Cactvs Toolkit Standard Property Definition Summary

Name Datatype Description Literature Enumerations Fields Parameters Computation Dependencies Invalidation CompModule
A_3D_BONDING_VECTOR floatvector 3D bonding vector (i.e. next open ligand shell position in VSEPR model to attach a ligand to). The length of this vector is always 1.0 regardless of the elements involved - this value is only to be used for directions, not as a bond length.

Currently, the implementatiion is limited to s/sp/sp2/sp3 geometries.
Compiled C module A_XYZ atomchange bondchange merge 3drelative 3dabsolute hadd mod_a_3d_bonding_vector.so
A_ALCHEMY_TYPE shortstring Atom type as used in the Alchemy program
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC atomchange bondchange a_alchemy_type.xpd
A_ALIHETERO_SUBSTITUENT_COUNT int Count the number of hetero (not C or H) ligands around a central atom which are not part of an aroamtic system
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ISAROMATIC atomchange bondchange mod_a_alihetero_substituent_count.so
A_ALIRING_COUNT short Number of aliphatic rings the atom is member of
countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
Compiled C module R_AROMATIC R_TYPE atomchange bondchange ring mod_a_aliring_count.so
A_ALKYL_SUBSTITUENT_COUNT short Number of alkyl substituents (carbon sp3 ligand with no hetero atoms except possibly the atom for which this property is computed). This follows the Lhasa definition of alkyl substituent groups. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 36
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER A_HETERO_SUBSTITUENT_COUNT atomchange bondchange atom bond mod_a_alkyl_substituent_count.so
A_ALLENE byte Flag for atoms in allenic system
no:terminal:odd:even
(builtin) A_VALENCE B_TYPE B_ORDER atomchange bondchange
A_ALLYLIC byte An allylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to a carbon-carbon double bond. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER B_ARORING_COUNT atomchange bondchange atom bond mod_a_allylic.so
A_ALPHA_ARO_COUNT int Number of aromatic systems in alpha position, without the atom being a member of these.
Compiled C module A_ISAROMATIC B_TYPE atomchange bondchange mod_a_alpha_aro_count.so
A_ALPHA_UNSAT_COUNT int Number of vinyl, aliphatic systems in alpha position, without the atom being a member of these. This corresponds to the Lilly SMARTS extension "AG>0" and is used to implement the /IWVy extension.
Compiled C module A_ARORING_COUNT A_UNSATURATION B_TYPE B_ORDER atomchange bondchange mod_a_alpha_unsat_count.so
A_ANNOTATION string Atom annotation string for 2D rendering, containing, for example, charge and radical information
chargerepeatlimit: { value: 2 datatype: string}
stereogroups: { value: 1 datatype: string}
stereo: { value: 7 datatype: string}
isotope: { value: 1 datatype: string}
radical: { value: 1 datatype: string}
mapping: { value: 1 datatype: string}
query: { value: 1 datatype: string}
flags: { value: 1 datatype: string}
nostereo: { value: 0 datatype: string}
auxproperty: { value: {} datatype: string}
auxfilter: { value: {} datatype: string}
auxpropertyprefix: { value: {} datatype: string}
auxpropertysuffix: { value: {} datatype: string}
style: { value: default datatype: string}
label: { value: 0 datatype: string}
(builtin) A_TYPE A_ISOTOPE A_FORMAL_CHARGE A_FREE_ELECTRONS A_ELEMENT A_LABEL_STEREO A_CIP_STEREO A_FLAGS A_DL_STEREO A_QUERY A_HASH_STEREO A_MAP_STEREO A_RADICAL A_STEREO_GROUP atomchange bondchange stereochange
A_AROBOND_COUNT byte Number of aromatic bonds atom participates in
Compiled C module B_ISAROMATIC atomchange bondchange mod_a_arobond_count.so
A_AROCONDENSED boolean Flags for atoms in condensed aromatic ring systems (i.e. atoms which are member in two or more aromatic rings that are connected by an overlapping ring portion, or share an annealed aromatic bond)
Compiled C module R_TYPE R_AROMATIC atomchange bondchange mod_a_arocondensed.so
A_ARORING_COUNT short Number of aromatic rings the atom is member of
countenvelopes: { value: 0 datatype: string}
(builtin) R_AROMATIC R_TYPE atomchange bondchange ring
A_ARORING_SIZE_BITS bitset Bit mask for aromatic ring sizes the atom participates in
ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
Compiled C module R_SIZE R_TYPE B_TYPE A_ARORING_COUNT R_AROMATIC bondchange ring mod_a_aroring_size_bits.so
A_AUTODOCK4_TYPE shortstring Atom type as used in the Autodock 4 program
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC atomchange bondchange a_autodock4_type.xpd
A_BENZYLIC byte A benzylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to an aromatic carbon atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_ARORING_COUNT atomchange bondchange atom bond mod_a_benzylic.so
A_BONDORDER_COUNT bytevector Count of different bond orders around an atom (array).
(builtin) B_ORDER atomchange bondchange
A_BOND_RANGE intpair Ids of first and last bond atom is bonded to
(builtin) B_SEQUENCE_NUMBER atomchange bondchange merge shuffle hadd mol
A_BRICS_LINKER_TYPE short BRICS fragmentation scheme linker type ChemMedChem 2008, 3, 1503-1507
none:C-R1:N-R2:O-R3:C-R4:N-R5:C-R6:C-R7:C-R8:n-R9:N-R10:S-R11:S-R12:C-R13:C-R14:C-R15:C-R16
never
A_BRIDGEHEAD boolean Flag indicating atom is a ring system bridgehead
Compiled C module A_RING_COUNT atomchange bondchange mod_a_bridgehead.so
A_C13_NMRSHIFT float C13 NMR shift, measured in ppm.
atomchange bondchange stereochange atom bond
A_CARBOCYCLE boolean Flag indicating an atom in a carbocycle ESSSR ring
Compiled C module R_TYPE R_HETEROATOM_COUNT atomchange bondchange atom bond mod_a_carbocycle.so
A_CARBON_FRAGMENT_SIZE int Size of the carbon skeleton the atom looked at is member of
Compiled C module B_TYPE A_ELEMENT A_TYPE atomchange bondchange mod_a_carbon_fragment_size.so
A_CENTRALITY double Centrality rating of the atom (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN)
Compiled C module A_TOPO_DISTANCE M_SPAN atomchange bondchange atom bond mod_a_centrality.so
A_CGR_CHANGE intpair Atom change when interpreting a CGR-encoded structure. The values are a flag for addition/removal (-1: delete in product, 0: no change, 1:add in product) and the formal charge delta when going from reagent to product
presence int
charge int
atomchange bondchange 3dabsolute atom bond reaction
A_CH2_CHAIN_LENGTH int The length of the unbranched CH2/CH3 chain the atom is a member of. Hetero or carbon atoms that do not have 2 or more hydrogen neighbors have a 0 value. Hydrogen atoms are assigned the value of their bonding partner.
Compiled C module A_TYPE A_ELEMENT B_TYPE A_RING_COUNT A_HEAVY_SUBSTITUENT_COUNT atomchange bondchange atom bond mod_a_ch2_chain_length.so
A_CHAIN_LENGTH int The size of the chain-heavy-atoms-only fragment the atom is a member of. Ring atoms have value 0. Hydrogen atoms inherit the value of their bond partner.
Compiled C module A_TYPE A_RING_COUNT B_TYPE atomchange bondchange atom bond mod_a_chain_length.so
A_CHARGE_STABILIZATION shortvector Stabilization for negative charges, radicals and positive charges (in this order) on carbon atom (potentially after cutting a bond which is not the source of a stabilizing effect) according to the Lhasa formula CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 43
minus int
plus int
radical int
Compiled C module atomchange bondchange atom bond mod_a_charge_stabilization.so
A_CIP_STEREO byte Stereo descriptor for atoms, based on CIP (R/S) rules
SS=-2:S=-1:undef=0:R=1:RR=2
(builtin) atomchange bondchange
A_CL_COUNT int Count the number of chlorine substituents around the atoms
Tcl script A_ELEMENT A_TYPE atomchange bondchange a_cl_count.xpd
A_COLOR color Atom rendering color
mode: { value: light datatype: string}
labellist: { value: 1 datatype: string}
colorlist: { value: green datatype: string}
defaultcolor: { value: gray20 datatype: string}
(builtin) A_ELEMENT A_TYPE never
A_COLOR_SCALE color Get color values in different coloration models useing some atom property as data
property: { value: A_SIGMA_CHARGE datatype: string constraints: property}
maxintensity: { value: 255 datatype: int}
minintensity: { value: 0 datatype: int}
maxvalue: { value: auto datatype: string}
minvalue: { value: auto datatype: string}
colorspace: { value: rgb enumeration: red:green:blue:grey,gray:rgb:fixed datatype: int}
invert: { value: 0 datatype: boolean}
rootscale: { value: 0 datatype: boolean}
zerobalance: { value: 0 datatype: boolean}
filter: { value: {} datatype: string constraints: filterlist}
rangecolors: { value: red 1 green 0 blue datatype: string}
Tcl script atomchange bondchange a_color_scale.xpd
A_COMMENT string free-form atom comment. This is used for exampole in reading PubChem ASN.1 structure data.
never
A_CONFORMER xyzvector Conformers of the ensemble, created by various methods
maxconformers: { value: 10 description: Maximum number of conformers to generate or store minvalue: 1 maxvalue: 99999 datatype: int}
Tcl script A_ELEMENT A_MOL_NUMBER A_TYPE B_TYPE A_FREE_ELECTRONS A_LABEL_STEREO B_LABEL_STEREO B_ORDER A_FLAGS A_FORMAL_CHARGE atomchange bondchange merge a_conformer.xpd
A_CONJUGATED boolean A conjugated atom according to the Lhasa definition. Conjugated atoms are those alpha to a multiply bonded atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
Compiled C module A_TYPE B_TYPE A_FG_PARTICIPATION B_ORDER atomchange bondchange atom bond mod_a_conjugated.so
A_CONJUGATED_SYSTEM_SIZE int The size of the conjugated system the atom participates in according to the Shoichet definition (see literature reference). Atoms not in such a system get value 0. J. Med. Chem. 2003, 46, 4477-4486
Compiled C module A_TYPE A_SP2 A_INAMIDE A_ARORING_COUNT B_TYPE atomchange bondchange atom bond mod_a_conjugated_system_size.so
A_COVALENCY_RADIUS float Default covalence radius
(builtin) A_ELEMENT A_TYPE atomchange
A_CSP2_0H boolean Flag for carbon atoms with sp2 hybridization and no hydrogen substituents
Tcl script A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp2_0h.xpd
A_CSP2_1H boolean Flag for carbon atoms with sp2 hybridization and one hydrogen substituent
Tcl script A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp2_1h.xpd
A_CSP2_2H boolean Flag for carbon atoms with sp2 hybridization and two hydrogen substituents
Tcl script A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp2_2h.xpd
A_CSPECIAL boolean Flag for carbon atoms plotted with symbols by common agreement
triplebond: { value: 1 datatype: string}
allene: { value: 1 datatype: string}
charged: { value: 1 datatype: string}
isotope: { value: 1 datatype: string}
specialbonds: { value: 1 datatype: string}
onlyhligands: { value: 1 datatype: string}
onlyterminalxligands: { value: 1 datatype: string}
never: { value: 0 datatype: string}
(builtin) B_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER A_TERMINAL_DISTANCE A_ISOTOPE A_TEXTLABEL atomchange bondchange merge hadd
A_CSP_0H boolean Flag for carbon atoms with sp hybridization and no hydrogen substituents
Tcl script A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp_0h.xpd
A_CSP_1H boolean Flag for carbon atoms with sp hybridization and one hydrogen substituent
Tcl script A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp_1h.xpd
A_DAYLIGHT_ALIRING_COUNT short Number of aliphatic rings the atom is member of, with Daylight definition of aromaticity
countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE atomchange bondchange ring mod_a_daylight_aliring_count.so
A_DAYLIGHT_ARORING_COUNT short Number of aromatic rings the atom is member of, using Daylight aromaticity from R_DAYLIGHT_AROMATIC instead of globally configurable R_AROMATIC
countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE atomchange bondchange ring mod_a_daylight_aroring_count.so
A_DAYLIGHT_ARORING_SIZE_BITS bitset Bit mask for aromatic ring sizes the atom participates in, using always Daylight aromaticity
ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
Compiled C module R_SIZE R_TYPE B_TYPE A_DAYLIGHT_ARORING_COUNT R_DAYLIGHT_AROMATIC bondchange ring mod_a_daylight_aroring_size_bits.so
A_DEGREE byte Number of explicit valences around atom. This corresponds to the absurdly impractical and dangerous 'D' attribute in SMILES and should be avoided to be used for anything else.
ignorequeryatoms: { value: 0 description: If set, query atoms are not counted to the degree value in the atom neighbor sphere datatype: boolean}
ignorestereoh: { value: 1 description: If set, non-implicit H at stereo centers is treated as implicit, assuming it was only added for stereochemistry encoding, not to make a structural statement datatype: boolean}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT A_LABEL_STEREO atomchange bondchange mod_a_degree.so
A_DISTANCE floatvector Interatomic 3D distances
(builtin) A_XYZ atomchange bondchange stereochange 3drelative shuffle hadd
A_DL_STEREO byte Stereo descriptor for atoms, based on D/L nomenclature rules
L=-1:undef=0:D=1
(builtin) atomchange bondchange
A_EC_FRAGMENTS dataset Structure fragments associated with the different spheres of the EC hashcode

Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction)
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int}
debug: { value: 0 description: If set, print debug info datatype: boolean}
usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean}
includehydrogens: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean}
lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange atom bond mod_a_ec_fragments.so
A_EC_HASH uint64vector Base atoms hashcodes for ECFP-style fingerprints.

Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction)
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int}
debug: { value: 0 description: If set, print debug info datatype: boolean}
usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean}
includeh: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean}
properties: { value: A_ELEMENT A_SUBSTITUENT_COUNT A_HCOUNT description: List of properties to use in the atom seed, values cast to integer datatype: string constraints: propertylist}
boolproperties: { value: A_RING_COUNT description: List of properties to use in the atom seed, values cast to boolean datatype: string constraints: propertylist}
exprproperties: { value: A_EQUILIBRATED_CHARGE*10 description: List of property expressions to use in the atom seed, values cast to int datatype: string constraints: list}
lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange atom bond mod_a_ec_hash.so
A_ELEMENT byte Atomic number (periodic table of elements index, H=1)
(builtin) A_SYMBOL never
A_ENOLIZABLE boolean An enolizable atom by the Lhasa definition. An enolizable atom must be saturated, non-bridgehead, have at least one hydrogen and be activated by a withdrawing bond. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 48
Compiled C module A_TYPE A_ELEMENT A_BRIDGEHEAD A_HCOUNT B_TYPE B_ORDER A_FG_SUBSTITUENTS atomchange bondchange atom bond mod_a_enolizable.so
A_EQUILIBRATED_CHARGE float Equilibrated nominal charge
fixnoxides: { value: 1 datatype: string}
(builtin) B_TYPE A_FORMAL_CHARGE A_PICENTER atomchange bondchange hadd
A_EXPLICIT_VALENCE byte Sum of bond orders of bonds which do not lead to implicit atoms (property A_IMPLICIT). Use with extreme caution, this is not a generally useful property. This maps to the "nbonds" property in Bruns/Watson query processing.
ignoreallh: { value: 1 description: If set, all hydrogens are assumed to be implicit datatype: boolean}
Compiled C module B_TYPE B_ORDER A_IMPLICIT A_TYPE A_ELEMENT atomchange bondchange atom bond mod_a_explicit_valence.so
A_EXTENDED_GROUPHASH uint64 Perturbed group hashcode
usebondorder: { value: aro description: Whether to mix in bond orders within group: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
usesubstitution: { value: none description: none: pure group, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string}
Compiled C module A_TYPE A_FRAMEWORK A_ELEMENT atomchange bondchange groupchange hadd group mod_a_extended_grouphash.so
A_EXTENDED_GROUPHASH_GROUP index Hash group id index for atom group hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *group* indexing, the ensemble part is used as in A_HASHGROUP for global grouping.
Compiled C module A_GROUP_NUMBER A_EXTENDED_GROUPHASH atomchange bondchange groupchange merge hadd group mod_a_extended_grouphash_group.so
A_EXTENDED_RINGHASH uint64 Perturbed ringsystem hashcode
usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
usesubstitution: { value: none description: none: pure ring system, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string}
Compiled C module A_TYPE A_FRAMEWORK A_ELEMENT atomchange bondchange hadd ring mod_a_extended_ringhash.so
A_EXTENDED_RINGHASH_GROUP index Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping.
Compiled C module A_RINGSYSTEM_NUMBER A_EXTENDED_RINGHASH atomchange bondchange merge hadd ring mod_a_extended_ringhash_group.so
A_FG_CHECK bitvector Functional group test (for example, in Patran FGS/FGNOT clauses) of atoms as per the LHASA definition,
If the atom is a carbon atom and the FG is carbon-centric, this is the A_FG_PARTICIPATION flag, otherwise a test for A_FG_SUBSTITUIENTS>1
none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide
1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving
ketone boolean
aldehyde boolean
acid boolean
thioacid boolean
ester boolean
amide*1 boolean
amide*2 boolean
amide*3 boolean
sulfonamide*1 boolean
sulfonamide*2 boolean
sulfonamide*3 boolean
carbonium boolean
isocyanate boolean
acid*halide boolean
thioester boolean
amine*3 boolean
aziridine boolean
amine*2 boolean
amine*1 boolean
nitroso boolean
diazo boolean
haloamine boolean
hydrazone boolean
oxime boolean
imine boolean
thiocyanate boolean
isocyanide boolean
nitrile boolean
azo boolean
hydroxylamine boolean
nitro boolean
enamine boolean
amine*oxide boolean
thiol boolean
episulfide boolean
sulfide boolean
sulfoxide boolean
sulfone boolean
c*sulfonate boolean
anhydride boolean
lactam boolean
phosphine boolean
phosphonate boolean
epoxide boolean
ether boolean
peroxide boolean
alcohol boolean
enol*ether boolean
nitrite boolean
o*sulfonate boolean
fluoride boolean
chloride boolean
bromide boolean
iodide boolean
gem*dihalide boolean
trihalide boolean
acetylene boolean
olefin boolean
vic*dihalide boolean
halohydrin boolean
glycol boolean
hydrate boolean
hemiketal boolean
ketal boolean
hemiacetal boolean
acetal boolean
azide boolean
disulfide boolean
allene boolean
vinylsilane boolean
lactone boolean
vinylw boolean
vinyld boolean
esterx boolean
amidz boolean
methylene boolean
carbonyl boolean
carboxyl boolean
halide boolean
amine boolean
amide boolean
sulfonamide boolean
selenide boolean
trialkylsilyl boolean
trialkylsiloxy boolean
silylenolether boolean
n*urea*h boolean
n*urea*c boolean
carbamate*h boolean
carbamate*c boolean
o*carbamate boolean
n*carbamate boolean
o*carbonate boolean
dithioacetal boolean
dithioketal boolean
requested boolean
withdrawing boolean
expandable*withdrawing boolean
nonexpandable*withdrawing boolean
donating boolean
leaving boolean
good*leaving boolean
Compiled C module A_FG_PARTICIPATION A_FG_SUBSTITUENTS A_ELEMENT A_TYPE atomchange bondchange atom bond mod_a_fg_check.so
A_FG_PARTICIPATION bitvector Functional group participation of atoms as per the LHASA definition
none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide,sulphonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving:origin
ketone boolean
aldehyde boolean
acid boolean
thioacid boolean
ester boolean
amide*1 boolean
amide*2 boolean
amide*3 boolean
sulfonamide*1 boolean
sulfonamide*2 boolean
sulfonamide*3 boolean
carbonium boolean
isocyanate boolean
acid*halide boolean
thioester boolean
amine*3 boolean
aziridine boolean
amine*2 boolean
amine*1 boolean
nitroso boolean
diazo boolean
haloamine boolean
hydrazone boolean
oxime boolean
imine boolean
thiocyanate boolean
isocyanide boolean
nitrile boolean
azo boolean
hydroxylamine boolean
nitro boolean
enamine boolean
amine*oxide boolean
thiol boolean
episulfide boolean
sulfide boolean
sulfoxide boolean
sulfone boolean
c*sulfonate boolean
anhydride boolean
lactam boolean
phosphine boolean
phosphonate boolean
epoxide boolean
ether boolean
peroxide boolean
alcohol boolean
enol*ether boolean
nitrite boolean
o*sulfonate boolean
fluoride boolean
chloride boolean
bromide boolean
iodide boolean
gem*dihalide boolean
trihalide boolean
acetylene boolean
olefin boolean
vic*dihalide boolean
halohydrin boolean
glycol boolean
hydrate boolean
hemiketal boolean
ketal boolean
hemiacetal boolean
acetal boolean
azide boolean
disulfide boolean
allene boolean
vinylsilane boolean
lactone boolean
vinylw boolean
vinyld boolean
esterx boolean
amidz boolean
methylene boolean
carbonyl boolean
carboxyl boolean
halide boolean
amine boolean
amide boolean
sulfonamide boolean
selenide boolean
trialkylsilyl boolean
trialkylsiloxy boolean
silylenolether boolean
n*urea*h boolean
n*urea*c boolean
carbamate*h boolean
carbamate*c boolean
o*carbamate boolean
n*carbamate boolean
o*carbonate boolean
dithioacetal boolean
dithioketal boolean
requested boolean
withdrawing boolean
expandable*withdrawing boolean
nonexpandable*withdrawing boolean
donating boolean
leaving boolean
good*leaving boolean
origin boolean
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_FORMAL_CHARGE atomchange bondchange atom bond mod_a_fg_participation.so
A_FG_SUBSTITUENTS shortvector Functional group substituents on carbon as per the LHASA definition
ketone short
aldehyde short
acid short
thioacid boolean
ester short
amide*1 short
amide*2 short
amide*3 short
sulfonamide*1 boolean
sulfonamide*2 boolean
sulfonamide*3 boolean
carbonium short
isocyanate short
acid*halide short
thioester short
amine*3 short
aziridine short
amine*2 short
amine*1 short
nitroso short
diazo short
haloamine short
hydrazone short
oxime short
imine short
thiocyanate short
isocyanide short
nitrile short
azo short
hydroxylamine short
nitro short
enamine short
amine*oxide short
thiol short
episulfide short
sulfide short
sulfoxide short
sulfone short
c*sulfonate short
anhydride short
lactam short
phosphine short
phosphonate short
epoxide short
ether short
peroxide short
alcohol short
enol*ether short
nitrite short
o*sulfonate short
fluoride short
chloride short
bromide short
iodide short
gem*dihalide short
trihalide short
acetylene short
olefin short
vic*dihalide short
halohydrin short
glycol short
hydrate short
hemiketal short
ketal short
hemiacetal short
acetal short
azide short
disulfide short
allene short
vinylsilane short
lactone short
vinylw short
vinyld short
esterx short
amidz short
methylene short
carbonyl short
carboxyl short
halide short
amine short
amide short
sulfonamide boolean
selenide short
trialkylsilyl short
trialkylsiloxy short
silylenolether short
n*urea*h short
n*urea*c short
carbamate*h short
carbamate*c short
o*carbamate short
n*carbamate short
o*carbonate short
dithioacetal short
dithioketal short
requested short
withdrawing short
expandable*withdrawing short
nonexpandable*withdrawing short
donating short
leaving short
good*leaving short
Compiled C module A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE atomchange bondchange atom bond mod_a_fg_substituents.so
A_FLAGS bitset Display attributes for atom like boxing, marks, Fisher center
^none:starred,star:inverted,inverse,invert:boxed:groupbox1,gbox1:groupbox2,gbox2:invisible,invis:secondary:bold,dgrey,dgray,dark:greyed,mgrey,mgray,medium:italic,light,lgrey,lgray:fischer,fischercenter,fisher:nosym,nosymbol:circled,circle:alpha:beta:gamma:label:top:bottom:left:right:core:ligand,coreligand:highlight:diamond:triangle:cross:active:nostereo:protected:interfering:participating:hshowhetero:hshowterminal:hshowall:ballstick:capped:spacefill:wireframe:selected:expanded:spare1:spare2:spare3:node:symbol:insuperatom,insuper:hidden:firsthidden:groupsymbol
starred boolean
inverted boolean
boxed boolean
groupbox1 boolean
groupbox2 boolean
invisible boolean
secondary boolean
bold boolean
greyed boolean
italic boolean
fischercenter boolean
nosymbol boolean
circled boolean
alpha boolean
beta boolean
gamma boolean
label boolean
top boolean
bottom boolean
left boolean
right boolean
core boolean
ligand boolean
highlight boolean
diamon boolean
triangle boolean
cross boolean
active boolean
nostereo boolean
protected boolean
interfering boolean
participating boolean
hshowheterolboolean boolean
hshowterminal boolean
hshowall boolean
ballstick boolean
capped boolean
spacefill boolean
wireframe boolean
selected boolean
expanded boolean
spare1 boolean
spare2 boolean
spare3 boolean
node boolean
symbol boolean
insuperatom boolean
hidden boolean
firsthidden boolean
groupsymbol boolean
(builtin) never
A_FMC0 float Fragment molecular connectivity level #0
Compiled C module atomchange bondchange mod_a_fmc0.so
A_FMC1 float Fragment molecular connectivity level #1
Compiled C module atomchange bondchange mod_a_fmc1.so
A_FMC2 float Fragment molecular connectivity level #2
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc2.so
A_FMC3 float Fragment molecular connectivity level #3
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc3.so
A_FMC4 float Fragment molecular connectivity level #4
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc4.so
A_FMC5 float Fragment molecular connectivity level #5
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc5.so
A_FORMAL_CHARGE byte Nominal atom charge
(builtin) A_FREE_ELECTRONS never
A_FRACTIONAL_XYZ floatvector Fractional/reciprocal atomic 3D-coordinates. This is used in the CIF I/O module.
x float
y float
z float
A_XYZ E_UNIT_CELL atomchange bondchange stereochange merge 3drelative 3dabsolute
A_FRAGMENT_ID string Fragment identifier for original atom source. This is used in D_CHEMDRAW_PAGE.
never
A_FRAMEWORK byte Framework classification 0=ring, 1=sidechain, 2=linker
ring:sidechain,chain:linker,bridge
(builtin) B_TYPE atomchange bondchange hadd ring
A_FREE_ELECTRONS byte Number of free electrons
(builtin) A_FORMAL_CHARGE never
A_FREE_VALENCE byte Number of free valences
(builtin) A_ELEMENT A_FORMAL_CHARGE A_VALENCE atomchange bondchange hadd
A_F_COUNT int Count the number of fluorine substituents around a central atom
Tcl script A_ELEMENT A_TYPE atomchange bondchange a_f_count.xpd
A_GENERIC_FORCEFIELD_TYPE string Generic Force Field atom type- Used in the IFF I/O module. Computation of this property is linked to various program-specific variants, which can be selected by a parameter.
forcefield: { value: none description: If set to none, use the first type alread present on structure, or fallback to Sybyl2 as last resort enumeration: tinker:macromodel:sybyl2:sybyl:alchemy:babel datatype: string}
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_generic_forcefield_type.xpd
A_GEOMETRY byte Enumerated value of the geometry of an atom (terminal, tetrahedral, etc.)
none:terminal,end,s:linear,sp:trigonalplanar,planar,sp2:tetrahedral,tetraeder,sp3:bipyramidal,tbp,trigonalbipyramidal,bipyramid,sp3d,dsp3:sawhorse,seesaw:tshaped,t-shaped:octahedral,octaeder,sp3d2,d2sp3:squarepyramidal:squareplanar,sp2d,dsp2:other
Compiled C module A_VERTEX_DEGREE A_FREE_ELECTRONS A_TYPE B_TYPE A_FORMAL_CHARGE A_ISAROMATIC A_PICENTER A_IUPAC_GROUP atomchange bondchange mod_a_geometry.so
A_GROUP_FRAMEWORK byte Framework classification 0=group, 1=sidechain, 2=linker, using groups as core elements instead of rings as in standard A_FRAMEWORK
group:sidechain:linker
Compiled C module B_TYPE atomchange bondchange groupchange hadd group mod_a_group_framework.so
A_GROUP_NUMBER int Number (1-indexed group list position) of atoms, with 0 for atoms which are not in a group. This property assumes that an atom is only a member in a single group, if any.
Compiled C module atomchange bondchange groupchange atom bond group mod_a_group_number.so
A_H1_NMRSHIFT float Proton NMR shift, measured in ppm.
atomchange bondchange stereochange atom bond
A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY double The absolute electrophilic reactivity as computed by a simple Hammet calculation. Used in Lhasa transforms.
delta: { value: 1 datatype: double}
rho: { value: -5 datatype: double}
Compiled C module A_HUCKEL_PI_ELECTRON_DENSITY atomchange bondchange pi mod_a_hammet_absolute_electrophilic_reactivity.so
A_HAMMET_ABSOLUTE_NUCLEOPHILIC_REACTIVITY double The absolute nucleophilic reactivity as computed by a simple Hammet calculation. Used in Lhasa transforms.
delta: { value: 1 datatype: double}
rho: { value: -5 datatype: double}
Compiled C module A_HUCKEL_PI_ELECTRON_DENSITY atomchange bondchange pi mod_a_hammet_absolute_nucleophilic_reactivity.so
A_HAMMET_DIFFERENTIAL_ELECTROPHILIC_REACTIVITY double The differential electrophilic reactivity as computed by a simple Huckel calculation. Used in Lhasa transforms.
Compiled C module A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY atomchange bondchange pi mod_a_hammet_differential_electrophilic_reactivity.so
A_HAMMET_RELATIVE_ELECTROPHILIC_REACTIVITY double The relative electrophilic reactivity as computed by a simple Huckel calculation, expressed as percent of max reactivity in the structure. Used in Lhasa transforms.
Compiled C module A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY atomchange bondchange pi mod_a_hammet_relative_electrophilic_reactivity.so
A_HAMMET_RELATIVE_NUCLEOPHILIC_REACTIVITY double The relative nucleophilic reactivity as computed by a simple Huckel calculation, expressed as percent of max reactivity in the structure. Used in Lhasa transforms.
Compiled C module A_HAMMET_ABSOLUTE_NUCLEOPHILIC_REACTIVITY atomchange bondchange pi mod_a_hammet_relative_nucleophilic_reactivity.so
A_HASH uint64 Basic atomic hashcode
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 0 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE atomchange bondchange hadd
A_HASHGROUP index Hash group id index for basic hash code
(builtin) A_MOL_NUMBER A_HASH atomchange bondchange merge hadd
A_HASH_STEREO byte Stereo descriptor for atoms, based on atomic hashcodes
M=-1:undef=0:P=1
useisotope: { value: 0 datatype: string}
(builtin) A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange hadd
A_HCOUNT byte Number of classically bonded hydrogen atoms
useimplicith: { value: 0 datatype: string}
(builtin) B_TYPE A_ELEMENT atomchange bondchange hadd
A_HEAVY_SUBSTITUENT_COUNT byte Number of classically bonded non-hydrogen atoms
(builtin) B_TYPE A_ELEMENT atomchange bondchange
A_HETERO_SUBSTITUENT_COUNT byte Count the number of hetero (not C or H) ligands around a central atom
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange mod_a_hetero_substituent_count.so
A_HSPECIAL byte Flag for hydrogen atoms plotted with symbols by common agreement: 0: no, 1:yes, 2:at cis/trans db, 3:at stereocenter, but not wedge
never: { value: 0 datatype: string}
(builtin) B_STEREOINFO A_STEREOINFO A_ELEMENT A_TERMINAL_DISTANCE B_ORDER A_CSPECIAL B_FLAGS A_FLAGS A_ISOTOPE A_RING_COUNT atomchange bondchange merge hadd
A_HUCKEL_ELECTROPHILIC_LOCALIZATION_ENERGY double The electrophilic localization energy as computed by a simple Huckel calculation. Used in Lhasa transforms.
Compiled C module P_HUCKEL_MO_OCCUPANCY atomchange bondchange pi mod_a_huckel_electrophilic_localization_energy.so
A_HUCKEL_HOMO_COEFFICIENT double The HOMO coefficient as computed by a simple Huckel method. Used in Lhasa transforms.
P_HUCKEL_MO_OCCUPANCY atomchange bondchange pi
A_HUCKEL_HOMO_ENERGY double The LUMO energy of the pi system on this atom as computed by a simple Huckel method
Compiled C module P_HUCKEL_HOMO_ENERGY atomchange bondchange pi mod_a_huckel_homo_energy.so
A_HUCKEL_LUMO_COEFFICIENT double The LUMO coefficient as computed by a simple Huckel method. Used in Lhasa transforms.
P_HUCKEL_MO_OCCUPANCY atomchange bondchange pi
A_HUCKEL_LUMO_ENERGY double The LUMO energy of the pi system on this atom as computed by a simple Huckel method
Compiled C module P_HUCKEL_LUMO_ENERGY atomchange bondchange pi mod_a_huckel_lumo_energy.so
A_HUCKEL_NUCLEOPHILIC_LOCALIZATION_ENERGY double The nucleophilic localization energy as computed by a simple Huckel calculation. Used in Lhasa transforms.
Compiled C module P_HUCKEL_MO_OCCUPANCY atomchange bondchange pi mod_a_huckel_nucleophilic_localization_energy.so
A_HUCKEL_PI_ELECTRON_DENSITY double Pi elektron density (sum of electron count in occupied orbitals multiplied with atomic MO coefficient) according to plain Huckel model
P_HUCKEL_MO_OCCUPANCY atomchange bondchange atom bond pi
A_HYBRIDIZATION byte Hybridization of atom
none:s:sp3:sp2:sp:sp3d:sp3d2
Compiled C module never mod_a_hybridization.so
A_HYDROGENS_NEEDED byte Number of hydrogen atoms missing to fill up to standard valency
maxsulphurvalence: { value: 2 datatype: string}
maxchlorinevalence: { value: 1 datatype: string}
maxphosphorvalence: { value: 3 datatype: string}
hypervalentaddition: { value: 0 datatype: string}
(builtin) B_TYPE A_IUPAC_GROUP A_FORMAL_CHARGE A_FREE_ELECTRONS A_VALENCE A_RADICAL atomchange bondchange shuffle
A_HYDROGEN_BONDING byte Classification of H-Bonding Donor/Acceptor Potential
none:acidic:donor:acceptor:basic
Compiled C module A_FORMAL_CHARGE A_ELEMENT B_TYPE B_ORDER A_FREE_ELECTRONS A_SIGMA_CHARGE A_ISAROMATIC R_AROMATIC A_IUPAC_GROUP atomchange bondchange mod_a_hydrogen_bonding.so
A_IMPLICIT boolean Flag for implicitly added atoms. This information is internally maintained by hydrogen addition etc. subroutines. The compute function copies this internal data into a property.
Compiled C module atomchange mod_a_implicit.so
A_IMPLICIT_HCOUNT byte Number of implicit (automatically added) hydrogens around atom. This is computed from the internal hydrogen origin memory of structures. If this information has been deleted, the result is always zero.
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange mod_a_implicit_hcount.so
A_INAMIDE boolean Flags for atoms in amide-type system (set for n,o,c). Or'ed bits 'extended 1' allow C=S, 'extended 2' allow C=N
extended: { value: 1 datatype: string}
(builtin) A_ELEMENT B_TYPE B_ORDER atomchange bondchange
A_INDEX int Index of atom in internal atom list, not ordered into blocked molecules
Compiled C module atomchange bondchange merge shuffle hadd atom mod_a_index.so
A_ISAROMATIC boolean Flag whether atom is member of aromatic ring or not
(builtin) R_AROMATIC R_TYPE atomchange bondchange ring
A_ISMETAL boolean Flag for metal atoms, as determined by the column in the built-in element table, where the criterion could be modified if necessary.
Compiled C module A_ELEMENT atomchange bondchange mod_a_ismetal.so
A_ISOLATED_RING boolean Flag indicating atom is part of an isolated ring
Compiled C module Y_RING_COUNT atomchange bondchange atom bond mod_a_isolated_ring.so
A_ISOTOPE short Absolute isotopic mass (12C=12.0000)
never
A_ISOTOPE_HASH uint64 Atomic hashcode with isotopes
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 1 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange hadd
A_ISOTOPE_HASHGROUP index Hash group id index for isotope hash code
(builtin) A_MOL_NUMBER A_ISOTOPE_HASH atomchange bondchange merge
A_ISOTOPE_LABELLING_DEGREE float Isotope labelling degree (0.0..1.0)
A_ISOTOPE atomchange
A_ISOTOPE_STEREO_HASH uint64 Stereospecific and isotope-aware atomic hashcode
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 1 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange stereochange hadd
A_ISOTOPE_STEREO_HASHGROUP index Hash group id index for stereospecific isotope hash code
(builtin) A_MOL_NUMBER A_ISOTOPE_STEREO_HASH atomchange bondchange merge
A_IS_CHARGED_METAL_ION boolean Boolean flag indicating an unbonded, charged metal ion
Tcl script A_TYPE A_ELEMENT A_FORMAL_CHARGE atomchange bondchange a_is_charged_metal_ion.xpd
A_IUPAC_GROUP byte New IUPAC group number in range 1-18, 19=lanthanides, 20=actinides
(builtin) A_ELEMENT A_TYPE atomchange
A_JSTDATA intquad Extended fields in JST-type molfile
atomchange bondchange stereochange merge
A_LABEL int Arbitrary atom label
(builtin) never
A_LABELCOLOR color X11 style color name of atom labels
Tcl script never a_labelcolor.xpd
A_LABEL_STEREO byte Stereo descriptor for atoms, based on atomic labels
M,-=-1:undef=0:P,+=1:U,C=2:Z,N=3:X=4
(builtin) never
A_LHASA_PATH_LABEL byte Path atom label (1-based) for matched Lhasa patterns
X_LHASA_SCORE atomchange bondchange atom bond
A_LIGAND_ANGLE_SUM float Allred/Rochow ligand angle sum for phosphor atoms
Tcl script atomchange bondchange 3drelative a_ligand_angle_sum.xpd
A_LIGAND_ENEG_SUM float
Tcl script atomchange bondchange a_ligand_eneg_sum.xpd
A_LIGAND_RANK intvector Priority-sorted list of ligands around stereocenters according to CIP rules. The vector fields are label values of the stereo-defining root substituents (which may be distand in case of atom-stereogenic allenes). The ligand with highest priority is listed first. Stereogenic electron pairs are not listed, and for such compounds there are only three listed ligands on the stereo atom. Atoms without stereo potential have an empty vector.
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER A_CIP_STEREO B_CIP_STEREO A_LABEL A_ALLENE atomchange bondchange stereochange hadd mod_a_ligand_rank.so
A_LILLY_SPINACH boolean Boolean flag whether the atom is part of what in Eli Lilly lingo is defined "molecular spinach". Atoms which are a ring atom, a ring bridge atom, or connected via a multiple bond to a ring or ring bridge are part of the scaffold and not spinach. J. Med. Chem. 2012, 55, 9763-9772
Compiled C module A_FRAMEWORK B_TYPE B_ORDER atomchange bondchange atom bond ring mod_a_lilly_spinach.so
A_LINEAR_CHAIN_LENGTH int The size of the linear-chain-heavy-atoms-only fragment the atom is a member of. Ring atoms or branch atoms have value 0. Hydrogen atoms inherit the value of their bond partner.
Compiled C module A_TYPE A_RING_COUNT B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange atom bond mod_a_linear_chain_length.so
A_MACROMODEL_TYPE short MacroModel atom type. Used for example in the MMD and MAESTRO I/O modules.
none:C1:C2:C3:CA:CB:CC:CD:CE:CF:CM:CP:CR:unused:C0:O2:O3:OA:OM:OW:OP:OQ:unused:O0:N1:N2:N3:NA:NB:NC:ND:N4:N5:NE:NF:NG:NH:NI:NM:NP:N0:H1:H2:H3:H4:H5:unused:unused:unused:H0:S1:SA:SM:S0:P0:B2:B3:F0:Cl:Br:I0:Si:Z0:Lp:00:Li:Na:K0:Rb:Cs:Ca:Ba:Mg:M2:M3:M4:M5:M6:M7:f2:f3:o2:o3:n2:n3:c1:c2:Zn:m3:m4:m5:m6:unused:unused:unused:unused:unused:unused:unused:unused:SP:S2:Cm:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:PI
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange a_macromodel_type.xpd
A_MAPPING int Atom mapping (for example for reactions), linking to same-value A_MAPPING atoms of complementary structure (reagent <-> product), 0 for unmapped atoms. A_MAPPING has no direct relationship to atom labels A_LABEL.
ignoreexpandedcarbon: { value: 0 datatype: string}
ignoreexpandedhetero: { value: 0 datatype: string}
ignoreexpandedhydrogen: { value: 0 datatype: string}
ignoreexpandedalicarbon: { value: 0 datatype: string}
ignoreexpandedarocarbon: { value: 0 datatype: string}
(builtin) atomchange bondchange merge atom bond reaction
A_MAP_STEREO byte Atom stereo descriptor based on reaction mapping
M,-=-1:undef=0:P,+=1
(builtin) A_MAPPING never
A_MDL_VALUE string Custom atom value in MDL files ('V' data lines in Molfiles)
never
A_MOL_LABEL int Label of molecule atom belongs to
(builtin) A_MOL_NUMBER M_LABEL atomchange bondchange merge shuffle hadd mol
A_MOL_NUMBER short Number (index+1) of molecule atom belongs to
(builtin) B_TYPE atomchange bondchange merge shuffle hadd
A_MORGAN uint64 Morgan numbering value (not the atom rank in the Morgan number, this is the full raw value)
includeh: { value: 1 datatype: boolean}
useelement: { value: 0 datatype: boolean}
Compiled C module A_TYPE B_TYPE A_ELEMENT A_VERTEX_DEGREE atomchange bondchange hadd bond mod_a_morgan.so
A_MORGAN_RANK int Ranking of atoms according to Morgan code value (rank 1 has highest rating)
Tcl script A_MORGAN atomchange bondchange merge hadd atom bond a_morgan_rank.xpd
A_N15_NMRSHIFT float Proton NMR shift, measured in ppm.
atomchange bondchange stereochange atom bond
A_NCBI_MMDB compound MMDB source information
mmdb-id int
molecule-id int
molecule-name stringvector
residue-id int
residue-name string
atom-id int
atom-name string
never
A_NCICADD_NORM_CHARGE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
A_NCICADD_RESONANCE_STEREO_DELETED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
A_NCICADD_TAUTO_STEREO_DELETED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
A_NEIGHBOR_COUNT byte Number of ALL bonded neighbor atoms
(builtin) bondchange hadd
A_NH2_COUNT int Count the number of -NH2 substituents around an atom
Tcl script A_ELEMENT A_HCOUNT atomchange bondchange a_nh2_count.xpd
A_NMRSHIFT float True shift values, computed from shielding parameters and method string
Tcl script A_SHIELDING atomchange bondchange stereochange 3drelative a_nmrshift.xpd
A_NORMAL_VIBRATIONS xyzvector Raman and IR normal vibrations of the structure
A_XYZ atomchange bondchange stereochange merge 3drelative mol atom bond
A_OSAWA_C13_NMRSHIFT float C13 NMR spectrum chemical shift., as computed by a simple QSAR function. This is defined only for simple alkanes and more a demo property than of practical use. Osawa, FMC wo mochiita 13C-NMR kagakushifto no yosoku ni kan suru kenkyuu; master thesis; TUT 1993
Tcl script A_FMC0 A_FMC1 A_FMC2 A_FMC3 A_FMC4 A_FMC5 atomchange bondchange a_osawa_c13_nmrshift.xpd
A_P31_NMRSHIFT float P31 NMR shift values, by default computed from A_SHIELDING shielding parameters
Tcl script A_SHIELDING atomchange bondchange stereochange 3drelative a_p31_nmrshift.xpd
A_PATTY_TYPE string Programmable atom typer
patternfile: { value: patty.sma datatype: diskfile constraints: readable}
trace: { value: 0 datatype: boolean}
Tcl script A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange hadd atom bond a_patty_type.xpd
A_PHENYL_COUNT int Count for the number or ESSSR phenyl rings the atom is part of
Compiled C module R_TYPE R_AROMATIC R_HETEROATOM_COUNT atomchange bondchange atom bond ring mod_a_phenyl_count.so
A_PICENTER byte Flag for atoms with pi system (1:free electrons, 2:multibond or epair)
(builtin) A_PSE_ROW A_FREE_ELECTRONS B_TYPE A_FORMAL_CHARGE B_ORDER atomchange bondchange hadd
A_PISYSTEM_ELECTRON_COUNT short Number of pi electrons in largest pi system the atom is a member of
Compiled C module P_ELECTRON_COUNT atomchange bondchange atom bond pi mod_a_pisystem_electron_count.so
A_PISYSTEM_SIZE short Size (atom count) of the largest pi system the atom is a member of
Compiled C module atomchange bondchange atom bond pi mod_a_pisystem_size.so
A_PI_CHARGE float Gasteiger Pi charges
A_TYPE A_SIGMA_CHARGE atomchange bondchange hadd
A_PI_ELECTRONEGATIVITY float Gasteiger Pi Eneg value
A_TYPE A_PI_CHARGE atomchange bondchange hadd
A_POLARIZABILITY float Atom polarizablities by the Kang & Jhon (sic) algorithm Y. K. Kang, M. S. Jhon, Theor. Chim. Acta 61, 41 (1982)
Compiled C module A_VB_NEIGHBOR_COUNT A_ELEMENT A_FREE_ELECTRONS A_FORMAL_CHARGE A_ISAROMATIC A_AROCONDENSED atomchange bondchange mod_a_polarizability.so
A_PSE_ROW byte Row number in PSE (1 for H,He, 2 for Li ..)
(builtin) A_ELEMENT A_TYPE atomchange
A_QNA_DESCRIPTORS floatpair Filimonov/Zakharov/Lagunin/Poroikov QNA atomic descriptors. The p value correlates with partial atomic hardness, and q with electronegativity. The use of the matrix exponent of the adjaceny matrix ensures a decreasing neighbor influence with increasing topological distance.

Further literature references:
Chemical Research in Toxicology, 2012, 25, 2378-2385, DOI 10.1021/tx300247r
SAR and QSAR in Environmental Research, 2009, 20, 679-709, DOI 10.1080/10629360903438370
Molecular Informatics 30, 2011, 241-250
p double
q double
Compiled C module A_TYPE A_ELEMENT E_EXP_CONNECTIVITY_MATRIX atomchange bondchange atom bond mod_a_qna_descriptors.so
A_QUERY compound Atom query attributes
element,std,normal,standard:any,*,?:list,whitelist:excllist,neglist,blacklist:hetero,q:halogen,x:noth,noh:heteroh,qh,notc,noc:metal,m:pull1,y:pull2,z:hdonor,hd:hacceptor,ha:insulator,r:terminator,t,ref,reference:anyh,ah:metalh,mh:halogenh,xh:g,group:gh,grouph:g*,groupx:gh*,grouphx:acy:ach:abc:abh:ayl:ayh:alk:alh:ael:aeh:ahc:ahh:aox:aoh:aam:aah:amox:amoxh:cyc:cyh:cbc:cbh:ary:arh:cal:cah:cel:ceh:chc:chh:har:hah:cxx:cxh:1a:2a:3a:4a:5a:6a:7a:8a:1b:2b:3b:4b:5b:6b:7b:8b:8x:8y:8z:1m:2m:3m:tr:ln:ac,an:4m:nm:alk*,*alk,allalk:alh*,*alh,allalh:chk:hea:hef:het:spinach:spinachh:xspinach:xspinachh:cspinach:cspinachh:spinach2:spinach2h:xspinach2:xspinach2h:cspinach2:cspinach2h ^none:stereo:charge:unsaturated,unsat,insaturated,insat:dontmatch,exclude:aromatic:aliphatic,inaromatic:mustmap:picenter:aroneighbor,aroneighbour:noaroneighbor,noaroneighbour:substituted:unsubstituted:fgneighbor,fgneighbor:nofgneighbor,nofgneighbour:aroneighbor_unmatched,aroneighbour_unmatched:noaroneighbor_unmatched,noaroneighbour_unmatched:substituted_unmatched:unsubstituted_unmatched:fgneighbor_unmatched,fgneighbor_unmatched:nofgneighbor_unmatched,nofgneighbour_unmatched:nostereook:nomappingok:nooverlap:exactchange:noextrah:noextrac:noextrax:stereoinversion,inversion:stereoretention,retention:saturated:branched:linear,chain:nochargeok:explicitzerocharge:noextrarings:filledvalence:unfilledvalence:stereochangeofpresence,changeofpresence:noisotopeok:offpath:rgroup:groupsaturated,gsaturated:groupunsaturated,groupinsaturated,gunsaturated,ginsaturated:groupacyclic,gacyclic:groupmonocyclic,gmonocyclic:grouppolycyclic,gpolycyclic:groupcyclic,gcyclic:groupsimple,groupnotpolycyclic,gsimple,gnotpolycyclic:wbond,withdrawingbond:nowbond,nowithdrawingbond,no_withdrawing_bond,no_wbond:branched:unbranched:tertbranched,tbranched:heterocyclic:carbocylic none:H:He:Li:Be:B:C:N:O:F:Ne:Na:Mg:Al:Si:P:S:Cl:Ar:K:Ca:Sc:Ti:V:Cr:Mn:Fe:Co:Ni:Cu:Zn:Ga:Ge:As:Se:Br:Kr:Rb:Sr:Y:Zr:Nb:Mo:Tc:Ru:Rh:Pd:Ag:Cd:In:Sn:Sb:Te:I:Xe:Cs:Ba:La:Ce:Pr:Nd:Pm:Sm:Eu:Gd:Tb:Dy:Ho:Er:Tm:Yb:Lu:Hf:Ta:W:Re:Os:Ir:Pt:Au:Hg:Tl:Pb:Bi:Po:At:Rn:Fr:Ra:Ac:Th:Pa:U:Np:Pu:Am:Cm:Bk:Cf:Es:Fm:Md:No:Lr
type byte
flags bitset
list intvector
substituentcount bitset
valencecount bitset
neighborcount bitset
hydrogencount bitset
ringsize bitset
ringcount bitset
rganchor int
rgmember int
rginstance int
rgattach int
tclproc string
fuzz int
query querytree
component int
heterosubstituentcount bitset
rbcount bitset
repeat bitset
charge bitset
pyfunction string
ringid int
ringsystemid int
fgs bitvector
fgnot bitvector
aliheterosubstituentcount bitset
freeelectroncount bitset
pielectroncount bitset
rgroupid int
pathid int
altpathid int
formula formulamatch
piformula formulamatch
never
A_RACEMATE byte Racemate distribution of stereocenter
undefined,undef:rac,racemat:pure
atomchange bondchange
A_RADICAL byte Flag for radical center
none,no:singlet:doublet,yes:triplet:quartet:quintet
(builtin) A_FREE_ELECTRONS never
A_RADIOACTIVE boolean Marker for radioactive isotope labels.
Tcl script A_ISOTOPE A_ELEMENT atomchange bondchange atom bond a_radioactive.xpd
A_RECAP_LINKER_TYPE byte Connection type on this placeholder atom in the RECAP algorithm. The original paper abuses isotope labels for this. J. Chem. Inf. Comput. Sci. 1998, 38, 511-522
none:urea:amide:ester:amines:cyclicamines:ether:olefin:aronitroalicarbon:lactam:arocarbonarocarbon:sulphonamide:aronitroarocarbon
never
A_RENDER_XY floatpair Render coordinate of atoms on images, etc. Only set by render functions is specifically requested.
A_XY E_STDBLE A_FLAGS atomchange bondchange groupchange mol atom bond ring group
A_RESIDUE compound Residue information, esp. for proteins from PDB
atomtag string
grouptag string
groupindex int
segmentid string
resid string
chain string
weight double
hetatm boolean
atomchange bondchange
A_RINGHASH uint64 Atom hash code for atoms which are part of ring systems
usebondorder: { value: none datatype: string}
(builtin) A_TYPE A_FRAMEWORK A_ELEMENT B_TYPE atomchange bondchange 3drelative 3dabsolute ring
A_RINGHASH_GROUP index Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping.
Compiled C module A_RINGSYSTEM_NUMBER A_RINGHASH atomchange bondchange merge hadd ring mod_a_ringhash_group.so
A_RINGLABEL int Renumbered labels of atoms in ring system- Atoms not in ring get label 0, the ring atoms start with one. The order of the labelled atoms follows their standard atom label rank.
Tcl script A_LABEL ring a_ringlabel.xpd
A_RINGS intvector Labels of the rings the atom is member in
(builtin) R_LABEL A_RING_COUNT R_TYPE atomchange bondchange merge ring
A_RINGSYSTEM_NUMBER int Number (1-indexed ringsystem list position) of atoms, with 0 for atoms which are not in a ringsystem.
Compiled C module Y_LABEL atomchange bondchange atom bond ring mod_a_ringsystem_number.so
A_RINGSYSTEM_SIZE short Number of ESSSR rings in the ringsystem the atom is a member of, 0 for chain atoms
Compiled C module atomchange bondchange ring mod_a_ringsystem_size.so
A_RING_BOND_COUNT byte Number of ring bonds atom is participating in
Compiled C module B_RING_COUNT bondchange ring mod_a_ring_bond_count.so
A_RING_COUNT short Number of simple (non-envelope) rings an atom is member of
countenvelopes: { value: 0 datatype: string}
(builtin) R_TYPE atomchange bondchange ring
A_RING_HETEROATOM_COUNT_BITS bitset A bit is set at bit position n for any ESSSR ring the atom is a member of which has n hetero atoms. Chain atoms have value 0. If the atom is a member of a carbocyclic ESSSR ring, bit position 0 is set.
Compiled C module R_HETEROATOM_COUNT R_TYPE atomchange bondchange atom bond mod_a_ring_heteroatom_count_bits.so
A_RING_SIZE_BITS bitset Bit mask for ring sizes the atom participates in
ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
Compiled C module R_SIZE R_TYPE B_TYPE A_RING_COUNT bondchange ring mod_a_ring_size_bits.so
A_RING_SUBSTITUENT_SIZE intpair Number of atoms and maximum bond distance in ring substituent
size int
depth int
(builtin) A_FRAMEWORK ring
A_SCIDEX_DATA dictionary Scidex-specific atom attribute support for MDL SD-files. Handles data encoded in "S SDX" lines.
atomchange bondchange atom bond
A_SEQUENCE_NUMBER int Sequential atom number (trad. atoms only)
(builtin) A_MOL_NUMBER M_ATOM_RANGE A_TYPE atomchange bondchange merge shuffle hadd mol
A_SHELL_ELECTRONS byte Number of shell electrons in unbonded atom
(builtin) A_ELEMENT A_TYPE atomchange bondchange
A_SHIELDING float Isotropic magnetic shielding (NMR spectroscopy). This is a field in the SHARC spectroscopy archive format.
atomchange bondchange stereochange merge 3drelative hadd
A_SHIELD_TENSOR tensor Anisotropic magnetic shielding tensor. Used as data field in the SHARC NMR archive format.
atomchange bondchange stereochange merge 3drelative hadd
A_SIGMA_CHARGE float Gasteiger sigma charges
Compiled C module A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 atomchange bondchange mod_a_sigma_charge.so
A_SIGMA_ELECTRONEGATIVITY float Gasteiger sigma electronegativities
A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_SP A_SP2 atomchange bondchange
A_SIMILARITY_PATTERN float Quantitative evaluation of fragment-bit similarity
cmplist: { value: {} datatype: string}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange a_similarity_pattern.xpd
A_SMALLEST_RING int Size of smallest ESSSR ring the atom is a member of (0 for non-ring atoms)
Compiled C module R_SIZE ring mod_a_smallest_ring.so
A_SMILES_INDEX int Atom index in SMILES string (-1 for implicit atoms not explicitly encoded in the SMILES string). The result data is automatically set when computing E_SMILES, which has many options which influence the atom sequence in the string.
E_SMILES A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL_STEREO B_LABEL_STEREO A_ISOTOPE A_MAPPING A_QUERY B_QUERY atomchange bondchange merge hadd mol
A_SMILES_RANK int Unique SMILES ranking of atoms
Compiled C module A_ELEMENT B_TYPE A_TYPE B_ORDER A_FORMAL_CHARGE atomchange bondchange merge hadd mod_a_smiles_rank.so
A_SP boolean Flags for atoms forced into sp hybridisation by charge equilibration or aromaticity
useimplicith: { value: 1 datatype: boolean}
Compiled C module A_ELEMENT B_TYPE B_ORDER A_HYDROGENS_NEEDED atomchange bondchange mod_a_sp.so
A_SP2 boolean Flags for atoms forced into sp2 hybridisation by charge equilibration or aromaticity
useimplicith: { value: 1 datatype: boolean}
Compiled C module A_FORMAL_CHARGE B_ORDER B_TYPE A_HYDROGENS_NEEDED A_ELEMENT atomchange bondchange mod_a_sp2.so
A_SPAN float Largest distance of this atom to any atom in molecule, divided by molecule span
Compiled C module B_TYPE M_SPAN A_TOPO_DISTANCE atomchange bondchange hadd atom bond mod_a_span.so
A_SPIRO byte Number of spiro ring joins atom is participating in ESSSR ring set
(builtin) A_RING_COUNT R_TYPE atomchange bondchange ring
A_SSMATCH int Ensemble is structure, property data encodes labels of matching substructure atoms, 0 for unmatched parts
sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
Tcl script never a_ssmatch.xpd
A_SSMATCH_COUNT int Atom match count for structure matching. This is set on the *structure* ensemble when specific match flags are set in the substructure match routine.
sshandle: { value: {} datatype: substructure}
Tcl script never a_ssmatch_count.xpd
A_SSMATCH_ENVIRONMENT datatree Classigied unmatched structure environment of the substructure atoms, i.e. data on the characteristics of the unmatched structure atoms sprouting from the structure atom matched by this substructure atom. Set by a substructure hit option, not directly computable.
atomchange bondchange atom bond
A_STANDARD_GROUP_LABEL int Label of group which contains the atoms which form a standard group
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
A_STEREOGENIC byte Can this atom be a stereocenter ?
no:maybe:checkno:yes,checkyes:ringct
(builtin) atomchange bondchange hadd
A_STEREOINFO byte Stereo descriptor availability info: 1:Label,2:R/S,4:D/L:8:hash,16:map
^none,st_none:label,st_label:cip,st_cip:dl,st_dl:hash,st_hash:map,st_map
(builtin) A_HASH_STEREO A_LABEL_STEREO A_CIP_STEREO A_DL_STEREO A_MAP_STEREO atomchange bondchange stereochange
A_STEREO_CHANGE byte Stereo change during course of reaction
unknown:inversion:retention:changeofpresence
atomchange bondchange atom bond
A_STEREO_GROUP short MDL-style stereo group. The enumeration values correspond to the official MDL names of these groups. They are read and set by SDF3000/RXN3000 file format modules, and also used in PubChem I/O via ASN.
abs=99:or15=-15:or14=-14:or13=-31:or12=-12:or11=-11:or10=-10:or9=-9:or8=-8:or7=-7:or6=-6:or5=-5:or4=-4:or3=-3:or2=-2:or1=-1:none=0:&1,and1=1:&2,and2=2:&3,and3=3:&4,and4=4:&5,and5=5:&6,and6=6:&7,and7=7:&8,and8=8:&9,and9=9:&10,and10=10:&11,and11=11:&12,and12=12:&13,and13=13:&14,and14=14:&15,and15=15
A_TYPE B_TYPE atomchange bondchange stereochange
A_STEREO_HASH uint64 Stereospecific basic atomic hashcode
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 0 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE atomchange bondchange stereochange hadd
A_STEREO_HASHGROUP index Hash group id index for basic stereospecific hash code
(builtin) A_MOL_NUMBER A_STEREO_HASH atomchange bondchange merge hadd
A_STMATCH int Ensemble is substructure, property data encodes labels of matching structure atoms, 0 for unmatched parts
sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
Tcl script never a_stmatch.xpd
A_STMATCH_COUNT int Atom match count for structure matching. This is set on the *substructure* ensemble when specific match flags are set in the substructure match routine.
sthandle: { value: {} datatype: structure}
Tcl script never a_stmatch_count.xpd
A_SUBSTITUENT_COUNT int Count the number of non-H neighbors around a central atom
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange mod_a_substituent_count.so
A_SUBSTITUENT_VECTOR float Angle of the mid of the largest gap in the 2D layout of the substituent sphere
excludeatoms: { value: {} datatype: string}
(builtin) A_XY atomchange bondchange hadd
A_SUPERATOMSTRING string Descriptive string for atoms and especially superatoms
never
A_SUPERATOM_SSMATCH string A_SUPERATOMSTRING of matching substructure superatom, empty for unmatched parts. This is set by the substructure match routine if suitable flags are set.
sshandle: { value: {} datatype: structure}
Tcl script never a_superatom_ssmatch.xpd
A_SURFACE_AREA double Estimated surface area from simple intersection of bonded VdW spheres on A_XYZ coordinates P. Labute, Methods in Molecular Biology, 275, 261ff
vdwscale: { value: 0.8 description: scaling parameter for VdW radii datatype: double}
bondsonly: { value: 1 description: if set, only compute sphere intersections of bonded atoms datatype: boolean}
Compiled C module A_XYZ A_TYPE A_ELEMENT A_ISAROMATIC A_VDW_RADIUS atomchange bondchange 3dabsolute hadd atom bond mod_a_surface_area.so
A_SURFACE_SPHERE_RADIUS float Radius of sphere used for surface calculation
A_XYZ atomchange bondchange stereochange 3drelative
A_SYBYL2_TYPE shortstring Atom type as used in the Sybyl mol2 format
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_sybyl2_type.xpd
A_SYBYL_TYPE byte Atom type as used in the Sybyl mol format (version 1, not mol2)
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_sybyl_type.xpd
A_SYMBOL shortstring Atomic symbol
querysymbol: { value: ? datatype: string}
(builtin) A_ISOTOPE A_ELEMENT A_QUERY never
A_SYMVISIBLE boolean Flag for atoms typically plotted with symbol
(builtin) A_HSPECIAL A_CSPECIAL A_TYPE A_ELEMENT A_FLAGS atomchange bondchange
A_TAUTOMER_SYSTEM int Tautomer system ID of the atoms. Atoms outside any tautomer system receive ID 0, the rest of the systems are numbered starting with one.
Compiled C module B_ISTAUTOMERIC atomchange bondchange atom bond mod_a_tautomer_system.so
A_TERMINAL_DISTANCE short Number of bonds from terminal atom (0 if itself terminal)
(builtin) B_TYPE atomchange bondchange
A_TEXTLABEL compound Arbitrary textual atom label plus alignment info for plots
{} @above:left:center:right:below
label string
align byte
level: { value: 0 datatype: string}
(builtin) never
A_TINKER_TYPE short Atom type as used in the Tinker xyz format
forcefield: { value: none datatype: string}
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_tinker_type.xpd
A_TOPO_DISTANCE shortvector Topological distance matrix (minimum number of bonds between atoms)
bondclasses: { value: VB datatype: string}
Compiled C module B_TYPE bondchange mod_a_topo_distance.so
A_TOTAL_CHARGE float Atomic charge on Sigma and Pi systems
(builtin) A_TYPE A_ELEMENT B_TYPE B_ORDER A_SIGMA_CHARGE A_PI_CHARGE atomchange bondchange
A_TRAJECTORY xyzvector 3D atomic path trajectory, for example from a molecular modelling study. This property is for example used in the I/O modules for the GROMACS, XBSA, XYZ and GHEMICAL formats.
A_TYPE B_TYPE B_ORDER A_ELEMENT atomchange
A_TRANSFORM_STATUS byte Atom status as result of SMIRKS transformation. None: not matched in transform, matched: matched, but unchanged, changed: element or attribute changed, new: fragment introduced by transform
none:matched:changed:new
atomchange bondchange atom bond
A_TYPE short Classification, 0:Undef,1:Normal,2:Search,4:Epair,8:3DPoint,16:Super,32:Deloc,64:Polymer,128:Annotation,256:Open,512:Enzyme,1024:Unspecified
^undef:normal,element:search,query:epair,electron,ep,lp:3dpoint,bq,du:super,superatom:anchor,delocalized,deloc,@:polymer,poly:annotation,annot:open:enzyme,e,protein:unspecified
never
A_UNDEF_FLOAT1 float Some undefined atom property read from file formats with anonymous atom data
atomchange bondchange stereochange merge 3drelative 3dabsolute
A_UNSATURATION byte Sum of bond orders in excess of one of all non-aromatic bonds atom is participating in
aroisunsaturated: { value: 1 description: If set, aromatic bonds count as unsaturated datatype: boolean}
Compiled C module A_TYPE B_TYPE B_ORDER B_ISAROMATIC atomchange bondchange mod_a_unsaturation.so
A_VALD double Molconn-Z atom value parameter
never
A_VALENCE byte Number of classical bond valences
(builtin) B_ORDER B_TYPE bondchange hadd
A_VAMP_CHARGE float Atomic Charge as computed by the Vamp program. This is computed indireclty by requesting computation of heat for formation via Vamp (property E_HEAT_OF_FORMATION).
A_XYZ atomchange bondchange
A_VB_NEIGHBOR_COUNT byte Number of classically bonded neighbor atoms
(builtin) B_TYPE bondchange hadd
A_VDW_INTERACTION floatvector Atom-by-atom nonbonding interaction coefficients, dependent on the elements of an atom pair. The result s a float vector on each atom. The vector length is the number of atoms. The element value at each index is computed by formula

hardness(a1)*hardness(a2).pow(VdwBumperRad(element1)+VdWBumperRad(element2),12).

The atom hardness value is either the standard atom hardness (default 0.3) or a special hydrogen hardness (default 0.09). The diagonals are set to 0, and interactions to non-standrd atoms to -1.

Note that is is only a helper property. it is not dependen on the actual atomic coordinates. It is used by the computation functions of properties E_NONBONDING_ENERGY and E_CONFORMER_ENERGY.
stdhardness: { value: 0.30 datatype: double}
hydrogenhardness: { value: 0.09 datatype: double}
Compiled C module A_TYPE A_ELEMENT atomchange atom mod_a_vdw_interaction.so
A_VDW_RADIUS float Default van-der-Waals radius
(builtin) A_ELEMENT A_TYPE atomchange
A_VECTOR floatvector Directional 3D vector originating from atoms, generic purpose
atomchange bondchange 3drelative 3dabsolute
A_VERTEX_DEGREE byte Number of neighbors which are real atoms and are connected by vb or complex bonds
Compiled C module A_TYPE B_TYPE atomchange bondchange hadd mod_a_vertex_degree.so
A_VIRTUAL_HCOUNT byte Sum of actual hydrogen count (A_HCOUNT) and hydrogens needed for full set (A_HYDROGENS_NEEDED)
Compiled C module A_HCOUNT A_HYDROGENS_NEEDED atomchange bondchange atom bond mod_a_virtual_hcount.so
A_VORONOI_COLOR color Color of Voronoi background cells in 2D structure plots
Tcl script atomchange bondchange atom bond a_voronoi_color.xpd
A_VORONOI_POLYGON xyvector Voronoi polygon around 2D display of atom
polygonsonly: { value: 1 datatype: boolean}
adddummies: { value: 1 datatype: boolean}
extradummies: { value: 1 datatype: boolean}
debug: { value: 0 datatype: boolean}
Compiled C module A_XY never mod_a_voronoi_polygon.so
A_WATERMARK_SENSITIVITY float Guestimated sensitivity of overall compound energy on atom movement for watermarking
datafile: { value: a_watermark_sensitivity.dat datatype: diskfile constraints: readable}
Tcl script A_ELEMENT A_TYPE B_ORDER B_TYPE atomchange bondchange atom bond ring a_watermark_sensitivity.xpd
A_WATERMARK_XYZ floatvector Atomic 3D-coordinates with watermarking
x float
y float
z float
key: { value: LNTSCSWW datatype: string}
message: { value: CACTVS Watermark datatype: string}
scale: { value: 100 datatype: double}
sigma: { value: 1.0 datatype: double}
spread: { value: 1 datatype: boolean}
markhydrogens: { value: 0 datatype: boolean}
alignpmi: { value: 1 datatype: boolean}
usesensitivity: { value: 0 datatype: boolean}
Compiled C module A_XYZ A_TYPE A_ELEMENT A_WATERMARK_SENSITIVITY atomchange bondchange stereochange mod_a_watermark_xyz.so
A_WEIGHT float Atomic weight
allisotopes: { value: 0 datatype: string}
(builtin) A_TYPE A_ISOTOPE A_ELEMENT atomchange
A_WILDMAN_CRIPPEN_TYPE shortstring Atom classification according to the Wildman-Crippen scheme (see litref) J. Chem. Inf. Comput. Sci 1999, 39, 868-873
Compiled C module A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE B_TYPE B_ORDER B_ISAROMATIC A_IUPAC_GROUP atomchange bondchange atom bond mod_a_wildman_crippen_type.so
A_XSYMBOL string Expanded element symbol, lists contain all elements
(builtin) A_ISOTOPE A_SYMBOL A_ELEMENT A_QUERY atomchange
A_XY floatpair Atomic 2D display coordinates
x float
y float
fixbridgeheadstereo: { value: 1 datatype: string}
align: { value: none datatype: string}
optimize: { value: 1 datatype: string}
ringalignment: { value: 1 datatype: string}
heteroringalignment: { value: 1 datatype: string}
bondlength: { value: 1.0 datatype: string}
wedgepairs: { value: none datatype: string}
wedgestyle: { value: default datatype: string}
pseudo3d: { value: 0 datatype: string}
template: { value: {} datatype: string}
aspectratio: { value: 1.2 datatype: string}
ignorewiggleh: { value: 0 datatype: string}
ignoreatoms: { value: {} datatype: string}
templatefile: { value: 2dtpl.cbin datatype: string}
maxops: { value: 210000 datatype: string}
usertemplatefiles: { value: {} datatype: string}
hbondfactor: { value: 0.62 datatype: string}
hwedgefactor: { value: 0.85 datatype: string}
(builtin) never
A_XYDISTANCE floatvector Atomic distance in 2D plot coordinates
Tcl script A_XY atomchange bondchange a_xydistance.xpd
A_XYZ floatvector Atomic 3D-coordinates J. Gasteiger, C. Rudolph, J. Sadowsky, <Automatic Generation of 3D Atomic Coordinates for Organic Molecules>, Tetrahedron Computer Methodol. (1992)
x float
y float
z float
usechembiogrid: { value: 0 datatype: string}
usepubchem: { value: 1 datatype: string}
usecorina: { value: 1 datatype: string}
usepubchemqc: { value: 0 datatype: string}
maxconformers: { value: 1 datatype: string}
corinaoptions: { value: preserve,stergen,r2d,ori,rc,flapn,msc=32,msi=1024,v3000 datatype: string}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS atomchange bondchange stereochange mod_a_xyz.so
B_1ST_ATOM int First atom of a bond
Tcl script A_LABEL atomchange bondchange merge b_1st_atom.xpd
B_2ND_ATOM int Second atom of a bond
Tcl script A_LABEL atomchange bondchange merge b_2nd_atom.xpd
B_3RING boolean Flag indicating bond is part of 3-membered ring
Tcl script atomchange bondchange b_3ring.xpd
B_4RING boolean Flag indicating bond is part of 4-membered ring
Tcl script atomchange bondchange b_4ring.xpd
B_5RING boolean Flag indicating bond is part of 5-membered ring
Tcl script atomchange bondchange b_5ring.xpd
B_6RING boolean Flag indicating bond is part of 6-membered ring
Tcl script atomchange bondchange b_6ring.xpd
B_7RING boolean Flag indicating bond is part of 7-membered ring
Tcl script atomchange bondchange b_7ring.xpd
B_ALLYLIC boolean A allylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to a carbon-carbon double bond, excluding bonds that lead back to the C=C double bond. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
A_ALLYLIC atomchange bondchange atom bond
B_ANGLE float Angle of atom triples, encoded as pseudo-bond
(builtin) A_XYZ atomchange bondchange 3drelative
B_ANNOTATION string Bond annoations (stereo information etc.), primarily for 2D plots
style: { value: default datatype: string}
stereo: { value: 1 datatype: string}
query: { value: 1 datatype: string}
label: { value: 0 datatype: string}
(builtin) B_FLAGS B_CISTRANS_STEREO B_CIP_STEREO B_LABEL_STEREO B_QUERY atomchange bondchange stereochange
B_ARORING_COUNT short Number of aromatic rings the bond is member of
countenvelopes: { value: 0 datatype: string}
(builtin) R_AROMATIC R_TYPE B_TYPE atomchange bondchange ring
B_ATOMS intpair Sequence numbers of atoms of traditional bond, with lower number listed first
property: { value: A_SEQUENCE_NUMBER datatype: string}
(builtin) A_SEQUENCE_NUMBER atomchange bondchange merge hadd
B_BENZYLIC boolean A benzylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to an aromatic carbon, excluding bonds that lead back to an aromatic atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
A_BENZYLIC atomchange bondchange atom bond
B_BRICS_FRAGMENTATION boolean Bond which would be cut in the BRICS fragmentation method ChemMedChem 2008, 3, 1503
atomchange bondchange atom bond
B_BUGGY1 int Test case of buggy property computation to test recovery mechanisms
Compiled C module atomchange bondchange mod_b_buggy1.so
B_BUGGY2 int Test case of buggy property computation to test recovery mechanisms
Compiled C module atomchange bondchange mod_b_buggy2.so
B_BUGGY3 int Test case of buggy property computation to test recovery mechanisms
Compiled C module B_BUGGY1 atomchange bondchange mod_b_buggy3.so
B_CENTRALITY double Centrality rating of the bond (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN)
Compiled C module A_TOPO_DISTANCE M_SPAN B_TYPE atomchange bondchange atom bond mod_b_centrality.so
B_CGR_CHANGE intpair Bond change when interpreting a CGR-encoded structure. The value are the bond orders on the reagent and product sides. Bonds which are created have a zero value on the reagent side. Bonds which are broken have a zero value on the product side. Bonds which change during CGR interpretation are encoded as 'link' type in B_TYPE, while constant bonds retain their original bond type. This property is set as windfall when computing property X_CGR. Hoonakker, F.; Lachiche, N.; Varnek, A. Condensed Graph of Reaction: Considas one single pseudo molecule. Int. J. Artif. Intell. Tools 2011, 20, 253–270.
reagent int
product int
atomchange bondchange 3dabsolute atom bond reaction
B_CIP_STEREO byte Bond chirality descriptor based on CIP (E/Z) rules
E=-1:undef=0:Z=1
(builtin) atomchange bondchange
B_CISTRANS_STEREO byte Bond chirality descriptor based on cis/trans rules
cis=-1:undef=0:trans=1
(builtin) atomchange bondchange
B_CLASSIFICATION bitset Simple bond classification bits
^none:ccbond:chbond:cxbond:xhbond:xxbond:single:double:triple:multiple:aromatic:xaromatic:caromatic:ring:smallring:mediumring:bigring:a-ring:a-aromatic:a-multiple:a-cxbond:b-ring:b-aromatic:b-multiple:b-cxbond
Compiled C module B_TYPE B_ORDER A_TYPE A_ELEMENT B_ISAROMATIC B_RINGS R_HETEROATOM_COUNT R_AROMATIC atom bond ring mod_b_classification.so
B_COLOR colorvector Bond rendering color
color: { value: white datatype: string}
(builtin) never
B_CONJUGATED boolean A conjugated bond according to the Lhasa definition. These are bonds which have a spanning atom alpha to a multiply bonded atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
A_CONJUGATED atomchange bondchange atom bond
B_DAYLIGHT_ARORING_COUNT short Number of aromatic rings the bond is member of, using explicit Daylight aromaticity in R_DAYLIGHT_AROMATIC instead of aromodel-configurable R_AROMATIC
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE B_TYPE atomchange bondchange ring mod_b_daylight_aroring_count.so
B_DELTA_PI_CHARGE float Difference of Gasteiger pi-charges of the bond atoms
Tcl script A_PI_CHARGE B_TYPE atomchange bondchange b_delta_pi_charge.xpd
B_DELTA_PI_ELECTRONEGATIVITY float Difference of Gasteiger pi-electronegativity of the bond atoms. The value is dependent on the order of the atoms in the bond.
Tcl script A_PI_ELECTRONEGATIVITY B_TYPE atomchange bondchange b_delta_pi_electronegativity.xpd
B_DELTA_SIGMA_CHARGE float Difference of Gasteiger sigma charges of the bond atoms
Tcl script A_SIGMA_CHARGE B_TYPE atomchange bondchange b_delta_sigma_charge.xpd
B_DELTA_SIGMA_ELECTRONEGATIVITY float Difference of Gasteiger sigma electronegativity of the bond atoms
Tcl script A_SIGMA_ELECTRONEGATIVITY B_TYPE atomchange bondchange b_delta_sigma_electronegativity.xpd
B_DELTA_TOTAL_CHARGE float Difference of Gasteiger charges (sum of pi and sigma parts) of the bond atoms
Tcl script A_TOTAL_CHARGE B_TYPE atomchange bondchange b_delta_total_charge.xpd
B_DELTA_TOTAL_WALK_COUNT double Difference in total walk count E_TOTAL_WALK_COUNT if bond is cut J. Chem. Inf. Comput. Sci. 2000, 40, 99-106
usexatoms: { value: 1 description: If set, use heteroatom vs. carbon for additional differentiation. By default, non-hydrogen atoms are anonymous datatype: boolean}
usebo: { value: 1 description: If set, use bond order for additional walks datatype: boolean}
Compiled C module M_HEAVY_ATOM_COUNT B_TYPE B_ORDER B_ISAROMATIC B_RING_COUNT A_TYPE A_ELEMENT E_TOTAL_WALK_COUNT atomchange bondchange mol atom bond mod_b_delta_total_walk_count.so
B_FG_SUBSTITUENTS bitvector Functional group substituents on bonds as per the LHASA definition
ketone boolean
aldehyde boolean
acid boolean
ester boolean
amide*1 boolean
amide*2 boolean
amide*3 boolean
carbonium boolean
isocyanate boolean
acid*halide boolean
thioester boolean
amine*3 boolean
aziridine boolean
amine*2 boolean
amine*1 boolean
nitroso boolean
diazo boolean
haloamine boolean
hydrazone boolean
oxime boolean
imine boolean
thiocyanate boolean
isocyanide boolean
nitrile boolean
azo boolean
hydroxylamine boolean
nitro boolean
enamine boolean
amine*oxide boolean
thiol boolean
episulfide boolean
sulfide boolean
sulfoxide boolean
sulfone boolean
c*sulfonate boolean
anhydride boolean
lactam boolean
phosphine boolean
phosphonate boolean
epoxide boolean
ether boolean
peroxide boolean
alcohol boolean
enol*ether boolean
nitrite boolean
o*sulfonate boolean
fluoride boolean
chloride boolean
bromide boolean
iodide boolean
gem*dihalide boolean
trihalide boolean
acetylene boolean
olefin boolean
vic*dihalide boolean
halohydrin boolean
glycol boolean
hydrate boolean
hemiketal boolean
ketal boolean
hemiacetal boolean
acetal boolean
azide boolean
disulfide boolean
allene boolean
vinylsilane boolean
lactone boolean
vinylw boolean
vinyld boolean
esterx boolean
amidz boolean
methylene boolean
carbonyl boolean
carboxyl boolean
halide boolean
amine boolean
amide boolean
selenide boolean
trialkylsilyl boolean
trialkylsiloxy boolean
silylenolether boolean
n*urea*h boolean
n*urea*c boolean
carbamate*h boolean
carbamate*c boolean
o*carbamate boolean
n*carbamate boolean
o*carbonate boolean
dithioacetal boolean
dithioketal boolean
requested boolean
withdrawing boolean
expandable*withdrawing boolean
nonexpandable*withdrawing boolean
donating boolean
leaving boolean
good*leaving boolean
Compiled C module A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE atomchange bondchange atom bond mod_b_fg_substituents.so
B_FLAGS bitset Display attributes for bond
^none:bold,fat:dotted:dashed:lowarrowtip,lowarrow:higharrowtip,higharrow:highwedgetip,highwedge,hightip,lowbase:lowwedgetip,lowwedge,lowtip,lowbase:slash,intersect,intersection:split,wintersect,wslash,wavyslash,wavyintersect,wavyintersection:lowparallelarrow,lowparallel,lowarrow:highparallelarrow,highparallel,higharrow:right:left:crossed:wavy,zigzag:circle,mark1:square,mark2:cross,mark3:anchor,mark4:wedgelocation,wedgehere,wedgeposition:selected:front:back:protected:colorsplit:highlight:doubleslash:hash:resonance:aromatic:invisible:secondary:edge
bold boolean
dotted boolean
dashed boolean
lowarrowtip boolean
higharrowtip boolean
highwedgetip boolean
lowwedgetip boolean
slash boolean
split boolean
lowparallelarrow boolean
highparallelarrow boolean
right boolean
left boolean
crossed boolean
wavy boolean
circle boolean
square boolean
cross boolean
anchor boolean
wedgelocation boolean
selected boolean
front boolean
back boolean
protected boolean
colorsplit boolean
highlight boolean
doubleslash boolean
hash boolean
resonance boolean
aromatic boolean
invisible boolean
secondary boolean
edge boolean
(builtin) never
B_FRAGMENT_CARBON_CHAIN_LENGTH int Maximum length of linked carbon atoms in the fragments containing the respective bond atoms as first path atom if the bond were cut.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_carbon_chain_length.so
B_FRAGMENT_CARBON_COUNT int Number of carbon atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT(carbon). For a bond to hydrogen, one value is zero and the other the molecule carbon count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_carbon_count.so
B_FRAGMENT_COMPLEXITY double The fragment complexity (M_COMPLEXITY equivalent) of the fragment containing the first and second atom after cutting the bond
B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring
B_FRAGMENT_DIRECTION short Indicator whether the bond, as seen from its first atom to its second atom, is the principal substituent connection (i.e. if the bond is cut, the second atom is in the smaller substituent, and the first atom in the core).
magic=-1:none:asstored:symmetrical:reversed:ringbond
criteria: { value: B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH description: Properties used as criteria to determine the core-side and substituent atoms of the bond, in order of decreasing significance datatype: string constraints: propertylist}
Compiled C module B_TYPE B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH B_RING_COUNT atomchange bondchange atom bond mod_b_fragment_direction.so
B_FRAGMENT_ELEMENT_COUNT shortvector Element counts in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_element_count.so
B_FRAGMENT_FORMULA string Hill formula of the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_FORMULA. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
format: { value: ascii enumeration: ascii:html datatype: string}
usequeryatoms: { value: 0 datatype: string}
Compiled C module B_FRAGMENT_ELEMENT_COUNT atomchange bondchange mol atom bond ring mod_b_fragment_formula.so
B_FRAGMENT_HASH uint64 The hashcode (M_HASHY equivalent) of the fragment containing the first and second atom after cutting the bond
Compiled C module B_TYPE B_ORDER B_ISAROMATIC B_HASHGROUP A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_hash.so
B_FRAGMENT_HEAVY_ATOM_COUNT int Number of heavy atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HEAVY_ATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heavy atom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_heavy_atom_count.so
B_FRAGMENT_HETEROATOM_COUNT int Number of heteroatoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HETEROATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heteroatom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_heteroatom_count.so
B_FRAGMENT_STEREO_HASH uint64 The hashcode (M_HASHSY equivalent) of the fragment containing the first and second atom after cutting the bond
Compiled C module B_TYPE A_TYPE B_ISAROMATIC B_STEREO_HASHGROUP A_ELEMENT A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange mol atom bond ring mod_b_fragment_stereo_hash.so
B_FRAMEWORK byte Framework classification 0=ring, 1=sidechain, 2=linker
ring:sidechain,chain:linker,bridge
(builtin) A_FRAMEWORK atomchange bondchange
B_HASH uint64 Bond hashcode
pathlength: { value: 30 datatype: string}
(builtin) A_FRAMEWORK A_HASH B_TYPE B_FRAMEWORK atomchange bondchange
B_HASHGROUP index Hash group id index for bond hash code
(builtin) B_MOL_NUMBER B_HASH atomchange bondchange merge
B_HASH_STEREO byte Hashcode-based bond chirality descriptor
M=-1:undef=0:P=1
useisotope: { value: 0 datatype: string}
(builtin) A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange
B_HETERO_AROMAT_COUNT short Count for the number of heteroaromatic rings the bond participates in
Tcl script B_ISAROMATIC R_HETEROATOM_COUNT R_AROMATIC atomchange bondchange ring b_hetero_aromat_count.xpd
B_ISALPHAARO boolean Flag for bonds which are not aromatic themselves but linked to aromatic atom
(builtin) A_ARORING_COUNT B_TYPE B_ARORING_COUNT atomchange bondchange ring
B_ISAROMATIC boolean Flag whether bond is aromatic or not
(builtin) R_AROMATIC R_TYPE B_TYPE atomchange bondchange ring
B_ISAROTAUTOMERIC short Tautosytem-number for bonds which are in a potentially tautomeric system, including those which would destroy an aromatic system
useimplicith: { value: 0 datatype: string}
maxpathlen: { value: 18 datatype: string}
arotautomers: { value: 1 datatype: boolean}
Compiled C module A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT atomchange bondchange hadd mod_b_isarotautomeric.so
B_ISTAUTOMERIC short Tautosystem number for bonds which are in a potentially tautomeric system
useimplicith: { value: 0 datatype: string}
maxpathlen: { value: 18 datatype: string}
arotautomers: { value: 0 datatype: string}
(builtin) A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT atomchange bondchange hadd
B_LABEL int Arbitrary bond label
(builtin) never
B_LABELCOLOR string X11 style color name of bond labels
color: { value: black datatype: color}
Tcl script never b_labelcolor.xpd
B_LABEL_STEREO byte Label-based bond chirality descriptor
M,MI,-=-1:undef=0:P,PL,+=1
(builtin) never
B_LENGTH float Bond length (taken from 3D-coordinates)
(builtin) A_XYZ atomchange bondchange stereochange 3drelative
B_MAPPING int Bond map computed from A_MAPPING. The compute ensemble must be part of a reaction, with corresponding A_MAPPING for reagent and product ensemble. Unmapped bonds (those not having mapped atoms on both sides) have value 0.
Tcl script atomchange bondchange atom bond reaction b_mapping.xpd
B_MAP_STEREO byte Bond stereo descriptor based on reaction mapping
M,MI,-=-1:undef=0:P,PL,+=1
(builtin) A_MAPPING never
B_MOL_LABEL int Label of molecule bond belongs to
(builtin) A_MOL_LABEL atomchange bondchange merge shuffle hadd mol
B_MOL_NUMBER short Number of molecule bond belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge shuffle hadd mol
B_MOVED_SIGMA_CHARGE float Charge moved during PEOE equilibration during Gasteiger sigma charge/eneg iternation
A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 atomchange bondchange
B_NCICADD_RESONANCE_CROSSED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
B_NCICADD_TAUTO_CROSSED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
B_ORDER byte Bond order
never
B_ORDER_ESTIMATE float Estimation of fractional bond order from 3D coordinates via element pair plus base length/exponent table. Uses external data file b_order_estimate.dat (usually located in ${data_directory}/propdata/b_order_estimate directory) for the atom pair parameters. Bonds perceived from close atom distances are created as type "link" if not yet present, and their frational bond order is larger than the threshold parameter.
threshold: { value: 0.25 description: Minimal found bond order to act upon datatype: double}
patternfile: { value: b_order_estimate.dat datatype: diskfile constraints: readable}
Tcl script A_XYZ A_ELEMENT never b_order_estimate.xpd
B_POLARIZABILITY float Average of atom polarizabilities involved in bond
Compiled C module A_TYPE A_POLARIZABILITY atomchange bondchange mod_b_polarizability.so
B_QUERY compound Bond attributes for structure queries
^none:stereo:aromatic,aro:aliphatic,ali,nonaromatic,inaromatic,unaromatic:ringsystem,ringcount:doublearo,doubleoraro,da,d/a:singlearo,singleoraro,sa,s/a:mustmap:nostereook:symmetric,symmetry:asymmetric,asymmetry:nooverlap:implicitbondorder,implicit,implicitbo:kekulecmp:any:multiaro,multioraro,ma,m/a:multiple,m:offpath:daylightaromatic,daylightaro:singledouble,s/d:singledoublearo,s/d/a
flags bitset
order bitset
ringsize bitset
ringcount bitset
aroringcount bitset
tclproc string
query querytree
varbo double
pyfunction string
never
B_RACEMATE byte Racemate distribution of stereobond
undefined,undef:rac,racemat:pure
atomchange bondchange
B_REACTION_CENTER int Reaction Center information from MDL rxn/rdf file, can also be computed from a reaction with atom mapping information
nocenter=-1:unmarked=0:center=1:nochange=2:madebroken=4:madebrokencenter=5:orderchange=8:orderchangecenter=9:madebrokenorderchange=12:madebrokenorderchangecenter=13
(builtin) B_TYPE A_MAPPING B_ORDER B_ISAROMATIC atomchange bondchange reaction
B_RECAP_FRAGMENTATION boolean Bond which would be cut in the RECAP fragmentation method J. Chem. Inf. Comput. Sci. 38, 1998, 511-522
atomchange bondchange atom bond
B_RINGS intvector Labels of the rings the bond is member in
(builtin) R_LABEL R_TYPE B_TYPE atomchange bondchange merge ring
B_RINGSIZE uint64 Bits indicate membership in ring of size N
ringset: { value: esssr datatype: string}
(builtin) R_TYPE B_TYPE atomchange bondchange ring
B_RING_COUNT short Number of simple (non-enevelope) rings a bond is member of
countenvelopes: { value: 0 datatype: string}
(builtin) B_TYPE R_TYPE atomchange bondchange ring
B_RING_HETEROATOM_COUNT_BITS bitset A bit is set at bit position n for any ESSSR ring the bond is a member of which has n hetero atoms. Chain and bridge bonds have value 0. If the bond is a member of a carbocyclic ESSSR ring, bit position 0 is set.
Compiled C module R_HETEROATOM_COUNT R_TYPE B_TYPE atomchange bondchange atom bond mod_b_ring_heteroatom_count_bits.so
B_RING_SIZE_BITS bitset Bit mask for ring sizes the bond participates in
Compiled C module R_SIZE R_TYPE B_TYPE bondchange ring mod_b_ring_size_bits.so
B_RING_SUBSTITUENT_PATTERN compound Compute relative alignment of ring atom substituents in cases where the ring plane is the stereo-defining anchor, This is done both for ring substituents which are on directly connected ring atoms and those which are distant (for example, 1.4 cis/trans relationships in six-membered rings) and where the ring acts as a pseudo-doublebond. In the first case, the property is set on the ring bond between the substituted ring atoms. In the second case, all bonds which are on one of the shortest paths between two same-ring atoms where the A_STEREOGENIC value is "ringct" get the descriptor. For a simple 1.4 cyclohexane, these are all ring atoms. Note that a 1.3-substituted cyclohexane gets no descriptors in this property: Neither share the substituted ring atoms a bond, nor is the ring acting as a pseudo doublebond. Across-ring stereodescriptors are not set if other ring substituents impress normal atom stereogenicity on the substituted ring atoms, which is for example the case in any 1.x.4 substituent pattern.

Field descriptor is the label-based stereo decriptor for the bond(s).
Value 1/P: low-label off-ring substituents on different sides of ring plane, 1.2-substituents
Value -1/M: Low-label off-ring substituents on same side of ring plane, 1.2-substituents
Value 2/p: low-label off-ring substituents on different sides of ring plane, distant substituents
Value -2/m: Low-label off-ring substituents on same side of ring plane, distant substituents
Value 0: no ring substituent stereo

Fields ligatom1a/ligatom2a are the low-label off-ring substitituent atoms.
Fields ligatom1b/ligatom2b are the secondary off-ring substituent atoms.
@m:M:none:P:p
descriptor byte
ligatom1a int
ligatom1b int
ligatom2a int
ligatom2b int
Compiled C module A_LABEL_STEREO R_TYPE A_LABEL B_TYPE A_STEREOGENIC atomchange bondchange stereochange ring mod_b_ring_substituent_pattern.so
B_ROTATABILITY byte Classification of bond rotatability. Ring bond flag must have precedence over multi-bond flag for E_EFFECTIVE_ROTOR_COUNT
undef:terminal:ring:multiple:spheric,round,roundligand:linear,linearligand:yes:locked:forced
Compiled C module B_TYPE B_ORDER A_TYPE A_ELEMENT A_INAMIDE A_TERMINAL_DISTANCE atomchange bondchange hadd mod_b_rotatability.so
B_SEQUENCE_NUMBER int Sequential bond number for CTX output
(builtin) B_MOL_NUMBER A_SEQUENCE_NUMBER A_TYPE atomchange bondchange merge shuffle hadd mol
B_SSMATCH int Ensemble is structure, property data encodes labels of matching substructure bonds, 0 for unmatched parts
sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
Tcl script never b_ssmatch.xpd
B_SSMATCH_ENVIRONMENT datatree Classigied unmatched structure environment of the substructure bonds, i.e. data on the characteristics of the unmatched structure bonds sprouting from the structure bond matched by this substructure bond. Set by a substructure hit option, not directly computable.
atomchange bondchange atom bond
B_STEREOGENIC byte Can this bond be a stereocenter ?
no:maybe:checkno:yes,checkyes:ringct
simple: { value: 0 datatype: string}
ringsizecheck: { value: 1 datatype: string}
electronegativitycheck: { value: 1 datatype: string}
(builtin) atomchange bondchange hadd
B_STEREOINFO byte Stereo descriptor availability info: 1:Label,2:E/Z,4:cis/trans,8:hash,16:map
^none:label:cip:cistrans:hash:map
(builtin) B_CISTRANS_STEREO B_LABEL_STEREO B_HASH_STEREO B_CIP_STEREO B_MAP_STEREO atomchange bondchange stereochange
B_STEREO_HASH uint64 Stereospecific bond hashcode
(builtin) A_FRAMEWORK A_STEREO_HASH B_FRAMEWORK B_TYPE atomchange bondchange
B_STEREO_HASHGROUP index Hash group id index for stereospecific bond hash code
(builtin) B_MOL_NUMBER B_HASH A_HASH_STEREO B_HASH_STEREO atomchange bondchange merge
B_STMATCH int Ensemble is substructure, property data encodes labels of matching structure bonds, 0 for unmatched parts
sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
Tcl script never b_stmatch.xpd
B_STRAINED boolean Flags for strained bonds according to the Lhasa definition. These are:
endocylic 3/4-membered ring bonds
endocyclic 5-membered ring bonds which are part of a [2.1.1], [2.2.1] or [3.2.1] bicyclic system
trans C=C double bonds in rings smaller than size 10
C=C double bonds exocyclic to 3/4-membered rings
Compiled C module R_TYPE B_TYPE B_ORDER A_TYPE A_LABEL A_ELEMENT B_LABEL_STEREO A_RING_COUNT bondchange ring mod_b_strained.so
B_TEXTLABEL compound Arbitrary textual bond label plus alignment info for plots
left=-1:center=0:right=1
label string
align byte
never
B_TORSION_ANGLE float Torsion angle of atom quartets, encoded as pseudo bond
(builtin) A_XYZ atomchange bondchange 3drelative
B_TRANSFORM_STATUS byte Bond status as result of SMIRKS transformation. Possible values are none: not matched in transform, matched: matched, but unchanged, changed: bond order or attribute changed, new: bond introduced by transform
none:matched:changed:new
atomchange bondchange atom bond
B_TYPE int Bond type
^none:link:normal,valence,vb:hbond,hydrogen:dative:3center:angle,dihedral,3atom:torsion,torsional,4atom:rgroup,rg:nobond,searchnot,not:deloc,delocalized:complex:ionic
never
C_COMMENT string Connection (edge) comment in free format
never
C_DIRECTED boolean Flag indicating whether connection/edge is directed. Global default is given in N_DIRECTED.
Compiled C module atomchange bondchange atom bond mod_c_directed.so
C_GRAPHICS compound Connection (edge) graphics
none:arc:bitmap:image:line:oval,ellipse,ellipsis:polygon:rectangle,rect:text:box:circle:rhombus,diamond:ver_ellipsis:hor_ellipsis:triangle:pentagon:hexagon:octagon:roundedrectangle,roundrectangle,roundrect,roundedrect
type int
attributes dictionary
usehtml: { value: 0 description: Whether to use HTML encoding of the text annotation datatype: boolean}
fontsize: { value: -1 description: Font size (negative value: unset) datatype: int}
font: { value: Verdana description: Font name datatype: string}
fontcolor: { value: black description: Font color (empty is unset) datatype: color constraints: emptycolor}
color: { value: black description: Connection line color (empty is unset) datatype: color constraints: emptycolor}
Tcl script C_NAME never c_graphics.xpd
C_IDENT string Connection (edge) ident string
Compiled C module never mod_c_ident.so
C_LABEL int Connection (edge) label of connections in network objects
Compiled C module never mod_c_label.so
C_LABEL_GRAPHICS compound Connection (edge) label graphics
none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon
type int
attributes dictionary
never
C_NAME string Connection (edge) name in free format
never
C_ONTOLOGY_LINK int Ontology link type
none:is_a:has_part:is_conjugate_base_of:is_conjugate_acid_of:is_tautomer_of:is_enantiomer_of:has_functional_parent:has_parent_hydride:is_substituent_group_from:has_role
never
C_PARTITION int Partition code for connections (edges). If a symbolic name is available, I/O modules modify the enumeration field of the property.
atomchange bondchange atom bond
C_TEXT string Connection (edge) text label
never
C_TYPE string Connection (edge) type in free format
never
C_URL url Connection reference URL
atomchange bondchange atom bond
C_WEIGHT double Graph connection (edge) weight
Compiled C module never mod_c_weight.so
D_AUTHOR compound Dataset author data, computation copies these from the internal object author fields
name string
author string
email string
phone string
orcid string
authorurl url
date date
version string
affiliation string
affiliationurl url
affiliationduns string
doi string
infourl url
street string
city string
zip string
state string
country string
literature string
keywords string
comment string
license string
licenseurl url
category string
repopath string
baseuuid string
versionuuid string
Tcl script never d_author.xpd
D_CHEMDRAW_PAGE diskfile
(switchable between blob diskfile)
Tabular display of structure collection in ChemDraw page
ncols: { value: 3 minvalue: 1 maxvalue: 20 datatype: int}
nrows: { value: 4 minvalue: 1 maxvalue: 20 datatype: int}
offset: { value: 0 minvalue: 0 datatype: int}
filename: { value: {} datatype: string constraints: writeable}
format: { value: cdx enumeration: cdx:cdxml datatype: int}
grid: { value: 1 datatype: boolean}
gridcolor: { value: black datatype: color}
gridselectcolor: { value: orange datatype: color}
papersize: { value: a4 enumeration: a3:a4:a5:a6:a7:b3:b4:b5:b6:letter:legal:executive datatype: int}
border: { value: 12.0 minvalue: 0 maxvalue: 99 datatype: double}
boxspacing: { value: 6.0 minvalue: 0 maxvalue: 99 datatype: double}
bonds: { value: 8 minvalue: 1 maxvalue: 25 datatype: int}
boxborder: { value: 3.0 minvalue: 0 maxvalue: 99 datatype: double}
orientation: { value: portrait enumeration: portrait:landscape datatype: int}
cdxversion: { value: 8.0 datatype: double}
journalstyle: { value: acs enumeration: default:acs,jacs datatype: int}
multipage: { value: 0 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: propertylist}
headerformat: { value: {} datatype: string}
headerfont: { value: Arial datatype: string}
headercolor: { value: black datatype: color}
headerhighlightcolor: { value: red datatype: color}
headerhighlightfilter: { value: {} datatype: string constraints: filtername}
headerfontstyle: { value: none datatype: string}
headerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
header2property: { value: {} datatype: string constraints: propertylist}
header2format: { value: {} datatype: string}
header2font: { value: Arial datatype: string}
header2color: { value: black datatype: color}
header2highlightcolor: { value: red datatype: color}
header2highlightfilter: { value: {} datatype: string constraints: filtername}
header2fontstyle: { value: none datatype: string}
header2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
footerproperty: { value: E_NAME datatype: string constraints: propertylist}
footerformat: { value: {} datatype: string}
footerfont: { value: Arial datatype: string}
footerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
footercolor: { value: black datatype: color}
footerhighlightcolor: { value: red datatype: color}
footerhighlightfilter: { value: {} datatype: string constraints: filtername}
footerfontstyle: { value: none datatype: string}
footer2property: { value: {} datatype: string constraints: propertylist}
footer2format: { value: {} datatype: string}
footer2font: { value: Arial datatype: string}
footer2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
footer2color: { value: black datatype: color}
footer2highlightcolor: { value: red datatype: color}
footer2highlightfilter: { value: {} datatype: string constraints: filtername}
footer2fontstyle: { value: none datatype: string}
headercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int}
footercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int}
Tcl script atomchange bondchange stereochange groupchange dataset d_chemdraw_page.xpd
D_COPYRIGHT string Copyright information
never
D_CREATION_TIME datetime Date of dataset generation
Tcl script never d_creation_time.xpd
D_DATE date Dataset creation date
atomchange bondchange atom bond
D_DESCRIPTION string Free-form description of dataset
never
D_DIVERSITY_SET dataset Select a diverse subset from the source dataset.
property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property}
query: { value: all description: Structure filter query expression datatype: string}
size: { value: 50 description: Target size minvalue: 1 datatype: int}
startindex: { value: -1 description: First structure source index, -1 is random datatype: int}
minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int}
Tcl script atomchange bondchange atom bond d_diversity_set.xpd
D_EMF_IMAGE diskfile Dataset rendered as WMF/EMF image, from assembled E_EMF_IMAGE structure renderings
ncols: { value: 3 minvalue: 1 datatype: int}
nrows: { value: 4 minvalue: 1 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
framewidth: { value: 1 datatype: int}
boxwidth: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int}
boxheight: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerheight: { value: 0 minvalue: 0 datatype: int}
footerheight: { value: 0 minvalue: 0 datatype: int}
comment: { value: {} datatype: string}
commenttype: { value: text enumeration: none:text:property,prop datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
format: { value: pwmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
font: { value: arialn datatype: string}
annotationfontsize: { value: -1 datatype: double}
offset: { value: 0 datatype: int}
imgproperty: { value: E_EMF_IMAGE datatype: string constraints: property}
padding: { value: 1 datatype: int}
boxbgcolor: { value: transparent datatype: color}
boxhighlightcolor: { value: red datatype: string}
selectlist: { value: {} datatype: intvector}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,grayscale,greyscale:color,colour datatype: int}
downloadfilename: { value: {} datatype: string}
Compiled C module E_EMF_IMAGE dataset mod_d_emf_image.so
D_FRAGMENT_NETWORK network Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies.
trace: { value: 0 description: If set, print trace information on the progress of the process datatype: boolean}
mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int}
maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int}
minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int}
bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list}
Tcl script dataset d_fragment_network.xpd
D_FRAGMENT_TABLE table Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies.
mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int}
maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int}
minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
columns: { value: E_SMILES E_HASHY count frequency source destination description: Result table columns datatype: string constraints: list}
maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int}
bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list}
Tcl script dataset d_fragment_table.xpd
D_FUZZY_MCSS structure Maximum common substructure of dataset, determined by non-deterministic fuzzy matching
maxfuzz: { value: 5 datatype: string}
Compiled C module atomchange bondchange stereochange dataset mod_d_fuzzy_mcss.so
D_GIF diskfile
(switchable between string blob diskfile url)
GIF image table of the contents of a dataset, assembled by tiles of E_GIF structure images
ncols: { value: 3 datatype: int}
nrows: { value: 4 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
framewidth: { value: 1 datatype: int}
boxwidth: { value: 200 datatype: int}
boxheight: { value: 200 datatype: int}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerheight: { value: 0 datatype: int}
footerheight: { value: 0 datatype: int}
comment: { value: {} datatype: string}
commenttype: { value: text enumeration: none:text:property datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
format: { value: gif enumeration: gif:png,png24:png8 datatype: string}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
headercolor: { value: black datatype: string}
footercolor: { value: black datatype: string}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: string}
font: { value: arialn datatype: string}
annotationfontsize: { value: -1 datatype: double}
interlace: { value: 0 datatype: boolean}
offset: { value: 0 description: First dataset object to use datatype: int}
imgproperty: { value: E_GIF datatype: string constraints: property}
padding: { value: 1 datatype: int}
boxbgcolor: { value: transparent datatype: color}
boxhighlightcolor: { value: red datatype: color}
selectlist: { value: {} description: Indices of dataset objects to draw with highlight background datatype: intvector}
downloadfilename: { value: {} description: Save file name if http header is used datatype: string}
fixiepngsize: { value: 1 description: Circumvent Windows bug in older releases datatype: boolean}
checkimgsize: { value: 1 datatype: boolean}
Compiled C module E_GIF dataset mod_d_gif.so
D_HASHISY uint64 Stereospecific and isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHISY dataset mod_d_hashisy.so
D_HASHIY uint64 Non-stereospecific but isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHIY dataset mod_d_hashiy.so
D_HASHSY uint64 Stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHSY dataset mod_d_hashsy.so
D_HASHY uint64 Non-stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHY dataset mod_d_hashy.so
D_HTML_PAGE blob
(switchable between blob diskfile)
filename: { value: {} description: Output file name, empty for tmp file datatype: string}
htmlpage: { value: 0 description: If set, write complete HTML page, otherwise write only ExtJS generator statements. datatype: boolean}
title: { value: {} description: Graph title datatype: string}
Tcl script atomchange bondchange atom bond dataset d_html_page.xpd
D_IDENT string Ident string of dataset
Tcl script atomchange bondchange atom bond d_ident.xpd
D_MATCHED_PAIRS compoundvector Identify matched pair molecules, or matched series molecules, in a dataset.
id int
datasetindex int
bond int
centrality double
size int
setindex int
structure structure
mode: { value: pairs description: In pairs mode, always find molecule pairs under any ID. In series mode, if there are more than 2 structures linked, group them all under a common ID. Example: F/Cl/Br-benzene, In pairs mode, find 3 structure pairs, in series mode, find one series with 3 members enumeration: pairs:series datatype: string}
copystructures: { value: 0 description: If set, duplicate the matched pair/set structures with highlighted bonds in B_FLAGS into the "structure" field of this property. If it is not set, only the id/dataset index/bond fields are filled and the structure field is set to NULL datatype: boolean}
cutxhbonds: { value: 1 description: If set, allow bonds between hydrogen and heteroatom to be part of a pair or set definition datatype: boolean}
cutchbonds: { value: 1 description: If set, allow bonds between hydrogen and carbon to be part of a pair or set definition datatype: boolean}
cutcxbonds: { value: 1 description: If set, allow bonds between carbon and heteroatom to be part of a pair or set definition datatype: boolean}
cutccbonds: { value: 1 description: If set, allow bonds between carbon to be part of a pair or set definition datatype: boolean}
cutxxbonds: { value: 1 description: If set, allow bonds between heteroatoms to be part of a pair or set definition datatype: boolean}
cutchainchainbonds: { value: 1 description: If set, allow bonds between two chain atoms to be part of a pair or set definition datatype: boolean}
cutringchainbonds: { value: 1 description: If set, allow bonds between a ring and a chain atom to be part of a pair or set definition datatype: boolean}
cutringringbonds: { value: 1 description: If set, allow non-ring bonds between ring atoms to be part of a pair or set definition datatype: boolean}
cutpreference: { value: first description: Define which bonds should be preferred if there a multiple possibilities to define a pair or set. All: report all possibilities, first: report first possibility found, core: report most central cut, peripheral: report most peripheral cut for any given set or series enumeration: all:first:core,central:peripheral datatype: string}
minheavyatoms: { value: 0 description: Minimum number of heavy atoms which must be present in the R-group part datatype: int}
maxheavyatoms: { value: 999 description: Maximum number of heavy atoms which must be present in the R-group part datatype: int}
formulafilter: { value: {} description: A formula match expression which possible R-groups must match datatype: formulamatch}
removesubsets: { value: 0 description: If set, remove (in series mode) sets which are a subset of a larger set datatype: boolean}
Compiled C module B_FRAGMENT_HASH B_FRAGMENT_DIRECTION B_FRAGMENT_ELEMENT_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_CENTRALITY B_STEREO_HASHGROUP A_RING_COUNT A_TYPE A_ELEMENT atomchange bondchange atom bond dataset mod_d_matched_pairs.so
D_MCSS structure Maximum common substructure of dataset
cmpflags: { value: bondorder datatype: string}
hitflags: { value: {} datatype: string}
exclflags: { value: st_h|ss_h datatype: string}
Compiled C module atomchange bondchange stereochange dataset mod_d_mcss.so
D_METADATA dictionary Dublin Core metadata for dataset
never
D_NAME string Free-form user-defined dataset name
never
D_NEW_FLAG boolean Dataset flag for new compounds. THis is primarily used in the CHAI file format.
never
D_PROGRAM string Program source of dataset
never
D_PS_PAGES diskfile Postscript dataset rendering
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 datatype: boolean}
ncols: { value: 2 datatype: int}
nrows: { value: 3 datatype: int}
papersize: { value: A4 enumeration: none:a3:a4:a5:a6:a7:b3:b4:b5:b6:letter,usletter:legal,uslegal:executive,exec,usexecutive,usexec datatype: string}
border: { value: 10 datatype: int}
title: { value: {} datatype: string}
comment: { value: {} datatype: string}
space: { value: 5 datatype: int}
frame: { value: line enumeration: none:line:shadow datatype: string}
boxproperty: { value: E_NAME datatype: string constraints: property}
orientation: { value: portrait enumeration: none:landscape,wide,quer,querformat:portrait,tall,hoch,hochformat datatype: string}
colormode: { value: bow enumeration: bow,bw:wob:cow,color:cob datatype: string}
headerfontsize: { value: 12 datatype: double}
footerfontsize: { value: 12 datatype: double}
labelfontsize: { value: 10 datatype: double}
pagelimit: { value: 100 minvalue: 1 maxvalue: 9999 datatype: int}
pageoffset: { value: 0 minvalue: 0 maxvalue: 9999 datatype: int}
psheader: { value: all enumeration: all:none:prolog:trailer datatype: string}
pagecount: { value: 0 minvalue: -1 maxvalue: 9999 datatype: int}
shadow: { value: 3 datatype: int}
eps: { value: 0 datatype: boolean}
binder: { value: none enumeration: none:left:top:right:bottom datatype: string}
binderwidth: { value: 30 datatype: int}
logotext: { value: {} datatype: string}
printpagecount: { value: -1 datatype: int}
headerheight: { value: 14 datatype: int}
footerheight: { value: 14 datatype: int}
labelheight: { value: 12 datatype: int}
nameheight: { value: 12 datatype: int}
namefontsize: { value: 10 datatype: int}
atomcolor: { value: {} description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string constraints: emptycolor}
downloadfilename: { value: {} datatype: string}
Compiled C module E_EPS_IMAGE atomchange bondchange stereochange groupchange dataset mod_d_ps_pages.so
D_SCAFFOLD_TABLE table A list of Ertl-type scaffolds extracted from a file. The table contains the counts and SMILES strings as columns, plus row-attached structures.
maxrecs: { value: -1 description: The maximum number of records to process, -1 is infinite datatype: int}
maxscaffolds: { value: -1 description: The maximum number of scaffolds to record, -1 is infinite datatype: int}
maxsimplification: { value: 1 description: The maximum number of scaffolds simplification steps to perform, -1 is infinite datatype: int}
compoundfilter: { value: all description: A compound filter expression (see 'ens scan' command) scaffolds must match datatype: string}
Tcl script E_SMILES E_SCAFFOLD_TREE_STRUCTURE atomchange bondchange stereochange atom bond d_scaffold_table.xpd
D_SCAFFOLD_TREE datatree The scaffolds of the structures in the dataset in sorted, hierarchical order. The first node a an empty root node, and its children are the irreducible scaffolds. The individual scaffold nodes of the tree contain SMILES strings as value and the (non-stereo/non-isotope) ensemble hashcode as name, followed by all more complex scaffolds which are reduced to the current scaffold by one simplification step. J. Chem. Inf. Model. 2007, 47, 47-58
maxlevel: { value: -1 description: Maximum tree depth to generate, -1 for unlimited datatype: int}
includeoriginals: { value: 0 description: If set, include the base structures. By default, only the scaffolds are included datatype: boolean}
hashcode: { value: E_HASHY description: The hashcode property to be used to check structure identity datatype: string constraints: property}
nodenameproperty: { value: E_HASHY description: Instance values of this property are stored as node names. datatype: string constraints: property}
auxproperties: { value: {} description: Instance data of these properties is appended to the right of the SMILES data in the nodes datatype: string constraints: propertylist}
Tcl script atomchange bondchange atom bond dataset d_scaffold_tree.xpd
D_SIMILARITY_MATRIX intmatrix Similarity matrix between structures in dataset, with dataset element indices as matrix indices
property: { value: E_SCREEN datatype: string constraints: property}
method: { value: tanimoto datatype: string}
Tcl script E_SCREEN atomchange bondchange merge atom bond dataset d_similarity_matrix.xpd
D_SIZE int Dataset size
Tcl script dataset d_size.xpd
D_SMALLWORLD_NETWORK network Sample implementation of R. Sayles SmallWorld network for accelerated MCSS searching
useelements: { value: 1 datatype: boolean}
usebondorders: { value: 1 datatype: boolean}
addsingleatomfragments: { value: 0 datatype: boolean}
Compiled C module E_HASHY B_HASHGROUP A_ELEMENT A_LABEL B_LABEL A_TYPE B_TYPE B_ISAROMATIC B_RING_COUNT A_SUBSTITUENT_COUNT E_NMOLECULES E_HEAVY_ATOM_COUNT atomchange bondchange atom bond dataset mod_d_smallworld_network.so
D_SOURCE string Free-form dataset source description
never
D_SUBSTRUCTURE_HIERARCHY network A tree-style network of substructure hierarchies of the structures in the dataset.
storestructures: { value: 0 description: If set, store the structures in the nodes in property V_STRUCTURE datatype: boolean}
storeimages: { value: 0 description: If set, store an image of the structures in the nodes in property V_GRAPHICS datatype: boolean}
directory: { value: img description: Image directory datatype: string constraints: directory}
imgparameters: { value: width 100 height 100 bgcolor black atomcolor element bondcolor white format png frame 0 bonds 6 description: Image parameters datatype: dictionary}
ssmatchflags: { value: -excludeh all description: Extra flags to pass to the substructure matcher datatype: string}
auxlinks: { value: 0 description: if set, create additional links to alternative matches in the same level datatype: boolean}
Tcl script atomchange bondchange atom bond dataset d_substructure_hierarchy.xpd
D_SVG_IMAGE diskfile
(switchable between string blob diskfile url xmlstring)
SVG image table of the contents of a dataset, assembled by tiles of E_SVG_IMAGE structure images
ncols: { value: 3 datatype: int}
nrows: { value: 4 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
framewidth: { value: 1 datatype: int}
boxwidth: { value: 200 datatype: int}
boxheight: { value: 200 datatype: int}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerheight: { value: 0 datatype: int}
footerheight: { value: 0 datatype: int}
comment: { value: {} datatype: string}
commenttype: { value: text enumeration: none:text:property datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
headercolor: { value: black datatype: string}
footercolor: { value: black datatype: string}
font: { value: arialn datatype: string}
usewebfont: { value: 0 datatype: boolean}
annotationfontsize: { value: -1 datatype: double}
offset: { value: 0 description: First dataset object to use datatype: int}
imgproperty: { value: E_SVG_IMAGE datatype: string constraints: property}
padding: { value: 1 datatype: int}
boxbgcolor: { value: transparent datatype: color}
boxhighlightcolor: { value: red datatype: color}
selectlist: { value: {} description: Indices of dataset objects to include, if empty, use all datatype: intvector}
downloadfilename: { value: {} description: Save file name if http header is used datatype: string}
id: { value: {} datatype: string}
title: { value: {} datatype: string}
standalone: { value: 1 datatype: boolean}
xmlheader: { value: 1 datatype: boolean}
metadata: { value: 1 datatype: boolean}
footerproperty: { value: {} datatype: string constraints: property}
headerproperty: { value: {} datatype: string constraints: property}
checkimgsize: { value: 1 datatype: boolean}
Compiled C module E_SVG_IMAGE dataset mod_d_svg_image.so
D_TREE_DATA_GIF diskfile
(switchable between string blob diskfile url)
Rendering of tree-style property data (must be of property datatype "datatree") as a GIF/PNG image using a modified Reingold-Tilford tree layout algorithm.
property: { value: D_SCAFFOLD_TREE description: Property to read rendered data from datatype: string constraints: property}
treeindex: { value: 0 datatype: string}
maxlevel: { value: -1 datatype: int}
boxwidth: { value: 100 datatype: int}
boxheight: { value: 100 datatype: int}
treedistance: { value: 10 description: Minimum horizontal distance between boxes on a level which do not have the same parent datatype: int}
siblingdistance: { value: 5 description: Minimum horizontal distance between boxes on a level which do have the same parent datatype: int}
leveldistance: { value: 25 description: Distance between lower box Y of parent level and upper box Y of child level datatype: int}
border: { value: 5 description: Unused pixels around tree datatype: int}
decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean}
showname: { value: 0 description: If set, include the node name in rendering datatype: boolean}
showcount: { value: 0 description: If set, include non-negative count node fields in rendering datatype: boolean}
interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean}
alignstructures: { value: 1 description: If structures are rendered, align them hierarchically datatype: boolean}
excluderoot: { value: 0 description: If set, do not render root node datatype: boolean}
framewidth: { value: 0 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
linecolor: { value: red datatype: color}
boxframecolor: { value: blue datatype: color}
boxbgcolor: { value: grey90 datatype: color}
format: { value: png enumeration: gif:png,png24:png8 datatype: string}
font: { value: arialn datatype: string}
fontsize: { value: 8.0 datatype: double}
filename: { value: {} description: Output file name, if data type is diskfile. If empty, generate /tmp file datatype: diskfile constraints: writeable}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
Compiled C module atomchange bondchange atom bond dataset mod_d_tree_data_gif.so
D_WATERMARK double Watermark detection in a set of structures with 3D coordinates
key: { value: LNTSCSWW description: Message encoder key datatype: string}
message: { value: CACTVS Watermark description: Encoded message datatype: string}
scale: { value: 100 datatype: double}
sigma: { value: 1.0 datatype: double}
spread: { value: 1 datatype: int}
markhydrogens: { value: 0 description: Include hydrogens in atoms encoding the message datatype: boolean}
alignpmi: { value: 1 description: Align 3D atomic coordinates to PMI datatype: boolean}
usesensitivity: { value: 0 description: If set, use A_WATERMARK_SENSITITIVY data to tune coordiante shifts to minimize energy distortions datatype: boolean}
Compiled C module A_XYZ A_ELEMENT A_TYPE A_SMILES_RANK A_WATERMARK_SENSITIVITY E_HASHY dataset mod_d_watermark.so
D_XYPLOTENERGY double Plot pseudo energy - debug property, not intended for production use
maximprove: { value: 100 datatype: int}
maxcycle: { value: 100 datatype: int}
uselast: { value: 0 datatype: boolean}
Compiled C module A_XY A_ELEMENT A_TYPE B_TYPE dataset mod_d_xyplotenergy.so
E_ACROS_URL url Catalog URL of structure for Acros Organics/Fisher Scientific
Tcl script atomchange bondchange atom bond e_acros_url.xpd
E_ACTIVE_AIDSET intvector Set of PubChem assay IDs testing this compound as active
Tcl script E_CID atomchange bondchange stereochange e_active_aidset.xpd
E_ADJACENCY_MATRIX intmatrix Standard non-canonical adjacency matrix for the representation of compounds, with bond orders in i/j elements and free electrons in i/i elements. If there is no bond, the matrix element value is zero.
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS atomchange bondchange atom bond e_adjacency_matrix.xpd
E_AIDSET intvector Set of PubChem assay IDs where this compoundwas tested
Tcl script E_CID atomchange bondchange stereochange e_aidset.xpd
E_AIDSET_URL url PubChem assay database URL
Tcl script E_AIDSET atomchange bondchange stereochange merge e_aidset_url.xpd
E_ALFA_AESAR_ID string Structure ID in the AlfaAesar catalog(www.alfa.com)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_alfa_aesar_id.xpd
E_ALFA_AESAR_URL url Data page in the AlfaAesar catalog (www.alfa.com)
Tcl script E_ALFA_AESAR_ID atomchange bondchange atom bond e_alfa_aesar_url.xpd
E_ALIRING_COUNT short Number of aliphatic rings the ensemble contains
ringtypes: { value: esssr description: Ringset to perform count on enumeration: ^none:sssr:esssr,triple:k:envelope datatype: int}
Compiled C module R_AROMATIC R_TYPE atomchange bondchange atom bond ring mod_e_aliring_count.so
E_AMINO_ACID_SEQUENCE string Amino acid sequence in 1- or 3-letter letter code. Can be computed from molecular structure with standard amino acid set.
nomenclature: { value: a description: Whether to use single-letter amino acid codes (a) or 3-letter codes (aaa) enumeration: a,letter1=1:aaa,letter3=3 datatype: int}
encodeterminals: { value: 0 description: If set, include H- and -OH terminal encodings datatype: boolean}
encodebridges: { value: 0 description: If set, encode SS disulfide bridges in (x) format datatype: boolean}
separator: { value: {} description: Separator character between AA encodings (can be empty) datatype: string}
Compiled C module M_AMINO_ACID_SEQUENCE atomchange bondchange mol atom bond mod_e_amino_acid_sequence.so
E_ANNOTATION choicevector Graphical annotation objects of an ensemble. Thre various graphicsl objects supported by this property are described as separate proerties referred as choice variant fields.
text compound
rectangle compound
ellipse compound
roundedrectangle compound
polyline compound
bracket compound
A_XY never
E_AOPWIKI_URL url Display URL in the AOP Wiki (Adverse Outcome Pathway, https://aopwiki.org)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_aopwiki_url.xpd
E_ARORING_COUNT short Count of aromatic rings in ESSSR
ringtypes: { value: esssr description: Ringset to perform count on enumeration: ^none:sssr:esssr,triple:k:envelope datatype: int}
Compiled C module R_AROMATIC R_TYPE atomchange bondchange atom bond ring mod_e_aroring_count.so
E_ASCII_IMAGE string
(switchable between string unicode)
ASCII (or Unicode) rendering of a chemical structure.

Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the last line.
width: { value: 40 minvalue: 25 maxvalue: 256 datatype: int}
height: { value: 30 minvalue: 25 maxvalue: 256 datatype: int}
showcharge: { value: 0 datatype: boolean}
useunicode: { value: 1 datatype: boolean}
bonds: { value: 10 minvalue: 3 maxvalue: 25 datatype: double}
usecolor: { value: 0 datatype: boolean}
usefontstyle: { value: 0 datatype: boolean}
showradical: { value: 0 datatype: boolean}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,exten ded,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,y es datatype: int}
csymbol: { value: all enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: white datatype: color}
highlightcolor: { value: red datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
frame: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
crop: { value: left|right|top|bottom enumeration: ^none:left:right:top:bottom datatype: bitset}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
usealtcharset: { value: 0 datatype: boolean}
leadnewline: { value: 0 datatype: boolean}
tailnewline: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
hcolor: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
unicodeforringbonds: { value: macrocycles enumeration: no,never:macrocycles,largerings:yes,always datatype: int}
badunicodechars: { value: 0x2571 0x2572 0x2573 0x2afd description: Codes of Unicode chars which should not be used, for example because they are missing in the terminal font comment:
0x2afd: double slash, 0x244a: double backslash,
0x2500: horizontal single line, 0x2501: horizontal bold single line, 0x2502: vertical single line,
0x2504: vertical bold single line, 0x2504: horizontal dotted line, 0x2506: vertical dotted line,
0x250c: corner lower right, 0x2510: corner lower left, 0x2514: corner upper right, 0x2518: corner upper left,
0x2550: horizontal double line, 0x2551: vertical double line, 0x2554: double corner lower right,
0x2557: double corner lower left, 0x255A: double corner upper right, 0x255D: double corner upper left,
0x2571: diagonal lower left to upper right, 0x2572: diagonal upper left to lower right, 0x2573: cross,
0x2630: horizontal triple line
datatype: string constraints: list}
lineprefix: { value: {} description: Characters to add to the 2nd and later lines, for example to compensate for database table formatting datatype: string}
Compiled C module A_TYPE A_ELEMENT A_FLAGS B_FLAGS A_QUERY B_QUERY A_FORMAL_CHARGE A_RESIDUE A_SYMBOL A_XSYMBOL A_XY A_HSPECIAL A_CSPECIAL A_COLOR A_ANNOTATION B_TYPE B_LABEL B_ORDER B_COLOR R_TYPE atomchange bondchange stereochange merge mol atom bond mod_e_ascii_image.so
E_ASTATECH_ID string Catalog ID from AstaTech (astatechinc.om)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_astatech_id.xpd
E_ASTATECH_URL url Catalog display URL for AstaTech catalog (astatechinc.om)
Tcl script E_ASTATECH_ID atomchange bondchange stereochange atom bond e_astatech_url.xpd
E_ASYNCSERVER string Dummy property to test asynchronous client/server property computation/communication
never
E_ATOMHASH_COUNT int Number of different basic atom hash codes
(builtin) E_HASHGROUP_COUNT_A atomchange bondchange merge
E_AUTHOR compound Information about the original author of a structure or related document
name string
author string
email string
phone string
orcid string
authorurl url
date date
version string
affiliation string
affiliationurl url
affiliationduns string
doi string
infourl url
street string
city string
zip string
state string
country string
literature string
keywords string
comment string
license string
licenseurl url
category string
repopath string
baseuuid string
versionuuid string
never
E_AUTODOCK4_TORSIONAL_FREEDOM byte Torsional freedom parameter for Audock 4. Used in the I/O modules for the Autodoc4 PDBQT file format.
atomchange bondchange stereochange 3drelative
E_AUXILIARY_SCREEN bitvector Auxiliary custom structure search screens, configurable via pattern parameter or file
patternfile: { value: {} datatype: diskfile constraints: readable}
patterns: { value: N=[N+]=[N-] datatype: string}
aromode: { value: strict enumeration: strict:lenient:default datatype: int}
Tcl script atomchange bondchange stereochange hadd e_auxiliary_screen.xpd
E_BARCODE blob
(switchable between string blob diskfile)
Barcodes in various formats as image data, returned either as a blob or disk file
code: { value: qrcode description: barcode encoding standard enumeration: code39,39:code39x,39x:code128,128:ucc,ean,ucc/ean,ean/ucc:qrcode,qr,qrc datatype: int}
format: { value: png description: image format enumeration: gif:png,png24:png8 datatype: string}
mode: { value: property description: encode either property data or directly specified data value enumeration: property:value datatype: int}
value: { value: E_IDENT datatype: string}
filename: { value: {} datatype: string constraints: writeable}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
width: { value: -1 minvalue: -1 maxvalue: 512 datatype: int}
height: { value: 15 minvalue: 8 maxvalue: 50 datatype: int}
checksum: { value: 1 datatype: boolean}
bgcolor: { value: white datatype: color}
fgcolor: { value: black datatype: color}
showtext: { value: default description: Whether to also print ASCII text on the label enumeration: no:default:yes datatype: int}
font: { value: arialn datatype: string}
fontsize: { value: 8 minvalue: 7 maxvalue: 24 datatype: int}
antialias: { value: 1 datatype: boolean}
widebarfactor: { value: 3 description: Multiplier for 'wide' bars for codes which support that minvalue: 2 maxvalue: 5 datatype: int}
linewidth: { value: 1 description: Minimum line width minvalue: 1 maxvalue: 3 datatype: int}
downloadfilename: { value: {} description: If http header is generated, default download filename at client side datatype: string}
eclevel: { value: Q description: error correction level for qr encoding enumeration: L:M:Q:H datatype: int}
Compiled C module never mod_e_barcode.so
E_BARCODE_ID string Barcode tracking ID
never
E_BEILSTEIN_NUMBER int Beilstein registry number for structure ensemble
Tcl script atomchange bondchange stereochange merge
E_BENZENOID_INDEX double The count of benzene ESSSR rings divided by the total number of aromatic ESSSR rings. Zero in case there are no aromatic rings. Roughley and Jordan, J. Med. Chem. 2011, 54, 3451-3479
Compiled C module R_TYPE R_AROMATIC R_HETEROATOM_COUNT atomchange bondchange atom bond mod_e_benzenoid_index.so
E_BINDINGDB_URL url Structure display URL for BindingDB database (www.bindingdb.org)
Tcl script atomchange bondchange atom bond e_bindingdb_url.xpd
E_BINDING_AFFINITY qualifiedfloat General binding affinity descriptor
atomchange bondchange stereochange atom bond
E_BIOCYC_ID string Database identifier in the BioCyc database (biocyc.org)
Tcl script E_CID atomchange bondchange stereochange atom bond e_biocyc_id.xpd
E_BIOCYC_URL url Display URL for a compound in the BioCyc database (biocyc.org)
Tcl script E_BIOCYC_ID atomchange bondchange stereochange atom bond e_biocyc_url.xpd
E_BOND_ORDER_COUNT intvector Count of bond orders (index 5==aromatic, other bond orders are index to count vector, bond order 0 for non-standard bonds)
special int
single int
double int
triple int
quadruple int
aromatic int
excludeh: { value: 0 datatype: boolean}
Compiled C module B_TYPE B_ORDER A_TYPE A_ELEMENT atomchange bondchange mod_e_bond_order_count.so
E_BP floatpair Boiling point in Kelvin, with optional temperature range
value float
range float
pressure: { value: 760 datatype: double}
pressureunit: { value: Torr datatype: string}
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE atomchange bondchange
E_BRACKET_ANNOTATION compound Bracket as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION.
{} {} {} ROUND:SQUARE:BRACES:CHEVRONS SINGLE:DOUBLE
coords floatvector
linecolor color
linewidth float
type int
orientation int
A_XY never
E_BRENDA_ID int Ligand ID in the BRENDA database (www.brenda-enzymes.org)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_brenda_id.xpd
E_BRENDA_URL url Ligand display URL in the BRENDA database (www.brenda-enzymes.org)
Tcl script E_BRENDA_ID atomchange bondchange stereochange atom bond e_brenda_url.xpd
E_BRENK_ALERTS stringvector Structural alerts as per Brenk et al. (see literature reference) Brenk, R. et al., ChemMedChem 3, 435 (2008)
Tcl script A_FORMAL_CHARGE A_ELEMENT B_ORDER B_ARORING_COUNT A_ARORING_COUNT atomchange bondchange atom bond e_brenk_alerts.xpd
E_BRICS_FRAGMENTS structure Fragmentation of the structure according to the Raray BRICS rules. ChemMedChem 2008, 3, 1503
shredderpatternfile: { value: brics_shred.smarts datatype: diskfile constraints: readable}
excludepatternfile: { value: brics_exclude.smarts datatype: diskfile constraints: readable}
trace: { value: 0 datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER B_FRAGMENT_CARBON_COUNT B_FRAGMENT_CARBON_CHAIN_LENGTH atomchange bondchange atom bond e_brics_fragments.xpd
E_BRUNS_WATSON_DEMERIT compound An implementaton of the Bruns/Watson structural MedChem filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a score between 0 (nothing found) up to an integer >= 100. 100 is the threshold where a comoiund should be rejected, values inbetween are scaled demerits. By default the check stops after the threshold has been reached - it can happen that the sum of demerits at that time has reached exactly 100 or a higher value. It is possible to force the use of the complete rule set by a parameter to tally up the complete set of disagreeable features. The rule set is editable and can be user-expanded. The query files are located at $DATADIR/propdata/e_bruns_watson_demerit. J. Med. Chem. 2012, 55, 9763-9772
demerit int
features dictionary
useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold has been reached, the evaluation stops. datatype: boolean}
reportallrules: { value: 0 description: If set, report on the match scores of all applied rules, not just the ones which change the demerit score datatype: boolean}
threshold: { value: 100 description: The threshold after which to stop further computation datatype: int}
Compiled C module E_BRUNS_WATSON_INITIAL_DEMERIT atomchange bondchange atom bond mod_e_bruns_watson_demerit.so
E_BRUNS_WATSON_INITIAL_DEMERIT compound Bruns/Watson non-substructural filters as published in J. Med. Chem. 2012, 55, 9763-9772.
The return value is a value between 0 and 100, where 100 is outright rejection, 0 no problems found, and values inbetween for demerit points.
J. Med. Chem. 2012, 55, 9763-9772
demerit int
features dictionary
heavy_atom_lower_cutoff: { value: 7 description: Reject compound if fewer heavy atoms found datatype: int}
heavy_atom_upper_cutoff: { value: 40 description: Reject compound if more heavy atoms found datatype: int}
heavy_atom_demerit_threshold: { value: 25 description: Demerit compound if more heavy atoms found datatype: string}
use_formal_charge: { value: 0 description: If set, use A_FORMAL_CHARGE for plus(minus rules. By default, use E_CHARGED_GROUP_COUNTS datatype: boolean}
useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold of 100 has been reached, the evaluation stops. datatype: boolean}
threshold: { value: 100 description: The threshold after which to stop further computation datatype: int}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT A_MOL_NUMBER A_HEAVY_SUBSTITUENT_COUNT A_RING_COUNT A_FORMAL_CHARGE A_ISOTOPE R_TYPE A_UNSATURATION A_CH2_CHAIN_LENGTH E_NSSSR atomchange bondchange atom bond mod_e_bruns_watson_initial_demerit.so
E_CAMEO_ID int Registration ID in Cameo Chemicals safety database (https://cameochemicals.noaa.gov).
Tcl script E_CAS atomchange bondchange stereochange atom bond e_cameo_id.xpd
E_CAMEO_URL url Data display URL in Cameo Chemicals safety database (https://cameochemicals.noaa.gov).
Tcl script E_CAMEO_ID atomchange bondchange stereochange atom bond e_cameo_url.xpd
E_CANONIC_TAUTOMER structure Canonic tautomer form of ensemble, selected from a rated collection of generated tautomers.
maxtautomers: { value: 500 description: Maximum number of tautomers to generate and rate datatype: int}
maxtransforms: { value: -1 description: Maximum number of tautomer transforms to apply datatype: int}
useneutralform: { value: 0 description: If set, compute on E_NEUTRALIZED_STRUCTURE instead of current structure datatype: boolean}
preservegroups: { value: 0 datatype: boolean}
Compiled C module A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange merge mol atom bond mod_e_canonic_tautomer.so
E_CARBON_COUNT int Number of carbon atoms in ensemble - the same as E_ELEMENT_COUNT(6)
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_carbon_count.so
E_CAS string Chemical Abstracts registry number for structure ensemble
useresolver: { value: 1 datatype: string}
usepubchem: { value: 1 datatype: string}
uselookchem: { value: 0 datatype: string}
Tcl script atomchange bondchange stereochange merge
E_CAS_URL url CommonChemistry URL linked via CAS number. By default the validity of the target is not verified - set parameter to perform this check.
verify: { value: 0 datatype: boolean}
Tcl script E_CAS atomchange bondchange stereochange merge e_cas_url.xpd
E_CATALOG compound Catalog data
producer stringvector
catnum stringvector
country stringvector
packsize intvector
purity shortvector
price intvector
atomchange bondchange stereochange merge
E_CATALOG_CAS stringvector CAS numbers of compound in catalog
never
E_CATALOG_NAMES stringvector Names of compound in a catalog
never
E_CCRIS_URL url Display URL in EPA CCRIS (Chemical Carcinogenesis Research Information System, https://toxnet.nlm.nih.gov/newtoxnet/ccris.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_ccris_url.xpd
E_CDXML_IMAGE diskfile
(switchable between blob diskfile xmlstring)
A standard structure rendering in the ChemDraw XML format. This is not a complete file which could be loaded into ChemDraw, but a building block to assemble CDXML files.
width: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int}
height: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int}
bonds: { value: 8 minvalue: 2 maxvalue: 32 datatype: int}
filename: { value: {} datatype: string constraints: writeable}
border: { value: 12 minvalue: 0 maxvalue: 256 datatype: int}
idstart: { value: -1 minvalue: -1 datatype: int}
frame: { value: 0 datatype: boolean}
xoffset: { value: 8 datatype: double}
yoffset: { value: 8 datatype: double}
framecolor: { value: black datatype: color}
markcolor: { value: blue datatype: color}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT B_FLAGS A_FLAGS atomchange bondchange stereochange merge mol atom bond mod_e_cdxml_image.so
E_CDXML_STRING xmlstring Structure encoded in CDXML (CambridgeSoft)
Tcl script atomchange bondchange stereochange merge hadd atom bond e_cdxml_string.xpd
E_CENTER compound Box, geometric and mass-weighted ensemble center
box floatvector
geo floatvector
mass floatvector
coordinateproperty: { value: A_XYZ datatype: string}
useh: { value: 1 datatype: string}
(builtin) E_XYZEXTENT A_WEIGHT A_XYZ atomchange bondchange 3drelative 3dabsolute
E_CHANGEDATE date Change data time stamp for molecule
Tcl script never e_changedate.xpd
E_CHARGE short Sum of charges in ensemble
(builtin) A_FORMAL_CHARGE atomchange
E_CHARGED_ATOM_COUNT int Number of atoms which are formally charged and not direclty adjacent to an atom of opposite formal charge (such as in ionic nitro groups).
Compiled C module A_TYPE A_FORMAL_CHARGE B_TYPE atomchange bondchange atom bond mod_e_charged_atom_count.so
E_CHARGED_GROUP_COUNTS intpair Counts of groups charged positively or negatively under neutral conditions in protic solvents. This is a simple guestimate from A_HYDROGEN_BONDING, using acidic and basic groups as starting points and combining close centers (i.e. a P(=O)(OH)2 group with 2 acidic protons only gets a single positive charge count).
positive int
negative int
Compiled C module M_CHARGED_GROUP_COUNTS atomchange bondchange atom bond mod_e_charged_group_counts.so
E_CHEBI_ID string ChEBI ID (www.ebi.ac.uk/chebi)
Tcl script E_STDINCHI atomchange bondchange stereochange merge e_chebi_id.xpd
E_CHEBI_URL url ChEBI structure data display URL
urlencoding: { value: 1 datatype: boolean}
Tcl script E_CHEBI_ID atomchange bondchange stereochange merge e_chebi_url.xpd
E_CHECKDATE date Check data time stamp for molecule
Tcl script never e_checkdate.xpd
E_CHEMAGORA_URL url Display link for ChemAogra (chemagora.jrc.ec.europa.eu)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_chemagora_url.xpd
E_CHEMBASE_ID int Record ID in Chembase (en.chembase.cn)
matchatomstereo: { value: 1 datatype: boolean}
matchbondstereo: { value: 1 datatype: boolean}
matchisotopes: { value: 1 datatype: boolean}
matchcharges: { value: 1 datatype: boolean}
matchradicals: { value: 1 datatype: boolean}
Tcl script atomchange bondchange atom bond e_chembase_id.xpd
E_CHEMBASE_URL url Display URL in ChemBase database (en.chembase.cn)
Tcl script E_CHEMBASE_ID atomchange bondchange atom bond e_chembase_url.xpd
E_CHEMBL_ASSAY_IDS stringvector ChEMBL assay IDs which test the substance
limit: { value: 5000 description: Maximum number of assay IDs to retrieve minvalue: 1 datatype: int}
Tcl script atomchange bondchange atom bond e_chembl_assay_ids.xpd
E_CHEMBL_ID string ChEMBL ID (https://www.ebi.ac.uk/chembl/)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange merge e_chembl_id.xpd
E_CHEMBL_MEDCHEM_FRIENDLY boolean Implementation of the simple CHEMBL MedChemFriendly filter, a simple substructure-based exclusion list.
Tcl script atomchange bondchange atom bond e_chembl_medchem_friendly.xpd
E_CHEMBL_URL url ChEMBL compound data display URL (https://www.ebi.ac.uk/chembl)
Tcl script E_CHEMBL_ID atomchange bondchange stereochange merge e_chembl_url.xpd
E_CHEMBUYERSGUIDE_IDS compoundvector Get company name and their catalog number by querying chembuyersguide.com via full-structure search.
name string
catalogno string
Tcl script atomchange bondchange atom bond e_chembuyersguide_ids.xpd
E_CHEMDB_ID string Structure ID in the NIH NIAID ChemDB database (https://chemdb.niaid.nih.gov)
Tcl script E_CAS atomchange bondchange atom bond e_chemdb_id.xpd
E_CHEMDB_URL url Data display URL for the NIH NIAID ChemDB database
Tcl script E_CHEMDB_ID atomchange bondchange stereochange atom bond e_chemdb_url.xpd
E_CHEMDIV_ID string ID of structure in ChemDiv (chemistryondemand.com) database
Tcl script E_SMILES atomchange bondchange atom bond e_chemdiv_id.xpd
E_CHEMDIV_URL url Data display URL for structure in catalog of chemdiv.com/chemistryondemand.com
atomchange bondchange stereochange atom bond
E_CHEMEO_ID string ID in the Chemeo properties database (www.chemeo.com)
Tcl script atomchange bondchange atom bond e_chemeo_id.xpd
E_CHEMEO_URL url Display URL for the Chemeo properties database (www.chemeo.com)
Tcl script atomchange bondchange atom bond e_chemeo_url.xpd
E_CHEMEXPER_URL url ChemExper data display URL (chemexper.com)
querytype: { value: fs enumeration: fs:ss datatype: int}
Tcl script E_CHEMEXPER_URL mol atom bond e_chemexper_url.xpd
E_CHEMICALBOOK_ID string Database ID for the chemicalbook.com site
Tcl script E_CAS atomchange bondchange stereochange atom bond e_chemicalbook_id.xpd
E_CHEMICALBOOK_URL url Data display URL for the chemicalbook.com site
Tcl script E_CAS atomchange bondchange stereochange atom bond e_chemicalbook_url.xpd
E_CHEMICALIZE_URL url URL to submit compound to chemicalize.org computational service by ChemAxon
Tcl script E_SMILES atomchange bondchange stereochange merge e_chemicalize_url.xpd
E_CHEMICAL_BEAUTY double Chemical beauty score (aka QED, quantitative estimate of drug likeness). Because we are using different logP and HA/HD algorithms, the results are not exactly identical to those from the publication, but close. Bickerton et al., Nature Chemistry, 4, 90 (2012)
weightingscheme: { value: max enumeration: max:mo:u datatype: int}
Tcl script E_BRENK_ALERTS E_WEIGHT E_XLOGP2 E_NHDONORS E_NHACCEPTORS E_NROTBONDS E_TPSA E_ARORING_COUNT atomchange bondchange stereochange atom bond e_chemical_beauty.xpd
E_CHEMIDPLUS_ID string ChemIDPlus structure id (from http://chem.sis.nlm.nih.gov)
Tcl script E_STDINCHIKEY mol atom bond e_chemidplus_id.xpd
E_CHEMIDPLUS_URL url ChemIDPlus URL
Tcl script E_CHEMIDPLUS_ID mol atom bond e_chemidplus_url.xpd
E_CHEMSPIDER_ID string chemspider.com structure record ID
Tcl script E_STDINCHI atomchange bondchange stereochange merge e_chemspider_id.xpd
E_CHEMSPIDER_URL url chemspider.com structure data display URL
Tcl script E_CHEMSPIDER_ID atomchange bondchange stereochange merge e_chemspider_url.xpd
E_CHEMSYNTHESIS_ID int ID of structure in ChemSynthesis database (www.chemsynthesis.com)
Tcl script atomchange bondchange merge mol e_chemsynthesis_id.xpd
E_CHEMSYNTHESIS_URL url Data sccess URL of structure in ChemSynthesis database (www.chemsynthesis.com)
Tcl script E_CHEMSYNTHESIS_ID atomchange bondchange merge mol e_chemsynthesis_url.xpd
E_CHIRALITY byte Stereo status and potential of ensemble
none:meso:unspecified:chiral:contradictory
Compiled C module M_CHIRALITY atomchange bondchange stereochange mol atom bond mod_e_chirality.so
E_CHIRAL_POTENTIAL intpair Number of possible chiral atom and bond centers
Tcl script A_STEREOGENIC B_STEREOGENIC A_TYPE atomchange merge atom bond e_chiral_potential.xpd
E_CID int PubChem CID structure identifier
trace: { value: 0 datatype: boolean}
Tcl script E_STDINCHIKEY atomchange bondchange stereochange merge hadd e_cid.xpd
E_CIF_BLOCK table _loop dataset of a CIF file
never
E_CLASSIFIED_BOND_COUNT intvector Counts of used-defined classes of bonds
bondtypes: { value: C-C C=C C*C C-X C=X C*X X-X X=X X*X C-H X-H description: The bond types to look for, in element/bondordersymbol/element notation datatype: string constraints: list}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange merge mod_e_classfied_bond_count.so
E_CLASSIFIED_SURFACE_AREA doublevector Estimated surface area classified by atom type P. Labute, Methods in Molecular Biology, 275, 261ff
total_double double
carbon double
hydrogen double
hetero double
aromatic double
aliphatic double
ring double
chain double
Compiled C module A_SURFACE_AREA A_ISAROMATIC A_ELEMENT A_TYPE A_RING_COUNT atomchange bondchange 3dabsolute hadd atom bond mod_e_classified_surface_area.so
E_CLASSYFIRE_CLASSIFICATION jsonstring ClassyFire classification (http://classyfire.wishartlab.com) Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.
Tcl script atomchange bondchange stereochange merge e_classyfire_classification.xpd
E_CLASSYFIRE_URL url ClassyFire display URL (http://classyfire.wishartlab.com) Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.
Tcl script E_STDINCHIKEY atomchange bondchange stereochange merge e_classyfire_url.xpd
E_CLEANNAME string Name cleaned from purity info and miscellaneous remarks
keeppurity: { value: 1 datatype: boolean}
keepstereo: { value: 1 datatype: boolean}
keepisotope: { value: 1 datatype: boolean}
keepsalt: { value: 1 datatype: boolean}
trace: { value: 0 datatype: boolean}
watch: { value: {} description: String to watch out for, output notification if found datatype: string}
Tcl script E_NAME never e_cleanname.xpd
E_CML_STRING string CML structure record as string
pedantic: { value: 1 datatype: boolean}
Tcl script atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond e_cml_string.xpd
E_CMSSPECTRUM compound Continuous mass spectrum. Filled by reading JCAMP spectrum file of CMS type.
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum floatvector
atomchange bondchange
E_COCONUT_ID string Structure key for the Coconut natural products database (http://coconut.naturalproducts.net)
Tcl script E_STDINCHI atomchange bondchange stereochange atom bond e_coconut_id.xpd
E_COCONUT_URL url Display URL for a natural product entry in the COCNUT database (coconut.naturalproducts.net)
Tcl script atomchange bondchange atom bond e_coconut_url.xpd
E_COD_ID int ID of structure in the Crystallography Open Database (www.crystallography.net)
Tcl script atomchange bondchange atom bond e_cod_id.xpd
E_COD_URL url URL to the Crystallography Open Database (www.crystallography.net)
Tcl script E_COD_ID atomchange bondchange atom bond e_cod_url.xpd
E_COLOR color Background color to use in plots
never
E_COMMENT stringvector Free form comment for ensemble
never
E_COMMONCHEMISTRY_URL url Display URL in the ACS CommonChemistry database (commonchemistryy.org)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_commonchemistry_url.xpd
E_COMPLEXITY float Ensemble complexity according to modified Bertz/Hendrickson algorithm W. D. Ihlenfeldt, Ph.D. Thesis, TU Munich 1991
Compiled C module M_COMPLEXITY M_HASH atomchange bondchange merge mol mod_e_complexity.so
E_COMPOSITION string Elemental composition
useimplicith: { value: 1 datatype: boolean}
Tcl script A_WEIGHT A_SYMBOL A_HYDROGENS_NEEDED atomchange e_composition.xpd
E_CONFORMER_ENERGY floatvector Estimation of energy of conformer
Compiled C module A_CONFORMER A_TYPE A_TOPO_DISTANCE A_VDW_INTERACTION atomchange bondchange stereochange merge 3drelative hadd mod_e_conformer_energy.so
E_CONNECTIVITY boolean Pseudo property for connectivity reconstruction
(builtin) never
E_CONNECTIVITY_MATRIX floatmatrix Connectivity matrix, configurable in several variants
usefe: { value: 0 description: If set, the diagonal contains the atom free electron count datatype: boolean}
usebo: { value: 0 description: If set, atom pair matrix elements contain the VB bond order, not just 1 for an existing bond datatype: boolean}
usearo: { value: 0 description: If set, and bond orders are use, the bond order for aromatic bonds is 1.5 (Kekule VB otherwise) datatype: boolean}
Compiled C module B_ORDER B_TYPE B_ISAROMATIC A_FREE_ELECTRONS atomchange bondchange atom bond mod_e_connectivity_matrix.so
E_CONSENSUSPATHDB_URL url Display URL in MPG ConsensusPathDB (http://consensuspathdb.org/)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_consensuspathdb_url.xpd
E_CONVENTION string Free-form description of structure encoding convention
never
E_COSMO_DATA dictionary COSMO runtime information
atomchange bondchange stereochange merge 3drelative
E_CREST_URL url Display URL in the CREST (Chemical attributes, Regulatory approaches and Experimental STudies, http://www.rmeonline.net/CREST/r1/start.php) database
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_crest_url.xpd
E_CTDBASE_ID string CTD database ID (ctdbase.org)
Tcl script E_CAS atomchange bondchange atom bond e_ctdbase_id.xpd
E_CTDBASE_URL url CTD database (ctdbase.org) data display URL
Tcl script E_CTDBASE_ID atomchange bondchange atom bond e_ctdbase_url.xpd
E_DATABASE compound Info about the database the molecule was read from
dbtype string
database string
host string
port int
table string
id int
time date
atomchange bondchange stereochange merge
E_DAYLIGHT_ARORING_COUNT short Count of aromatic rings in ESSSR, always using Daylight aromaticity definition
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE atomchange bondchange atom bond ring mod_e_daylight_aroring_count.so
E_DBREFERENCE stringvector Generic free-form database references associated with ensemble
never
E_DECORATED_STRUCTURES dataset Exhaustive set of structures generated by decorating a core with any combination of user-supplied substituents.
substituents: { value: {} description: Substituent fragments in line notation. The first atom of these is their attachment point datatype: string constraints: list}
coreatomfilters: { value: hydrogen chbond description: These atoms on the core will be replaced by combinations of fragments datatype: string constraints: filterlist}
duphash: { value: E_HASHY description: Hash code used to remove duplicates datatype: string constraints: property}
Tcl script atomchange bondchange atom bond e_decorated_structures.xpd
E_DEGLYCOSILATED_STRUCTURE structure Structure with glycolisation fragments removed
spinach1: { value: C1-2O0-1H3- datatype: string}
spinach2: { value: O0-2N0-1C0-2H+ datatype: string}
Tcl script atomchange bondchange stereochange shuffle atom bond e_deglycosilated_structure.xpd
E_DENSITY float Density of compound at room temperature in kg/L
Tcl script A_ELEMENT A_ISOTOPE atomchange bondchange e_density.xpd
E_DICTIONARY_OF_NATURAL_PRODUCTS_ID string Entry ID in dictionary of natural products (dnp.chemnetbase.com)
Tcl script E_MRV_STRING atomchange bondchange stereochange atom bond e_dictionary_of_natural_products_id.xpd
E_DICTIONARY_OF_NATURAL_PRODUCTS_URL url Display URL in dictionary of natrual products (dnp.chemnetbase.com)
Tcl script E_DICTIONARY_OF_NATURAL_PRODUCTS_ID atomchange bondchange atom bond e_dictionary_of_natural_products_url.xpd
E_DIPOLEMOMENT compound Dipole Moment. The computation links indirectly vie E_HEAT_OF_FORMATION to a VAMP run.
pointcharge floatvector
hybrid floatvector
sum floatvector
A_XYZ atomchange bondchange stereochange 3drelative
E_DOTSURFACE xyzvector Coordinates of points on dot-surface
distance: { value: 0 description: dot distance to VDW surface (nm) datatype: double}
density: { value: 30 description: average number of dots per atom datatype: int}
A_XYZ A_ELEMENT atomchange bondchange stereochange 3drelative 3dabsolute
E_DRUGBANK_ID string Drugbank ID, looked up over the Internet
Tcl script E_SMILES atomchange bondchange stereochange merge e_drugbank_id.xpd
E_DRUGBANK_URL url Drugbank data display URL
Tcl script E_DRUGBANK_ID atomchange bondchange stereochange merge e_drugbank_url.xpd
E_DRUGINFO_URL url Display URL for the NIH DrugInfo prtal (druginfo.nlm.nih.gov)
Tcl script E_UNII atomchange bondchange atom bond e_druginfo_url.xpd
E_EC50 compound EC50 aids screen data
concentration float
concunit shortstring
flag shortstring
ecconc float
nexperiments short
atomchange bondchange merge
E_ECHA_URL url Display number for a structure in the EU ECHA (European Chemicals Agency) registration system.
E_CAS atomchange bondchange stereochange atom bond
E_ECHEMPORTAL_URL url Link into the OECD echemportal.org site
Tcl script E_CAS atomchange bondchange atom bond e_echemportal_url.xpd
E_EC_FINGERPRINT bitvector
(switchable between bitvector bytevector shortvector intvector)
An ECFP-style fingerprint implementation. This property merges atomic enviroment hash codes from property A_EC_HASH for different numbers of spheres into a fingerprint or count vector. The number of enviroment spheres used is controlled by the settings of A_EC_HASH - this is a vector, and each element is the hashed atom enviroment including an additional sphere.

If changed from default data type bitvector to bytevector, shortvector or intvector, the number of found atom environments in A_EC_HASH is counted.
diameter: { value: -1 description: Maximum neighbor distance to consider. Must be <= length of A_EC_HASH vector, use -1 to use vector length minvalue: -1 maxvalue: 15 datatype: int}
length: { value: 1024 description: Folded bitvector length minvalue: 16 maxvalue: 32768 datatype: int}
counts: { value: 0 description: Whether to use counts enumeration: no:linear:exponential datatype: int}
debug: { value: 0 description: If set, print debug info datatype: boolean}
Compiled C module A_EC_HASH atomchange bondchange atom bond mod_e_ec_fingerprint.so
E_EC_NUMBER string The European Community registration number for a compound with the European Chemicals Agency (ECHA, echa.europa.eu). This replaces the EINECS system (property E_EINECS_ID). Note that this identifier is very different from the enzyme commission EC number for proteins.
usepubchem: { value: 0 datatype: boolean}
useecha: { value: 1 datatype: boolean}
Tcl script E_CID E_CAS atomchange bondchange stereochange atom bond e_ec_number.xpd
E_EEROS_URL url Data display URL for compound in Wiley Electronic Encyclopedia of Reagents for Organic Synthesis (https://onlinelibrary.wiley.com/doi/book/10.1002/047084289X)
Tcl script E_STDINCHIKEY atomchange bondchange atom bond e_eeros_url.xpd
E_EFFECTIVE_ROTOR_COUNT double Effective rotor count, computed from rotatable bonds (B_ROTATABILITY) and fractional values for ring flexibility.
usecanonictautomer: { value: 0 description: If set, compute on standard tautomer instead of current structure datatype: boolean}
Tcl script B_ROTATABILITY atomchange bondchange e_effective_rotor_count.xpd
E_EGAN_BIOAVAILABILITY_FLAG boolean Veber bioavailability flag (E_XLOGP2<=5.88 && E_TPSA<=131.6) Journal of Medicinal Chemistry, Vol. 43, pp. 3867-3877, 2000
Compiled C module E_XLOGP2 E_TPSA atomchange bondchange atom bond mod_e_egan_bioavailability_flag.so
E_EIGENVALUES floatvector MO Eigenvalues
A_XYZ atomchange bondchange
E_EINECS_ID string EINECS ID. Note that this is now an outdated identifier with the launch of the EU REACH system. It should be replaced by the ECHA (https://echa.europa.eu) European Commission EC number (property E_EC_NUMBER, this is not the same as the Enzyme Commission protein EC number).
Tcl script E_SDF_STRING atomchange bondchange stereochange merge e_einecs_id.xpd
E_ELECTRONIC_ENERGY float Measured or computed electronic energy, as returned by, for example, a QM program. This property currently is used for reading VAMP data.
atomchange bondchange
E_ELEMENT_COUNT shortvector Count of element types of atoms of ensemble
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
(builtin) A_ELEMENT A_TYPE atomchange merge hadd
E_ELLIPSE_ANNOTATION compound Ellipse as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
A_XY never
E_EMBL_SIDER_URL url Data display link in the EMBL Sider database (http://sideeffects.embl.de)
Tcl script E_CID atomchange bondchange stereochange atom bond e_embl_sider_url.xpd
E_EMBL_STITCH_URL url Data display URL in the STITCH database (http://stitch.embl.de)
Tcl script E_CID atomchange bondchange stereochange atom bond e_embl_stitch_url.xpd
E_EMF_IMAGE diskfile
(switchable between blob diskfile url)
Metafile WIN32 structure drawing
width: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int}
height: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue" datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: string}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: smiles datatype: string}
metadata: { value: 1 datatype: boolean constraints: writeable}
filename: { value: {} datatype: diskfile}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.4 datatype: double}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
usehatch: { value: 0 datatype: boolean}
format: { value: wmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 1.5 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
crop: { value: -1 datatype: int}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Arial datatype: string}
usesubscripts: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR A_ANNOTATION B_FLAGS A_FLAGS atomchange bondchange stereochange merge hadd mol mod_e_emf_image.so
E_EMOLECULES_ID string EMolecules Web database ID (www.emolecules.com)
catalog: { value: all enumeration: SC:BB:all datatype: string}
Tcl script E_SMILES atomchange bondchange stereochange merge e_emolecules_id.xpd
E_EMOLECULES_URL url EMolecules (www.emolecules.com) Web database display URL
Tcl script E_EMOLECULES_ID atomchange bondchange stereochange merge e_emolecules_url.xpd
E_ENAMINE_ID string Catalog ID for the Enamine catalog (enaminestore.com)
Tcl script atomchange bondchange stereochange atom bond e_enamine_id.xpd
E_ENAMINE_URL url Data display URL for the Enamine catalog (enaminestore.com)
Tcl script E_ENAMINE_ID atomchange bondchange stereochange atom bond e_enamine_url.xpd
E_ENANTIOMER structure Enantiomer of ensemble (i.e. all tetrahedral stereochemistry is reversed)
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange merge e_enantiomer.xpd
E_ENERGY float Ensemble energy
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange stereochange merge 3drelative
E_ENS_COUNT int Pseudo-property: Number of ens in ensemble - always 1, needed for generality in processing bind sets in "scan" queries
Compiled C module atomchange bondchange atom bond mod_e_ens_count.so
E_EPA_ACTOR_URL url EPA Actor data access
Tcl script E_CAS atomchange bondchange stereochange e_epa_actor_url.xpd
E_EPA_COMPTOX_URL url Data display URL for the new EPA CompTox portal
Tcl script E_STDINCHIKEY atomchange bondchange atom bond e_epa_comptox_url.xpd
E_EPA_HPVIS_URL url Data display URL in US EPA High Production Volume Information System (HPVIS), https://www.epa.gov/hpvis
Tcl script E_CAS atomchange bondchange atom bond e_epa_hpvis_url.xpd
E_EPRSPECTRUM compound EPR spectrum, usually read from JCAMP file
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum floatvector
atomchange bondchange stereochange
E_EPS_IMAGE diskfile
(switchable between blob diskfile)
A 2D-plot of the structure as EPS image file
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: string}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: string}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: string}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: string}
comment: { value: E_NAME datatype: string}
structure: { value: none enumeration: none:smiles:stdinchi:cactvs:molfile datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3,tetrahedral:sp2,planar:all datatype: string}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.3 datatype: double}
colormode: { value: mono datatype: string}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: string}
frame: { value: 0 datatype: boolean}
linespacing: { value: 2.5 datatype: double}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filterlist}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filterlist}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Helvetica datatype: string}
contractgroups: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
downloadfilename: { value: {} datatype: string constraints: writeable}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange merge hadd mod_e_eps_image.so
E_EXACT_MASS floatpair Exact mass of most abundant compound isotope combination, assuming natural abundance
weight double
abundance double
useimplicith: { value: 1 description: Whether to include implicit hydrogens in the computation datatype: boolean}
Compiled C module atomchange merge atom mod_e_exact_mass.so
E_EXPANDED_QUERY_STRUCTURES dataset
Tcl script atomchange bondchange stereochange atom bond e_expanded_query_structures.xpd
E_EXPERIMENT string Experimental setup used to obtain structure data
never
E_EXP_CONNECTIVITY_MATRIX floatmatrix Exponent of the connectivity matrix, as per the work of Alexey Lagunin Molecular Informatics 30, 2011, 241-250
multiplier: { value: -0.5 description: multiplier for all matrix elements applied before exponent computation datatype: double}
Compiled C module E_CONNECTIVITY_MATRIX atomchange bondchange atom bond mod_e_exp_connectivity_matrix.so
E_FDA_OBJECT_CODE compound FDA data code triple from SPL file, identiying for example the type of structure extracted
code string
codesystem string
displayname string
atomchange bondchange atom bond
E_FDA_SPL_URL url
Tcl script E_UNII atomchange bondchange atom bond e_fda_spl_url.xpd
E_FDA_SRS_URL url Link into FDA SRS (structure registration system) database
Tcl script E_UNII atomchange bondchange atom bond e_fda_srs_url.xpd
E_FEATURES bytevector Count of structural features defined as parameters by SMARTS expressions
carboxylic_acid byte
acid_halogenide byte
aldehyde byte
ketone byte
amine byte
primary_amine byte
secondary_amine byte
tertiary_amine byte
quarternary_amine byte
hydrazine byte
urea byte
12diamine byte
pyridine byte
thp byte
piperidine byte
piperazine byte
morpholine byte
thiomorpholine byte
amide byte
ester byte
alpha_aminoacid byte
betaaminoacid byte
alpha_ketoacid byte
betaketoacid byte
alcohol byte
phenol byte
thiol byte
thiophenol byte
ether byte
thioether byte
epoxide byte
acetal byte
enol byte
lactone byte
oxime byte
nitro byte
isocyanate byte
thioisocyanate byte
anhydride byte
cyanide byte
sulfonic_acid byte
sulfonic_acid_halogenide byte
sulfonamide byte
phosphoric_acid byte
boronic_ester byte
silyl_hydride byte
siloxyl byte
aliphatic_halogen byte
aromatic_halogen byte
trifluoromethyl byte
11_diphenyl_methyl byte
alpha_haloketone byte
chalcone byte
aromatic_nitrogen byte
aromatic_oxygen byte
aromatic_sulphur byte
cc_doublebond byte
cc_triplebond byte
phenyl byte
patterns: { value: {{carboxylic acid} C(=O)O[#1]} {{acid halogenide} C(=O)[Cl,Br,I,F]} {aldehyde CC(=O)[#1]} {ketone CC(=O)C} {amine N([Cx1,cx1,#1])([Cx1,cx1,#1])[Cx1,cx1,#1]} {{primary amine} [Cx1,cx1][NH2;v3]} {{secondary amine} [NH;v3]([Cx1,cx1])([Cx1,cx1])} {{tertiary amine} [N;v3]([Cx1,cx1])([Cx1,cx1])[Cx1,cx1]} {{quarternary amine} [N;v4](C)(C)(C)C} {hydrazine [N;R0][N;R0]} {urea [N;x0]C(=O)[N;x0]} {{1.2-diamine} [NH2]CC[NH2]} {pyridine n1ccccc1} {tetrahydropyrrole N1CCCC1} {piperidine [N;A]1CCCCC1} {piperazine N1CCNCC1} {morpholine N1CCOCC1} {thiomorpholine S1CCOCC1} {amide CC(=O)N([C,c,#1])[C,c,#1]} {ester CC(=O)[O;R0]C} {{alpha-aminoacid} NCC(=O)O} {{beta-aminoacid} NCCC(=O)O} {{alpha-ketoacid} O=CC(=O)O} {{beta-ketoacid} O=CCC(=O)O} {alcohol [C;X4;A]O[#1]} {phenol [c]O[#1]} {thiol [C;X4;A]S[#1]} {thiophenol [c]S[#1]} {ether [Cx1,cx1][O;!r3][Cx1,cx1]} {thioether [Cx1,cx1][S;!r3][Cx1,cx1]} {epoxide C1OC1} {acetal [Cx1,cx1]O[Cx2]O[Cx1,cx1]} {enol C=CO} {lactone [C;R](=O)[O;R]} {oxime C=NO} {nitro N(=O)O} {isocyanate N=C=O} {thioisocyanate N=C=S} {anhydride {C(=O)OC(=O)C}} {cyanide C#N} {{sulfonic acid} S(=O)(=O)O[#1]} {{sulfonic acid halogenide} S(=O)(=O)[F,Cl,Br,I]} {sulfonamide S(=O)(=O)N} {{phosphoric acid derivative} P(=[O,S,N])[N,O,S,F,Cl,Br,I]} {{boronic ester} C[B](O[C,#1])O[C,#1]} {{silyl hydride} [SiH]} {{siloxyl} [Si]O} {{aliphatic halogen} [C;A][F,Cl,Br,I]} {{aromatic halogen} [c][F,Cl,Br,I]} {trifluoromethyl C(F)(F)F} {{1.1-diphenyl-methyl} c1ccccc1C(c1ccccc1)[!C;!c;!#1]} {{alpha-haloketone} CC(=O)C[F,Cl,Br,I]} {chalcone CC(=O)[C;A]=[C;A]} {{aromatic nitrogen} [n]} {{aromatic oxygen} [o]} {{aromatic sulphur} [s]} {{C-C double bond} [C;A]=[C;A]} {{C-C triple bond} C#C} {{phenyl ring} c1ccccc1} datatype: string}
Tcl script A_ELEMENT B_ORDER B_TYPE atomchange bondchange merge hadd atom bond ring e_features.xpd
E_FELDMAN_FINGERPRINT bitvector Feldman and Hodes, JCICS 1975 15(3) 147-152
Python script atomchange bondchange atom bond e_feldman_fingerprint.xpd
E_FG_COUNT shortvector Count of functional groups in ensemble, summed up from molecular FG counts in M_FG_COUNT
Compiled C module M_FG_COUNT atomchange bondchange mod_e_fg_count.so
E_FICTS_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICTS datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICTS_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHISY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficts_id.xpd
E_FICTS_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICTU_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICTu datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICTU_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHIY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_fictu_id.xpd
E_FICTU_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICUS_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICuS datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICUS_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHISY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficus_id.xpd
E_FICUS_STRUCTURE structure Standardized structure for FICUS computations. Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICUU_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICuu datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICUU_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHIY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficuu_id.xpd
E_FICUU_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICXX_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICxx datatype: string}
scope: { value: private datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICXX_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHIY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficxx_id.xpd
E_FICXX_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FILE compound Info about the file the molecule was read from
filename string
startrecord int
endrecord int
line int
format string
offset int64
length int
atomchange bondchange merge
E_FLEXNOVO_FILTER boolean Test whether structure passes the FlexNovo smarts pattern filter (which removes reactive or non-druglike componds)
patternfile: { value: flexnovo_exclude.sma datatype: diskfile constraints: readable}
trace: { value: 0 datatype: boolean}
Tcl script atomchange bondchange atom bond e_flexnovo_filter.xpd
E_FLG_FICTS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_FICTU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_FICUS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_FICUU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUTS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUTU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUUS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUUU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FORMAT string Original format in data file (I/O module name)
never
E_FORMULA string Molecular formula of ensemble
usecharges: { value: 0 datatype: string}
format: { value: ascii datatype: string}
useimplicith: { value: 1 datatype: string}
usequeryatoms: { value: 0 datatype: string}
(builtin) A_ISOTOPE atomchange merge
E_FRAGMENT_COMPOSITION intvector Get composition of structure using a user-defined hierarchical fragment database with SMILES/SMARTS fragment definition. Larger fragments, and fragments with more specialized attributes have precedence. Multiple solutions may be found and are attached as E_FRAGMENT_COMPOSITION/n. The result is an int vector with the counts for each fragment in their definition file order.

The default fragment set is for the UNIFAC method. Various other fragment files for Joback, Lyderson, Sedlbaur methods are also supplied in the data directory.
fragfile: { value: unifac.sma datatype: diskfile constraints: readable}
explicith: { value: 0 datatype: boolean}
debug: { value: 0 datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange merge hadd e_fragment_composition.xpd
E_FRAGMENT_COUNT dictionary Counts of all (filtered) fragments the structure, The result is a dictionary with SMARTS keys, and occurence count values.
minsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int}
maxsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int}
hydrogen: { value: 0 datatype: boolean}
mode: { value: absolute description: In relative mode, scale to total count 1 enumeration: absolute:relative datatype: int}
keeparo: { value: 0 description: If set, lock A_ISAROMATIC datatype: boolean}
aroquery: { value: 0 description: If set, rewrite SMARTS to match only aromatic fragments where applicable datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange merge atom bond e_fragment_count.xpd
E_FRAGMENT_TREE_CUTS datatree Topological fragment hierarchy tree - cut bond classification
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
E_FRAGMENT_TREE_HASH datatree Topological fragment hierarchy tree - hashcodes
maxcuts: { value: 3 datatype: int}
minsize: { value: 2 datatype: int}
cutphenyl: { value: 0 datatype: boolean}
queryhash: { value: 0 datatype: boolean}
dupcheck: { value: hierarchical enumeration: hierarchical:global datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange mod_e_fragment_tree_hash.so
E_FRAGMENT_TREE_LABELS datatree Topological fragment hierarchy tree - atom labels of fragments
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
E_FRAGMENT_TREE_SMARTS datatree Topological fragment hierarchy tree - SMARTS of fragments
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
E_FRAGMENT_TREE_TABLE table Summary of fragmentation routes
Tcl script E_FRAGMENT_TREE_HASH E_FRAGMENT_TREE_CUTS E_FRAGMENT_TREE_LABELS atomchange bondchange e_fragment_tree_table.xpd
E_FREQUENCY string Generic computed frequencies. Used in Gaussian Archive I/O module
atomchange bondchange merge 3drelative hadd
E_FSP3 double Carbon flatness score - the ratio of SP3 hybridized carbon atoms to total carbon atom count Lovering, F. et al., J.Med.Chem. 2009, 52, 6752-6756
Compiled C module A_TYPE A_ELEMENT A_HYBRIDIZATION atomchange bondchange atom bond mod_e_fsp3.so
E_GC compound Measured gas-chromatograph spectrum. Used for example in JCAMP I/O module
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
reference string
purity float
source string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
spectrum floatvector
atomchange bondchange
E_GDL_ID int Substance ID in German hazardous chemicals database (http://www.gefahrstoff-info.de)
Tcl script E_CAS atomchange bondchange atom bond e_gdl_id.xpd
E_GDL_URL url Data display URL in German hazardous chemicals database (http://www.gefahrstoff-info.de)
Tcl script E_GDL_ID atomchange bondchange atom bond e_gdl_url.xpd
E_GENETOX_URL url Display URL in EPA GENE-TOX (Genetic Toxicology Data Bank, https://toxnet.nlm.nih.gov/newtoxnet/genetox.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_genetox_url.xpd
E_GENOTOXIC_ALERTS shortvector Check for problematic potentially genotoxic groups CE&N Sep 27, 2010 p16ff
patternfile: { value: genotoxic.sma datatype: diskfile constraints: readable}
Tcl script atomchange bondchange merge hadd mol atom bond ring e_genotoxic_alerts.xpd
E_GEOOPT_METHOD string Geometry optimization method description string. Used for example in the Gaussian Input, Gaussian Archive and Sharc file forms.
atomchange bondchange 3drelative 3dabsolute
E_GI50 compound GI50 tumor screen data
concunit shortstring
lcconc float
panel shortstring
cell string
panelnumber short
cellnumber short
nlog_gi50 float
ntest_this short
ntest_max short
atomchange bondchange merge
E_GIF diskfile
(switchable between string blob diskfile url)
A 2D-plot of the structure as a GIF or PNG file
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
interlace: { value: 1 datatype: boolean}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
secondarycolor: { value: #00D000 datatype: color}
highlightbonds: { value: {} datatype: intvector}
highlightatoms: { value: {} datatype: intvector}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
crop: { value: -1 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
format: { value: gif enumeration: gif:png:png8:bmp datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string}
footerproperty: { value: {} datatype: string}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
font: { value: arialn datatype: string}
symbolfontsize: { value: -1 datatype: int}
annotationfontsize: { value: -1 datatype: int}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
showisotope: { value: 1 datatype: boolean}
isotopemapping: { value: none datatype: string}
showstereoh: { value: 1 datatype: boolean}
suppressedmols: { value: {} datatype: intvector}
linewidth: { value: 1.4 datatype: double}
showempty: { value: 0 datatype: boolean}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
showmapping: { value: 0 datatype: boolean}
showstereogroups: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
frame: { value: 0 datatype: boolean}
framecolor: { value: black datatype: diskfile}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: int}
footerfontsize: { value: -1 datatype: int}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circlefilter: { value: {} datatype: string}
circleatoms: { value: {} datatype: intvector}
atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 2.0 datatype: double}
fixiepngsize: { value: 1 datatype: string}
rawcoordinates: { value: 0 datatype: boolean}
checkintersection: { value: 0 datatype: boolean}
usegrouplabels: { value: 0 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
colormode: { value: color datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
saverendercoordinates: { value: 0 datatype: boolean}
labelproperty: { value: {} datatype: string}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange groupchange merge hadd mod_e_gif.so
E_GOLM_URL url Data display link into the GOLM metabolome database (http://gmd.mpimp-golm.mpg.de)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_golm_url.xpd
E_GOOGLE_SCHOLAR_URL url URL for data in the Google Scholar search engine
Tcl script E_STDINCHI E_STDINCHIKEY E_CAS atomchange bondchange stereochange atom bond e_google_scholar_url.xpd
E_GPCR_LIGAND_LIKENESS compound GPCR ligand structural likeness, computed as maximum similarity score with standard similarity property E_SCREEN on a diverse 1K cpds subset of the GLL database. Gatica, Cavasotto, J. Chem. Inf. Model. 2011, 52, 1
similarity byte
structure structure
Tcl script E_SCREEN atomchange bondchange atom bond e_gpcr_ligand_likeness.xpd
E_GRAPHICS_TEXT stringvector Head- and footline for graphics plots
never
E_GRID_VOLUME floatvolume Generic floating-point volume grid data. Used for exmapl ein the STF and Gausscube file I/O modules.
atomchange bondchange stereochange merge 3drelative hadd atom bond ring
E_GROUP_COUNT int Number of groups defined for the ensemble
Compiled C module atomchange bondchange groupchange atom bond mod_e_group_count.so
E_GUIDETOPHARMACOLOGY_ID int Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org)
Tcl script E_SMILES atomchange bondchange stereochange merge e_guidetopharmacology_id.xpd
E_GUIDETOPHARMACOLOGY_URL url Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org)
Tcl script E_GUIDETOPHARMACOLOGY_ID atomchange bondchange stereochange merge e_guidetopharmacology_url.xpd
E_HALIDE_FRACTION double Fraction of molecular weight contributed by halogen atoms
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_halide_fraction.so
E_HASH uint64 Basic ensemble hashcode
(builtin) M_HASHGROUP M_HASH atomchange bondchange merge
E_HASH128 uint128 Perturbed ensemble hashcode, extended to 128 bits
Compiled C module M_HASHGROUP128 M_HASH128 atomchange bondchange merge hadd mod_e_hash128.so
E_HASHGROUP_COUNT_A intvector Population of basic atom hash groups
(builtin) A_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_AI intvector Population of isotope atom hash groups
(builtin) A_ISOTOPE_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_AIS intvector Population of isotopic stereospecific basic atom hash groups
(builtin) A_ISOTOPE_STEREO_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_AS intvector Population of stereospecific basic atom hash groups
(builtin) A_STEREO_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_B intvector Population of bond hash groups
(builtin) B_HASH atomchange bondchange merge
E_HASHGROUP_COUNT_BS intvector Population of stereospecific bond hash groups
(builtin) B_STEREO_HASH atomchange bondchange merge
E_HASHGROUP_COUNT_M intvector Population of perturbed molecule hash groups
(builtin) M_HASHY atomchange bondchange merge hadd
E_HASHGROUP_COUNT_MI intvector Population of isotopic perturbed molecule hash groups
(builtin) M_HASHIY atomchange bondchange merge hadd
E_HASHGROUP_COUNT_MIS intvector Population of isotopic stereospecific perturbed molecule hash groups
(builtin) M_HASHISY atomchange bondchange merge hadd
E_HASHGROUP_COUNT_MS intvector Population of stereospecifc perturbed molecule hash groups
(builtin) M_HASHSY atomchange bondchange merge hadd
E_HASHISY uint64 Perturbed isotope stereo ensemble hashcode
(builtin) M_ISOTOPE_STEREO_HASHGROUP_Y M_HASHISY atomchange bondchange merge hadd
E_HASHIY uint64 Perturbed isotope ensemble hashcode
(builtin) M_ISOTOPE_HASHGROUP_Y M_HASHIY atomchange bondchange merge hadd
E_HASHS uint64 Stereospecific basic ensemble hashcode
(builtin) M_STEREO_HASHGROUP M_HASHS atomchange bondchange merge
E_HASHSY uint64 Perturbed stereospecific ensemble hashcode
useisotope: { value: 0 datatype: string}
(builtin) M_STEREO_HASHGROUP_Y M_HASHSY atomchange bondchange merge hadd
E_HASHY uint64 Perturbed ensemble hashcode
useisotope: { value: 0 datatype: string}
(builtin) M_HASHGROUP_Y M_HASHY atomchange bondchange merge hadd
E_HEAT_OF_FORMATION float Measured or computed Heat of Formation. The computation procedure tries to run a simple VAMP job. This proeprties acts as the cornerstone for a standard set of QM-related properties via windfall/indirect property definition relationships.
filename: { value: {} datatype: string}
prgpath: { value: /usr/local/bin/vamp datatype: string}
method: { value: AM1 datatype: string}
Tcl script A_XYZ atomchange bondchange e_heat_of_formation.xpd
E_HEAVY_ATOM_COUNT int Number of non-hydrogen atoms in the ensemble
Compiled C module A_ELEMENT A_TYPE atomchange bondchange mol atom bond mod_e_heavy_atom_count.so
E_HEAVY_BOND_COUNT int Count of VB bonds which do not contain hydrogen
Compiled C module A_TYPE A_ELEMENT B_TYPE atomchange mod_e_heavy_bond_count.so
E_HETEROATOM_CARBON_RATIO double Number of hetero atoms devided by number of carbon atoms
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_heteroatom_carbon_ratio.so
E_HETEROATOM_COUNT int Number of hetero (not C or H) atoms in the ensemble
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_heteroatom_count.so
E_HISTORY compoundvector Record history
program string
version string
patchlevel string
pgmdate date
user string
date date
machine string
never
E_HIT2LEAD_ID int Catalog number from www.hit2lead.com (aka ChemBridge)
database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
Tcl script E_SDF_STRING atomchange bondchange atom bond e_hit2lead_id.xpd
E_HIT2LEAD_URL url Display URL for a hit2lead (www.hit2lead.com, aka ChemBridge) database entry
database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
Tcl script E_HIT2LEAD_ID atomchange bondchange atom bond e_hit2lead_url.xpd
E_HMDB_ID string ID of structure in the HMDB database (www.hmdb.ca)
Tcl script E_SMILES atomchange bondchange atom bond e_hmdb_id.xpd
E_HMDB_URL url Display URL of structure in the HMDB database (www.hmdb.ca)
Tcl script E_HMDB_ID atomchange bondchange atom bond e_hmdb_url.xpd
E_HSDB_URL url Display URL for the HSDB (http://toxnet.nlm.nih.gov/newtoxnet/hsdb.htm) database
Tcl script E_CAS atomchange bondchange atom bond e_hsdb_url.xpd
E_HYDROGEN_BOND_CENTER_COUNT int Number of heavy atoms that can act as hydrogen donor or acceptor
Tcl script A_HYDROGEN_BONDING never e_hydrogen_bond_center_count.xpd
E_HYDROGEN_COMPLETE boolean Boolean flag indicating whether there are no open hydrogen sites
Compiled C module A_HYDROGENS_NEEDED atomchange bondchange hadd atom bond mod_e_hydrogen_complete.so
E_IC50 compound IC50 aids screen data
concentration float
concunit shortstring
flag shortstring
icconc float
nexperiments short
atomchange bondchange merge
E_ICSC_CARD_ID shortstring International Chemical Safety Cards ID (from www.ilo.org)
Tcl script E_CAS atomchange bondchange atom bond e_icsc_card_id.xpd
E_ICSC_CARD_URL url International Chemical Safety Cards display URL (from www.ilo.org)
Tcl script E_ICSC_CARD_ID atomchange bondchange atom bond e_icsc_card_url.xpd
E_IDENT string Short ensemble identification string
(builtin) never
E_IDENTIFIER_NORM_DATASET dataset Debug property for FICUS suite
atomchange bondchange atom bond
E_IDENTIFIER_NORM_EXEMPTION_LIST stringvector Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_IDTF_MODEL blob
(switchable between blob diskfile mapfile)
3D structure model in Intel IDTF format
style: { value: spacefill enumeration: ballstick:capped:spacefill:wireframe:all datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
bondradius: { value: 15 datatype: double}
ignoreh: { value: 0 datatype: boolean}
vdwscaling: { value: 25 datatype: double}
atomhighlightcolor: { value: red datatype: color}
highlightatoms: { value: {} datatype: intvector}
bondhighlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
showbondorder: { value: 0 datatype: boolean}
bondcolor: { value: atomsplit datatype: string}
structure: { value: 0 datatype: boolean}
showlabel: { value: 0 datatype: boolean}
labelcolor: { value: purple datatype: color}
addlights: { value: 0 datatype: boolean}
addview: { value: 0 datatype: boolean}
glossfactor: { value: 75 datatype: double}
labelsize: { value: 15 datatype: int}
tesselation: { value: octahedron 4 20 20 datatype: string}
dynamictesselation: { value: 1 datatype: boolean}
downloadfilename: { value: {} datatype: string}
suppressedatoms: { value: {} datatype: intvector}
suppressedbonds: { value: {} datatype: intvector}
Compiled C module A_XYZ A_ELEMENT B_TYPE B_ORDER B_FLAGS A_FLAGS A_COLOR B_COLOR atomchange bondchange stereochange merge 3drelative 3dabsolute hadd mod_e_idtf_model.so
E_IMAGEMAP string HTML imagemap associated with a GIF/PNG image (property E_GIF)
name: { value: {} datatype: string}
mode: { value: mol enumeration: atom:bond:mol datatype: int}
target: { value: {} datatype: string}
url: { value: {} datatype: string}
title: { value: {} datatype: string}
Tcl script E_GIF never e_imagemap.xpd
E_IMAGE_SCALING doublevector 2D coordinate scaling information (A_XY) for rendering in an image of specified size. The fields are the coordinate scale factor, the x and y offsets (these three values place the drawing into the 0..w/h-1 pixel area), the relative scale factor for the structure needed to fit into the "bonds" size box (1.0 if it fits into the box), and suggested symbol and annotation font sizes in points.
factor double
xoffset double
yoffset double
scale double
symbolfontsize double
annotationfontsize double
width: { value: 25ß description: Image width (pixel) datatype: int}
height: { value: 250 description: Image height (pixel) datatype: int}
border: { value: 10 description: Image border (pixel) minvalue: 0 maxvalue: 100 datatype: int}
bonds: { value: 8 description: Number of standard bonds across image minvalue: 1 maxvalue: 20 datatype: int}
hidefragment: { value: {} description: Structure fragment to hide and exclude from computation datatype: structure}
Compiled C module A_XY atomchange bondchange atom bond mod_e_image_scaling.so
E_INACTIVE_AIDSET intvector Set of PubChem assay IDs testing this compound as inactive
Tcl script E_CID atomchange bondchange stereochange e_inactive_aidset.xpd
E_INCHI string First release InChI identifier (E_STDINCHI following the current standard is preferred)
options: { value: DONOTADDH FIXEDH RECMET NOWARNINGS description: Set of default option words as used in the original NIST software comment: Supported option words: MISMATCHISERROR OUTERRINCHI Key XHash1 XHash2 SNON NEWPSOFF DONOTADDH LooseTSACheck SREL ChiralFlagOFF SUU SLUUD FIXEDH RECMET KET 15T PT_22_00 PT_16_00 PT_06_00 PT_39_00 LargeMolecules Polymers Polymers105 NPZz NoWarnings FoldCRU FoldSRU FrameShift: NoFrameShift NoEdits SATZZ FNUDOFF FixSp3bugOFF FBOFF FB2OFF SPXYZOFF SASXYZOFF Polymers105+. Record processing and output options NOLABELS SAVEOPT AUXNONE NoInCXhI INPAUX START: END: RECORD: MergeHash have no effect. datatype: string constraints: list}
fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean}
stereoperception: { value: 1 description: If set, perceive stereochemistry, if no, use what is presently set on the structure datatype: boolean}
stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int}
autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean}
prefix: { value: 1 description: If set, include InChI= prefix in output datatype: boolean}
stripstereolayer: { value: 0 datatype: boolean}
stripisotopelayer: { value: 0 datatype: boolean}
stripfixedhlayer: { value: 0 description: If set, the /f layer *and* the following /h and /q layers are stripped datatype: boolean}
stripreconnectlayer: { value: 0 datatype: boolean}
stripchargelayer: { value: 0 datatype: boolean}
Compiled C module B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE B_STEREOGENIC B_ISAROMATIC A_ALLENE atomchange bondchange stereochange merge atom bond mod_e_inchi.so
E_INCHIKEY string Hash of InChI string
prefix: { value: 1 datatype: boolean}
Compiled C module E_INCHI atomchange bondchange stereochange atom bond mod_e_inchikey.so
E_INCHI_AUXINFO string InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting E_INCHI
B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd atom bond
E_INPUTDATE date Time stamp for molecule
Tcl script never e_inputdate.xpd
E_IONIZATION_POTENTIAL float Measured or computed Ionization potential. This can be computed indirectly via E_HEAT_OF_FORMATION by a VAMP run.
A_XYZ atomchange bondchange
E_IRIS_URL url Display URL in EPA IRIS (Integrated Risk Information System, https://toxnet.nlm.nih.gov/newtoxnet/iris.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_iris_url.xpd
E_IRSPECTRUM compound Measured or computed IR spectrum. The compuation function attempts to get an IR spectrum from the NIST WebBook, or run a simple VAMP job depending on the "source" parameter, which should be set to "NIST" or "VAMP".
experimental boolean
origin string
author string
date datetime
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum xyvector
peaks floatvector
peakshape stringvector
peakintensity floatvector
peakname stringvector
filename: { value: {} description: temporary job file datatype: diskfile constraints: writeable}
prgpath: { value: /usr/local/bin/vamp datatype: diskfile constraints: existing}
method: { value: AM1 datatype: string}
freqfactor: { value: 0.98 datatype: string}
cofreqfactor: { value: 0.90 datatype: string}
source: { value: NIST enumeration: NIST:VAMP datatype: int}
Tcl script A_XYZ atomchange bondchange 3drelative e_irspectrum.xpd
E_IRSPECTRUM_IMAGE diskfile
(switchable between string blob diskfile url)
IR spectrum rendering
height: { value: 250 datatype: int}
width: { value: 500 datatype: int}
bgcolor: { value: white datatype: color}
title: { value: {} datatype: string}
filename: { value: {} datatype: string constraints: writeable}
format: { value: gif enumeration: png,png24:gif:png8 datatype: string}
titlecolor: { value: black datatype: color}
framecolor: { value: black datatype: color}
signalcolor: { value: #DD0000 datatype: color}
ystyle: { value: transmittance enumeration: transmittance:absorbance datatype: int}
xdirection: { value: reverse enumeration: normal:reverse datatype: int}
xstyle: { value: 1/cm enumeration: 1/cm:um datatype: int}
Tcl script E_IRSPECTRUM atomchange bondchange merge mol e_irspectrum_image.xpd
E_ISOTOPE_ATOMHASH_COUNT int Number of different isotopic basic atom hash codes
(builtin) E_HASHGROUP_COUNT_AI atomchange bondchange merge
E_ISOTOPE_COUNT int Number of isotopically labelled atoms
Compiled C module A_TYPE A_ISOTOPE atomchange merge atom bond mod_e_isotope_count.so
E_ISOTOPE_HASH128 uint128 Perturbed isotope-sensitive ensemble hashcode, extended to 128 bits
Compiled C module M_ISOTOPE_HASHGROUP128 M_ISOTOPE_HASH128 atomchange bondchange merge hadd mod_e_isotope_hash128.so
E_ISOTOPE_MOLHASH_COUNT int Number of different isotopic perturbed molecule hash codes
(builtin) E_HASHGROUP_COUNT_MI atomchange bondchange merge hadd
E_ISOTOPE_STEREO_ATOMHASH_COUNT int Number of different isotopic stereospecific basic atom hash codes
(builtin) E_HASHGROUP_COUNT_AIS atomchange bondchange merge
E_ISOTOPE_STEREO_HASH128 uint128 Perturbed isotope-sensitive and stereo-sensitive ensemble hashcode, extended to 128 bits
Compiled C module M_ISOTOPE_STEREO_HASHGROUP128 M_ISOTOPE_STEREO_HASH128 atomchange bondchange merge hadd mod_e_isotope_stereo_hash128.so
E_ISOTOPE_STEREO_MOLHASH_COUNT int Number of different isotopic stereospecific perturbed molecule hash codes
(builtin) E_HASHGROUP_COUNT_MIS atomchange bondchange merge hadd
E_ISOTOPE_STEREO_TAUTO_HASH uint64 Perturbed tautomer-tolerant ensemble isotope stereo hashcode
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASHISY atomchange bondchange stereochange merge mod_e_isotope_stereo_tauto_hash.so
E_ISOTOPE_STEREO_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant ensemble isotope stereo hashcode, 128 bit version
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_ISOTOPE_STEREO_HASH128 atomchange bondchange stereochange merge mod_e_isotope_stereo_tauto_hash128.so
E_ISOTOPE_TAUTO_HASH uint64 Perturbed tautomer-tolerant ensemble stereo hashcode, with isotope labels but without stereochemistry
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
setcount: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
stereobondmalus: { value: 0 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASHIY atomchange bondchange merge mod_e_isotope_tauto_hash.so
E_ISOTOPE_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant ensemble isotope hashcode, 128 bit version
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_ISOTOPE_HASH128 atomchange bondchange stereochange merge mod_e_isotope_tauto_hash128.so
E_ITER_URL url Display URL in EPA ITER (International Toxicity Estimates for Risk, https://toxnet.nlm.nih.gov/newtoxnet/iter.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_iter_url.xpd
E_IUPAC_ALLOWED_NAME string Allowed IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_allowed_name.xpd
E_IUPAC_OECAS_NAME string IUPAC name (OEChem CAS-like Style). This is a field in PubChem and used by the ASN I/O module.
atomchange bondchange stereochange
E_IUPAC_PREFERRED_NAME string Preferred IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_preferred_name.xpd
E_IUPAC_SYSTEMATIC_NAME string Systematic IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_systematic_name.xpd
E_IUPAC_TRADITIONAL_NAME string Traditional IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_traditional_name.xpd
E_IUPHAR_ID int Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org)
Tcl script E_SMILES atomchange bondchange stereochange merge e_iuphar_id.xpd
E_IUPHAR_URL url Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org)
Tcl script E_GUIDETOPHARMACOLOGY_ID atomchange bondchange stereochange merge e_iuphar_url.xpd
E_JCAMP_SPECTRA_BLOCK compound Embedded JCAMP spectral data block. Currently only used in E_NMRSPECTRUM to support the newer NTUPLES data table JCAMP style, with real/imaginary spectrum and real/imaginary FID possibly stored all in one file.
name string
symbol string
{#points} int
firstx double
lastx double
firsty double
lasty double
xfactor double
yfactor double
xunit string
yunit string
data floatvector
atomchange bondchange atom bond
E_JCHECK_URL url Data display URL in Japanese JCHECK databases (www.safe.nite.go.jp)
Tcl script E_CAS E_MITI_ID atomchange bondchange atom bond e_jcheck_url.xpd
E_JGLOBAL_ID string Database ID for the J-GLOBAL registry (https://jglobal.jst.go.jp)
Tcl script atomchange bondchange atom bond e_jglobal_id.xpd
E_JGLOBAL_URL url Display URL for the J-GLOBAL registry (https://jglobal.jst.go.jp)
Tcl script atomchange bondchange atom bond e_jglobal_url.xpd
E_JHOTI_FRAGMENTLIKENESS_VIOLATIONS byte Congreve, Carr, Murray, Jhoti, Drug. Discov. Today 2003, 8, 876
Tcl script E_WEIGHT E_NHDONORS E_NHACCEPTORS E_XLOGP2 atomchange bondchange atom bond e_jhoti_fragmentlikeness_violations.xpd
E_JME_STRING string JME editor structure encoding
Compiled C module A_ELEMENT B_ORDER B_TYPE A_TYPE A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange stereochange hadd mol atom bond ring mod_e_jme_string.so
E_JSTDATA stringvector JST extended molfile data in skip section
atomchange bondchange stereochange merge
E_KEGG_BRITE_CLASSIFICATION stringvector Compound classification codes as per the KEGG BRITE database (http://www.genome.jp/kegg/brite.html). Compounds must be present in KEGG database, i.e. have a KEGG ID.
Tcl script atomchange bondchange atom bond e_kegg_brite_classification.xpd
E_KEGG_COMPOUND_ID string KEGG ID (www.genome.jp)
Tcl script atomchange bondchange stereochange merge e_kegg_compound_id.xpd
E_KEGG_COMPOUND_URL url KEGG compound display URL (www.genome.jp)
Tcl script E_KEGG_COMPOUND_ID atomchange bondchange stereochange merge e_kegg_compound_url.xpd
E_KEGG_DRUG_ID string KEGG drug ID (www.genome.jp)
Tcl script atomchange bondchange stereochange merge e_kegg_drug_id.xpd
E_KEGG_DRUG_URL url KEGG drug display URL (www.genome.jp)
Tcl script E_KEGG_DRUG_ID atomchange bondchange stereochange merge e_kegg_drug_url.xpd
E_KEKULESET dataset Generated set of alternative Kekule forms of the structure- The generated forms are duplicate-filtered by symmetry hashcodes - that means there is only a single Kekule form for benzene, pyridine, pyrimidine (1.3-diazine) or pyrazine (1.4-diazine) - but two for pyridazine (1.2-diazine, with a double or single bond between the adjacent nitrogens).
maxkekuleforms: { value: 512 datatype: int}
Compiled C module A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange merge atom bond mod_e_kekuleset.so
E_KEYWORDS stringvector Keywords associated with ensemble
never
E_KLIFS_ID int Database ID for the KLIFS database (http://klifs.vu-compmedchem.nl)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_klifs_id.xpd
E_KLIFS_URL url Data display URL for the KLIFS database (http://klifs.vu-compmedchem.nl)
Tcl script E_KLIFS_ID atomchange bondchange stereochange atom bond e_klifs_url.xpd
E_KNAPSACK_ID string Database ID of compund in KNAPSACK database (http://www.knapsackfamily.com)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_knapsack_id.xpd
E_KNAPSACK_URL url Data display URL for the Knapsack database (www.knapsackfamily.com)
Tcl script E_KNAPSACK_ID atomchange bondchange stereochange atom bond e_knapsack_url.xpd
E_LC50 compound LC50 tumor screen data
concunit shortstring
lcconc float
panel shortstring
cell string
panelnumber short
cellnumber short
nlog_lc50 float
ntest_this short
ntest_max short
atomchange bondchange merge
E_LEVEL int Ensemble level
never
E_LHASA_REAGENT_SCAN_VERIFICATION compound Test conditions for Lhasa transform reagent scan verification. The value consists of a transform ID this test applies to, and a bit set indicating which starting material reagent condition this structure should match (0 if none)
{} {none:intramolecular:intermolecular1:intermolecular2:intermolecular3:intermolecular4}
transformid int
reagentmatches bitset
atomchange bondchange stereochange atom bond
E_LINCS_ID string Dabase ID of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_lincs_id.xpd
E_LINCS_URL url Display URL of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu)
Tcl script E_LINCS_ID atomchange bondchange stereochange atom bond e_lincs_url.xpd
E_LINKTEXTS stringvector Toplevel link texts of HTML URLs leading to this molecule
never
E_LIPIDMAPS_ID string Structure ID for the Lipidmaps database
Tcl script atomchange bondchange stereochange atom bond e_lipidmaps_id.xpd
E_LIPIDMAPS_URL url
Tcl script atomchange bondchange atom bond e_lipidmaps_url.xpd
E_LIPINSKI_ACCEPTOR_COUNT int Number of hydrogens on N and O atoms - H-bond acceptors according to simple Lipinski definition.
For a more refined definition, use property E_NHACCEPTORS.
Compiled C module A_TYPE A_ELEMENT A_FREE_ELECTRONS atomchange bondchange atom bond mod_e_lipinski_acceptor_count.so
E_LIPINSKI_DONOR_COUNT int Number of oxygen and nitrogen atoms according to really simple Lipinski definition. For a more refined definition, use E_NHDONORS.
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_lipinski_donor_count.so
E_LITERATURE_REFERENCE stringvector Auxiliary literature references
never
E_LOOKCHEM_URL url PubChem compound database URL
Tcl script atomchange bondchange stereochange merge e_lookchem_url.xpd
E_MACCS_KEYS bitvector MDL MACCS fingerprint (166 bits)
Tcl script atom bond e_maccs_keys.xpd
E_MANUFACTURERS compoundvector Data about manufactorers of a chemical
catno string
manufacturer string
catalog string
price float
currency string
amount float
unit string
info string
purity string
atomchange bondchange stereochange merge
E_MAP_ANNOTATION compoundvector Map markers to be used in conjuction with D_ANNOTATED_MAP
{} {none:circle:triangle:invtriangle:square:diamond:pentagon:hexagon}
tag string
object string
size int
outlinecolor color
fillcolor color
textcolor color
header string
footer string
atomchange bondchange stereochange 3drelative atom bond
E_MARKED boolean Flag for marked structures
never
E_MASSBANK_URL url Display URL for MassBank (https://massbank.eu) entry
Tcl script atomchange bondchange atom bond e_massbank_url.xpd
E_MASS_PATTERN xyvector Mass distribution pattern
cutoff: { value: 0.01 description: Minimum abundancy to include in output vector minvalue: 0.00 maxvalue: 1.00 datatype: double}
useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
Compiled C module A_ELEMENT A_TYPE A_ISOTOPE atomchange mod_e_mass_pattern.so
E_MATRIX_SCIENTIFIC_IDS stringvector ID of the compound Matrix Scientific catalog
Tcl script atomchange bondchange stereochange atom bond e_matrix_scientific_ids.xpd
E_MATRIX_SCIENTIFIC_URLS urlvector URL Matrix Scientific catalog entry
Tcl script E_MATRIX_SCIENTIFIC_IDS atomchange bondchange atom bond e_matrix_scientific_urls.xpd
E_MAX_CHAIN_FRAGMENT_SIZE int The maximum value of A_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-hydrogen atoms.
Compiled C module A_CHAIN_LENGTH atomchange bondchange atom bond mod_e_max_chain_fragment_size.so
E_MAX_CONJUGATED_SYSTEM_SIZE int The maximum size of a conjugated system in the ensemble according to the Shoichet definition (see literature reference). J. Med. Chem. 2003, 46, 4477-4486
Compiled C module A_CONJUGATED_SYSTEM_SIZE atomchange bondchange atom bond mod_e_max_conjugated_system_size.so
E_MAX_LINEAR_CHAIN_FRAGMENT_SIZE int The maximum value of A_LINEAR_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-branching non-hydrogen atoms.
Compiled C module A_LINEAR_CHAIN_LENGTH atomchange bondchange atom bond mod_e_max_linear_chain_fragment_size.so
E_MCULE_ID string Get database ID of structure in MCULE (mcule.com) database
Tcl script E_SMILES atomchange bondchange atom bond e_mcule_id.xpd
E_MCULE_URL url Display URL for MCULE (mcule.com) database
Tcl script E_MCULE_ID atomchange bondchange atom bond e_mcule_url.xpd
E_MDL_NAME string Name as extracted from MDL Molfile header
never
E_MDL_NUMBER string MDL substance number
Tcl script atomchange bondchange atom bond e_mdl_number.xpd
E_MEREG string MDL external registry number
never
E_MESH_ID string MESH ID, extracted from E_MESH_TERMS at the toplevel
Tcl script E_MESH_TERMS atomchange bondchange atom bond e_mesh_id.xpd
E_MESH_TERMS compoundvector Mesh terms associated with structure retrieved from PubChem
id int
terms stringvector
url url
ontotree datatree
Tcl script E_CID atomchange bondchange stereochange merge atom bond e_mesh_terms.xpd
E_MESH_URL url MESH display URL, extracted from E_MESH_TERMS at the toplevel
Tcl script E_MESH_TERMS atomchange bondchange atom bond e_mesh_url.xpd
E_MESO boolean Check whether at least one molecule is a meso compound, and all other molecules are either also meso, or not stereogenic
Tcl script M_MESO M_STEREO_STATUS atomchange bondchange stereochange merge mol atom bond e_meso.xpd
E_MESOMER_SET dataset A generator for all duplicate-filtered mesomers accessible by moving existing charges along pi systems. Does not create new charges.
Tcl script atomchange bondchange atom bond e_mesomer_set.xpd
E_METABOLIGHTS_ID string Structure access key for MetaboLights database (https://www.ebi.ac.uk/metabolights)
Tcl script E_INCHI atomchange bondchange stereochange atom bond e_metabolights_id.xpd
E_METABOLIGHTS_URL url Structure data display URL for MetaboLights database (https://www.ebi.ac.uk/metabolights)
Tcl script E_METABOLIGHTS_ID atomchange bondchange atom bond e_metabolights_url.xpd
E_METABOLOMICSWORKBENCH_CLASSIFICATION dictionary Compund description in the Metabolomics Workbench (www.metabolomicsworkbench.org)
Tcl script E_METABOLOMICSWORKBENCH_ID atomchange bondchange stereochange atom bond e_metabolomicsworkbench_classification.xpd
E_METABOLOMICSWORKBENCH_ID int Compund registration ID in the Metabolomics Workbench (www.metabolomicsworkbench.org)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_metabolomicsworkbench_id.xpd
E_METACYC_URL url Link into the MetaCyc database (metacyc.org)
Tcl script atomchange bondchange atom bond e_metacyc_url.xpd
E_METADATA dictionary Dublin Core metadata for structure
never
E_METHOD string QM method description string
atomchange bondchange
E_MIF_IMAGE diskfile
(switchable between string blob diskfile xmlstring)
Ensemble image in MIF FrameMaker format
width: { value: 180 datatype: int}
height: { value: 180 datatype: boolean}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.2 datatype: double}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: string}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 1.5 datatype: double}
unit: { value: {} datatype: string}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: color constraints: emptycolor}
voronoifilter: { value: {} datatype: string constraints: filtername}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Arial datatype: string}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module atomchange bondchange stereochange merge atom bond mod_e_mif_image.so
E_MINIMOL blob Ultracompact structure representation for structure database applications, with precomputed data for most common substructure attributes. Queries with extended attributes are still possible by converting the Minimol into a standard ensemble. The format is designed to be expanded into a simple memory blob for matching, minimizing malloc/free oberhead. In scripting interpreters, "ens create" auto-detects and decodes binary and hex-encoded Minimols.
version: { value: 3 datatype: int}
Compiled C module A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO B_ORDER B_TYPE A_TYPE A_STEREO_GROUP atomchange bondchange stereochange hadd mol atom bond mod_e_minimol.so
E_MIREG string MDL internal registry number. This is a standard field in RD files.
never
E_MITI_ID string Japanese hazardous substance registration number (www.safe.nite.go.jp)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_miti_id.xpd
E_MNA dictionary MNA (multilevel neighborhood of atoms) fragment set, as defined by Poroikov et al. J. Chem. Inf. Comput. Sci. 1999, 39, 666-670
levels: { value: 1 2 description: Neighbor sphere radii to include in the result set datatype: intvector}
Tcl script A_SYMBOL atomchange bondchange atom bond e_mna.xpd
E_MOL2_STRING string Sybyl MOL2 structure encoding as string
Tcl script atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond e_mol2_string.xpd
E_MOLAR_REFRACTIVITY double Molar refractivity computed by the Wildman-Crippen method (see litref) J. Chem. Inf. Comput. Sci. 1999, 39, 868-873
Compiled C module A_WILDMAN_CRIPPEN_TYPE atomchange bondchange atom bond mod_e_molar_refractivity.so
E_MOLBASE_URL url Supplier data display page from molbase.com
Tcl script atomchange bondchange atom bond e_molbase_url.xpd
E_MOLD2_DESCRIPTORS floatvector MOLD2 descriptor collection, computed with original source encapsulated as a Cactvs module. The MOLD2 code unfortunately uses statically allocated data structures, and thus has a limit on 150 atoms, 400 paths and 9 ligands per atom. Larger structures fail. J. Chem. Inf. Model., 2008, 48 (7), pp 1337-1344
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Compiled C module atomchange bondchange merge mod_e_mold2_descriptors.so
E_MOLHASH_COUNT int Number of different pertured molecule hash codes
(builtin) E_HASHGROUP_COUNT_M atomchange bondchange merge hadd
E_MOLINSTINCTS_ANALYSIS_URL url Access URL for structure analysis in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_analysis_url.xpd
E_MOLINSTINCTS_CONSTANT_PROPERTY_URL url Display URL for constant properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_constant_property_url.xpd
E_MOLINSTINCTS_DESCRIPTOR_PROPERTY_URL url Display URL for molecular descriptor properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_descriptor_property_url.xpd
E_MOLINSTINCTS_DRUG_PROPERTY_URL url Display URL for molecular drug properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_drug_property_url.xpd
E_MOLINSTINCTS_ID string ID in MolInstincts database (www.molinstincts.com)
Tcl script atomchange bondchange atom bond e_molinstincts_id.xpd
E_MOLINSTINCTS_QUANTUM_PROPERTY_URL url Display URL for molecular quantum properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_quantum_property_url.xpd
E_MOLINSTINCTS_SPECTRA_URL url Display URL for structure spectra in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_spectra_url.xpd
E_MOLNAME string Ensemble name as free format string, no associated with any specific naming convention
atomchange bondchange merge
E_MOLPORT_ID string ID of structure in the MOLPORT database (www.molport.com)
Tcl script E_SMILES atomchange bondchange stereochange merge e_molport_id.xpd
E_MOLPORT_URL url Display URL in the Molport portal (www.molport.com)
E_MOLPORT_ID atomchange bondchange stereochange merge
E_MONOISOTOPIC_MASS float Mass computed with most abundant isotope only, not natural abundance
useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
Compiled C module A_ELEMENT A_TYPE A_ISOTOPE atomchange mod_e_monoisotopic_mass.so
E_MP floatpair Melting Point in Kelvin, with optional range
value float
range float
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE atomchange bondchange
E_MQN shortvector Reymond molecular quantum numbers L. Ruddigkeit, L. C. Blum, J.-L. Reymond, J. Chem. Inf. Model. 2013, 53, 56-65
c int
f int
cl int
br int
i int
s int
p int
an int
cn int
ao int
co int
hac int
asb int
adb int
atb int
csb int
cdb int
ctb int
rbc int
hbam int
hba int
hdbm int
hdb int
neg int
pos int
asv int
adv int
atv int
aqv int
cdv int
dtv int
cqv int
r3 int
r4 int
r5 int
r6 int
r7 int
r8 int
r9 int
rg10 int
afr int
bfr int
Compiled C module A_TYPE B_TYPE A_ELEMENT B_RING_COUNT B_ORDER A_RING_COUNT B_ROTATABILITY R_TYPE R_SIZE E_CHARGED_GROUP_COUNTS atomchange bondchange atom bond mod_e_mqn.so
E_MRV_STRING string MRV structure encoding
Tcl script A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange stereochange merge hadd atom bond e_mrv_string.xpd
E_MSDS_URL url URL of MSDS from Matrix Scientific Website
Tcl script atomchange bondchange atom bond e_msds_url.xpd
E_MSSPECTRUM compound Mass spectrum. The computation function attempts a NIST WebBook retrieval.
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
mass floatvector
signal floatvector
label stringvector
Tcl script A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange stereochange e_msspectrum.xpd
E_MSSPECTRUM_IMAGE diskfile
(switchable between string blob diskfile url)
MS spectrum rendering
height: { value: 250 datatype: int}
width: { value: 500 datatype: int}
bgcolor: { value: white datatype: color}
title: { value: {} datatype: string}
filename: { value: {} datatype: string constraints: writeable}
format: { value: gif enumeration: png,png24:gif:png8 datatype: string}
titlecolor: { value: black datatype: color}
framecolor: { value: black datatype: color}
signalcolor: { value: #DD0000 datatype: color}
Tcl script E_MSSPECTRUM atomchange bondchange merge mol e_msspectrum_image.xpd
E_MS_ACADEMIC_URL url URL for data in Maicrosoft Academic Search
Tcl script E_STDINCHI E_CAS atomchange bondchange stereochange atom bond e_ms_academic_url.xpd
E_MULTIPLICITY byte Spin multiplicity of the whole molecular ensemble. Used in Gaussion Archive I/O module.
atomchange bondchange merge hadd
E_MURCKO_SCAFFOLD structure Compute various Murcko-Style scaffolds J. Med. Chem. (1996), 39(15), 2887-2893
heteroatomreplacement: { value: none description: Whether to change hetero atoms into a generic hetero atom, or into carbon enumeration: none:generic,het,x:carbon,c datatype: int}
hydrogenate: { value: none description: If set, hydrogenate aliphatic or any double bonds enumeration: none:aliphatic:all datatype: int}
minringsize: { value: 0 description: Minimum required un-annealed ring size for retention minvalue: 0 datatype: int}
preserveexodb: { value: 0 description: If set, preserve exo-ring double bond stub datatype: boolean}
Tcl script atomchange bondchange atom bond e_murcko_scaffold.xpd
E_MURRAY_DRUGLIKENESS_VIOLATIONS byte Number of failed tests according to the Jhoti-Murray rules. This is a stricter form of the Lipinski Rule-of-5 criterion. Jhoti, Williams, Rees, Murray, Nat.. Rev. Drug. Discov. 2013, 12, 644
Tcl script E_NHDONORS E_NHACCEPTORS E_WEIGHT E_XLOGP2 E_NROTBONDS E_TPSA atomchange bondchange atom bond e_murray_druglikeness_violations.xpd
E_NAME string Long ensemble identification string
pubchemlookup: { value: 0 datatype: string}
lmchlookup: { value: 0 datatype: string}
useformula: { value: 1 datatype: string}
(builtin) never
E_NAMEKEYSET stringvector List of chemical keys of alternative compound names in phonetic encoding, derived from the names in E_NAMESET
maxlen: { value: 100 description: maxiumum number of characters to include datatype: int}
expand: { value: 0 description: expand common chemistry-specific spelling variants datatype: boolean}
Compiled C module E_NAMESET never mod_e_namekeyset.so
E_NAMESET stringvector List of alternative compound names The computation function retrieves a full set names registered in the NCI resolver.
Tcl script E_HASHISY atomchange bondchange stereochange e_nameset.xpd
E_NATOMS int Number of atoms in ensemble
(builtin) atomchange merge hadd
E_NATURAL_PRODUCT_LIKENESS double Natrual product-likeness score according to the Ertl/Roggo/Schuffenhauer algorithm Ertl, Roggo, Schuffenhauer, J. Chem. Inf. Model. 2008, 48, 68-74
Tcl script atomchange bondchange atom bond e_natural_product_likeness.xpd
E_NBHASH int Number of different bond hash codes
(builtin) E_HASHGROUP_COUNT_B atomchange bondchange merge
E_NBHASHS int Number of different stereospecific bond hash codes
(builtin) E_HASHGROUP_COUNT_BS atomchange bondchange merge
E_NBONDS int Number of bonds in ensemble
(builtin) atomchange bondchange merge hadd
E_NCBI_ACTIVITY byte Activity summary (Outcome)
inactive=1:active=2:inconclusive=3:unspecified=4:probe=5
never
E_NCBI_BIBLIO_AFFILIATION choice NCBI author affiliation
str string
std compound
never
E_NCBI_BIBLIO_AFFILIATION_LIST choicevector NCBI author affiliations
str string
std compound
never
E_NCBI_BIBLIO_ARTICLE_FROM choice Article container reference
journal compound
book compound
proc compound
never
E_NCBI_BIBLIO_ARTICLE_ID_SET choicevector Article reference ID set
pubmed int
medline int
doi string
pii string
pmcid int
pmcpid string
pmpid string
other compound
never
E_NCBI_BIBLIO_AUTHORS choice NCBI author reference
std compoundvector
ml stringvector
str stringvector
never
E_NCBI_BIBLIO_AUTHOR_LIST compound NCBI author reference
names choice
affil choice
never
E_NCBI_BIBLIO_FULL_AUTHOR compound NCBI author reference
{} primary=1:secondary=2 compiler=1:editor=2:patent-assignee=3:translator=4
name choice
level int
role int
affil choice
is-corr boolean
never
E_NCBI_BIBLIO_FULL_AUTHOR_SET compoundvector NCBI author reference
{} primary=1:secondary=2 compiler=1:editor=2:patent-assignee=3:translator=4
name choice
level int
role int
affil choice
is-corr boolean
never
E_NCBI_BIBLIO_IMPRINT compound Document imprint data
{} {} {} {} {} {} {} {} {} published:submitted:in-press:other=255 {} {} none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255
date date
volume string
issue string
pages string
section string
pub choice
cprt date
part-sup string
language string
prepub int
part-supi string
retract compound
pubstatus int
history compoundvector
never
E_NCBI_BIBLIO_MEETING compound Meeting reference
number string
date date
place choice
never
E_NCBI_BIBLIO_PATENT_ID choice Patent ID reference
number string
app-number string
never
E_NCBI_BIBLIO_PATENT_PRIORITY compoundvector Patent priorities
country string
number string
date date
never
E_NCBI_BIBLIO_PUBSTATUS_HISTORY compoundvector Publication status history
none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255
pubstatus int
date date
never
E_NCBI_BIBLIO_RETRACTION compound Document retraction information
none:retracted:notice:in-error:erratum
type int
exp string
never
E_NCBI_BIBLIO_STD_AFFILIATION compound NCBI structured affiliation
affil string
div string
city string
sub string
country string
street string
email string
fax string
phone string
postal-code string
never
E_NCBI_BIBLIO_TITLE choicevector NCBI bibliographic title reference
name string
tsub string
trans string
jta string
iso-jta string
ml-jta string
coden string
issn string
abr string
isdn string
never
E_NCBI_DBTAG compound NCBI database reference
db string
tag string
never
E_NCBI_DBTRACKING compound NCBI substance db source data
name string
source-id string
date date
description string
pub choice
never
E_NCBI_IMAGE diskfile A 2D-plot default image of the structure as a GIF or PNG file
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
interlace: { value: 1 datatype: boolean}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: string}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
crop: { value: -1 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
format: { value: png8 datatype: string}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 0 datatype: boolean}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
showstereoh: { value: 0 datatype: boolean}
symbolfontsize: { value: -1 datatype: int}
annotationfontsize: { value: -1 datatype: double}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int}
highlightgroups: { value: {} datatype: string}
boxgroups: { value: {} datatype: string}
font: { value: arialbd.ttf datatype: string}
groupcolor: { value: purple datatype: color}
showisotope: { value: 1 datatype: boolean}
isotopemapping: { value: none datatype: string}
suppressedmols: { value: {} datatype: string}
linewidth: { value: 1.4 datatype: double}
showempty: { value: 0 datatype: boolean}
voronoicolorproperty: { value: {} datatype: color constraints: emptycolor}
voronoifilter: { value: {} datatype: string constraints: filtername}
showmapping: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: string constraints: emptycolor}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
frame: { value: 0 datatype: boolean}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: int}
footerfontsize: { value: -1 datatype: int}
circlecolorproperty: { value: {} datatype: string}
circlefilter: { value: {} datatype: string constraints: filtername}
width: { value: 300 datatype: int}
height: { value: 300 datatype: int}
bgcolor: { value: grey96 datatype: color}
bondcolor: { value: split datatype: string}
atomcolor: { value: type datatype: string}
asymbol: { value: xsymbol datatype: string}
border: { value: 16 datatype: int}
bonds: { value: 8 datatype: int}
commenttype: { value: none enumeration: none:text:property,prop datatype: string}
metadata: { value: 0 datatype: boolean}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 2 datatype: double}
fixiepngsize: { value: 1 datatype: boolean}
rawcoordinates: { value: 0 datatype: boolean}
checkintersection: { value: 0 datatype: boolean}
showstereogroups: { value: 1 datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION A_ELEMENT atomchange bondchange stereochange merge hadd mod_e_ncbi_image.so
E_NCBI_MMDB compound MMDB source information
mmdb-id int
molecule-id int
molecule-name stringvector
residue-id int
residue-name string
atom-id int
atom-name string
never
E_NCBI_PERSON_ID choice NCBI person reference
dbtag compound
name compound
str string
consortium string
never
E_NCBI_PUBLICATION choice Publication in PubMed style
gen compound
sub compound
medline compound
muid int
article compound
journal compound
book compound
proc compound
patent compound
pat-id compound
man compound
equiv choicevector
pmid int
never
E_NCBI_PUBLICATION_ARTICLE compound Article reference
title choicevector
authors compound
from choice
ids choicevector
never
E_NCBI_PUBLICATION_BOOK compound Book reference
title choicevector
coll choicevector
authors compound
imp compound
never
E_NCBI_PUBLICATION_GENERAL compound General publication reference
cit string
authors compound
muid int
journal choicevector
volume string
issue string
pages string
date date
serial-number int
title string
pmid int
never
E_NCBI_PUBLICATION_JOURNAL compound Journal reference
title choicevector
imp compound
never
E_NCBI_PUBLICATION_MANUSCRIPT compound Manuscript reference
{} {} unknown:manuscript:letter:thesis
cit compound
man-id string
type int
never
E_NCBI_PUBLICATION_MEDLINE compound Medline reference
{} {} {} {} {} {} {} {} {} {} {} {} publisher:premedline:medline
uid int
em date
cit compound
abstract string
mesh compoundvector
substance compoundvector
xref compoundvector
idnum stringvector
gene stringvector
pmid int
pub-type stringvector
mlfield compoundvector
status int
never
E_NCBI_PUBLICATION_MEDLINE_FIELD_DOCREF_SET compoundvector Docrefs of NCBI medline field of publication
none:medline:pubmed:ncbigi
type int
uid int
never
E_NCBI_PUBLICATION_MEDLINE_FIELD_SET compoundvector NCBI medline field of publication
other:comment:erratum
type int
str string
ids compoundvector
never
E_NCBI_PUBLICATION_MEDLINE_MESH_QUALIFIER_SET compoundvector Medline mesh term qualifiers
mp boolean
subh string
never
E_NCBI_PUBLICATION_MEDLINE_MESH_SET compoundvector Medline mesh references
mp boolean
term string
qual compoundvector
never
E_NCBI_PUBLICATION_MEDLINE_RN_SET compoundvector Medline substance references
nameonly:cas:rc
type int
cit string
name string
never
E_NCBI_PUBLICATION_MEDLINE_SI_SET compoundvector Medline crossreferences
none:ddbj:carbbank:embl:hdb:genbank:hgml:mim:msd:pdb:pir:prfseqdb:psd:swissprot:gdb
type int
cit string
never
E_NCBI_PUBLICATION_PATENT compound Patent reference
title string
authors compound
country string
doc-type string
number string
date-issue date
class stringvector
app-number string
app-date date
applicants compound
assignees compound
priority compoundvector
abstract string
never
E_NCBI_PUBLICATION_PATENT_ID compound Patent ID reference
country string
id choice
doc-type string
never
E_NCBI_PUBLICATION_PROCEEDINGS compound Proceedings reference
book compound
meeting compound
never
E_NCBI_PUBLICATION_SET choicevector Publication in PubMed style
gen compound
sub compound
medline compound
muid int
article compound
journal compound
book compound
proc compound
patent compound
pat-id compound
man compound
equiv string
pmid int
never
E_NCBI_PUBLICATION_SUBMISSION compound Submission reference
{} {} unknown:paper:tape:floppy:email:other=255
authors compound
imp compound
medium int
date date
descr string
never
E_NCBI_RESONANCE_SCORE int Score of low-energy resonance form selected for standardization
A_ELEMENT B_ORDER B_TYPE A_TYPE atomchange bondchange merge
E_NCBI_STANDARDIZER_HASH uint64 NCBI standardization hashcode (no h, no charges, bond order)
Tcl script A_ELEMENT B_ORDER A_TYPE B_TYPE atomchange bondchange merge e_ncbi_standardizer_hash.xpd
E_NCBI_STD_NAME compound NCBI standardized name reference
last string
first string
middle string
full string
initials string
suffix string
title string
never
E_NCBI_SUBSTANCE_COMMENT stringvector Substance comments
never
E_NCBI_SUBSTANCE_ID compound NCBI substance identifier. If set to zero, use data in E_NCBI_SUBSTANCE_SOURCE
id int
version int
never
E_NCBI_SUBSTANCE_ID_LIST intvector NCBI substance identifier list, usually for a CID/SID mapping
never
E_NCBI_SUBSTANCE_SOURCE choice NCBI substance source data
individual choice
db compound
mmdb compound
never
E_NCBI_SUBSTANCE_SYNONYMS stringvector Substance synonyms
Tcl script E_CID never e_ncbi_substance_synonyms.xpd
E_NCBI_SUBSTANCE_XREF choicevector NCBI substance crossreference data
regid string
rn string
mesh string
pmid int
gi int
mmdb int
sid int
cid int
dburl url
sburl url
asurl url
protein-gi int
nucleotide-gi int
taxonomy int
aid int
mim int
gene int
probe int
biosystem int
geogse int
geogsm int
patent string
protein-accession string
nucleotide-accession string
doi string
citation string
never
E_NCBI_THUMBNAIL diskfile
(switchable between string blob diskfile url)
A 2D-plot thumbnail of the structure as a GIF or PNG or SVG file
hsymbol: { value: special datatype: string}
csymbol: { value: special datatype: string}
hcolor: { value: {} datatype: string}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: string}
footercolor: { value: black datatype: string}
interlace: { value: 1 datatype: boolean}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
filename: { value: {} datatype: string}
highlightcolor: { value: red datatype: string}
highlightbonds: { value: {} datatype: string}
httpheader: { value: 0 datatype: int}
crop: { value: -1 datatype: string}
wedges: { value: 1 datatype: string}
wiggles: { value: sp2 datatype: string}
format: { value: png8 description: Format svg uses E_SVG_IMAGE property computation, the others E_GIF enumeration: gif:png:png8:bmp:svg datatype: int}
markcolor: { value: blue datatype: string}
logofile: { value: {} datatype: string}
logoscale: { value: 1 datatype: string}
dashes: { value: 1 datatype: string}
headerproperty: { value: {} datatype: string}
footerproperty: { value: {} datatype: string}
bead: { value: 0 datatype: string}
showcharge: { value: 1 datatype: string}
showradical: { value: 1 datatype: string}
showstereo: { value: 1 datatype: string}
symbolfontsize: { value: -1 datatype: string}
annotationfontsize: { value: -1 datatype: string}
antialiasing: { value: 3 datatype: string}
highlightgroups: { value: {} datatype: string}
boxgroups: { value: {} datatype: string}
groupcolor: { value: purple datatype: string}
showisotope: { value: 1 datatype: string}
isotopemapping: { value: none datatype: string}
showstereoh: { value: 0 datatype: string}
suppressedmols: { value: {} datatype: string}
linewidth: { value: 1.4 datatype: string}
showempty: { value: 0 datatype: string}
voronoicolorproperty: { value: {} datatype: string}
voronoifilter: { value: {} datatype: string}
showmapping: { value: 0 datatype: string}
font: { value: {} datatype: string}
annotationcolor: { value: {} datatype: string}
showchirality: { value: none datatype: string}
frame: { value: 0 datatype: string}
linespacing: { value: 2.0 datatype: string}
headerfontsize: { value: -1 datatype: string}
footerfontsize: { value: -1 datatype: string}
circlecolorproperty: { value: {} datatype: string}
circlefilter: { value: {} datatype: string}
width: { value: 100 datatype: string}
height: { value: 100 datatype: string}
bgcolor: { value: grey96 datatype: string}
bondcolor: { value: black datatype: string}
atomcolor: { value: type datatype: string}
asymbol: { value: box datatype: string}
border: { value: 6 datatype: string}
bonds: { value: 8 datatype: string}
commenttype: { value: none datatype: string}
metadata: { value: 0 datatype: string}
wigglecount: { value: 4 datatype: string}
wiggleamplitude: { value: 2 datatype: string}
fixiepngsize: { value: 1 datatype: string}
rawcoordinates: { value: 0 datatype: string}
checkintersection: { value: 0 datatype: string}
showstereogroups: { value: 0 datatype: string}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION A_ELEMENT atomchange bondchange stereochange merge hadd mod_e_ncbi_thumbnail.so
E_NCICADD_PARENT_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: ncicad_parent datatype: string}
scope: { value: private datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_NCICADD_PARENT_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 0 resonance 0 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHISY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 0 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 0 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ncicadd_parent_id.xpd
E_NCICADD_PARENT_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_NCICADD_TEST_ERROR_BITSET bitvector Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_NCICADD_TEST_STATUS_BITSET bitvector Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_NCOLLISIONS int Number of atomic close contacts
Compiled C module A_XYZ A_ELEMENT A_TYPE atomchange 3drelative mod_e_ncollisions.so
E_NCONFORMERS int Number of conformations in A_CONFORMER
Tcl script A_CONFORMER atomchange bondchange merge e_nconformers.xpd
E_ND20 float Substance refractive index (20 oC, sodium D line 589.3 nm)
atomchange bondchange atom bond
E_NENVELOPE short Total number of envelope rings in ensemble
(builtin) R_TYPE atomchange bondchange merge ring
E_NESSSR short Total number of extended SSSR rings in ensemble, including all basic SSSR rings
(builtin) R_TYPE atomchange bondchange merge ring
E_NEUTRALIZED_STRUCTURE structure Structure with neutralized charges and charge pairs
Compiled C module A_FORMAL_CHARGE atomchange bondchange stereochange mod_e_neutralized_structure.so
E_NHACCEPTORS short Number of hydrogen bond acceptors
Tcl script A_HYDROGEN_BONDING atomchange bondchange e_nhacceptors.xpd
E_NHDONORS short Number of atoms which are bonded to hydrogens which may act as H-bridge donors
countdonorhs: { value: 0 datatype: boolean}
Tcl script A_HYDROGEN_BONDING atomchange bondchange e_nhdonors.xpd
E_NIKKAJI_ID string ID of the compound in the Japanese Nikkaji substance dictionary
atomchange bondchange stereochange atom bond
E_NIOSH_URL url NIOSH (http://www.cdc.gov/niosh-rtecs) data display URL
Tcl script E_RTECS_NUMBER atomchange bondchange atom bond e_niosh_url.xpd
E_NIST_SOLUBILITY_URL url Dislay URL for compound solubility in any registered solvent (https://srdata.nist.gov/solubility/)
Tcl script E_CAS atomchange bondchange atom bond e_nist_solubility_url.xpd
E_NIST_WEBBOOK_ID string NIST WebBook ID (webbook.nist.gov)
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER A_ISOTOPE atomchange bondchange stereochange mol atom bond e_nist_webbook_id.xpd
E_NIST_WEBBOOK_URL url NIST WebBook URL (webbook.nist.gov)
Tcl script E_NIST_WEBBOOK_ID mol atom bond e_nist_webbook_url.xpd
E_NMOLECULES int Number of molecules in ensemble
(builtin) atomchange bondchange merge shuffle mol
E_NMRDB_PREDICTOR_URL url nmrdb.org URL linking to a dynamic NMR spectra prediction for the structure
Tcl script E_SMILES mol atom bond e_nmrdb_predictor_url.xpd
E_NMRSHIFTDB_ID int NMRShiftDB URL
baseurl: { value: http://www.nmrshiftdb.org description: Base URL for Internet access datatype: url}
Tcl script E_INCHI mol atom bond e_nmrshiftdb_id.xpd
E_NMRSHIFTDB_URL url NMR Shift DB display URL (http://nmrshiftdb.nmr.uni-koeln.de)
baseurl: { value: http://www.nmrshiftdb.org description: Base URL for Internet access datatype: url}
Tcl script E_NMRSHIFTDB_ID atomchange bondchange atom bond e_nmrshiftdb_url.xpd
E_NMRSIGMA_METHOD string NMR shielding computation method description string. Used in SHARC/SHGI and Gaussian Input I/O modules.
atomchange bondchange 3drelative 3dabsolute
E_NMRSPECTRUM compound NMR spectrum
experimental boolean
nucleus string
origin string
author string
date date
spectrometer string
parameters string
specificparams dictionary
reference string
temperature float
purity float
source string
description string
solvent string
procedure string
resolution double
coding string
spectrum compound
imagspectrum compound
fid compound
imagfid compound
shift floatvector
multiplicity stringvector
integral floatvector
ja floatvector
jb floatvector
jc floatvector
jadist shortvector
jbdist shortvector
jcdist shortvector
assignment stringvector
assignmentmethod string
range floatvector
state string
standard string
source: { value: nmrshiftdb enumeration: nmrshiftdb datatype: int}
nucleus: { value: 13C description: Nucleus, with isotope mass prefixed, i.e. 13C, 1H, etc. datatype: string}
tryretrieval: { value: 1 datatype: boolean}
tryprediction: { value: 1 datatype: boolean}
Tcl script atomchange bondchange e_nmrspectrum.xpd
E_NMRSPECTRUM_IMAGE diskfile
(switchable between string blob diskfile url)
NMR spectrum rendering
datafield: { value: spectrum datatype: string}
height: { value: 250 datatype: int}
width: { value: 500 datatype: int}
bgcolor: { value: white datatype: color}
title: { value: {} datatype: string}
filename: { value: {} datatype: string constraints: writeable}
format: { value: png enumeration: png,png24:gif:png8 datatype: string}
titlecolor: { value: black datatype: color}
framecolor: { value: black datatype: color}
signalcolor: { value: #DD0000 datatype: color}
Tcl script E_NMRSPECTRUM atomchange bondchange merge mol e_nmrspectrum_image.xpd
E_NONBONDING_ENERGY float Estimate of NBE computed from VdW-Sphere Interaction in A_XYZ coordinates
Compiled C module A_XYZ A_TYPE A_TOPO_DISTANCE A_VDW_INTERACTION atomchange bondchange stereochange merge 3drelative hadd mod_e_nonbonding_energy.so
E_NOTEBOOK_ID string Laboratory notebook registration ID
A_ELEMENT A_TYPE B_TYPE B_ORDER never
E_NO_HYDROGEN_QUERY_SCREEN bitvector Bitvector optimized for standard superstructure queries, with focus on ring systems and ring substitutions as well as the capability to generalized heteroatoms and standard element classes (halogens, N/O/S, etc.).
size: { value: 1952 description: Vector size minvalue: 256 maxvalue: 4096 datatype: int}
power: { value: 2 description: Count step escalation minvalue: 1 maxvalue: 3 datatype: int}
nbitsperpath: { value: 4 description: Bit positions to ser per unique path minvalue: 1 maxvalue: 16 datatype: int}
maxcount: { value: 3 description: Maximum path count to use minvalue: 1 maxvalue: 16 datatype: int}
minpathlen: { value: 2 description: Minimum length of paths fo hash minvalue: 2 maxvalue: 5 datatype: int}
maxpathlen: { value: 5 description: Maximum length of pathes to hash minvalue: 2 maxvalue: 10 datatype: int}
maxpathsperatom: { value: -1 description: Maximum nmber of paths to find per atom, -1 is unlimited minvalue: -1 maxvalue: 9999 datatype: int}
isquery: { value: 0 description: Whether structure is a query sub/superstructure, or a complete structure datatype: boolean}
ignoreh: { value: 1 description: If set, do not create any codes involving hydrogen datatype: boolean}
tauto: { value: 0 description: If set, do not set any bits with H, or involving bond orders in tauo systems datatype: boolean}
debug: { value: 0 description: If set, print found paths datatype: boolean}
useringcombos: { value: 1 description: If set, add ring combo screen bits datatype: boolean}
tracebit: { value: -1 description: Trace which pattern sets this bit position minvalue: -1 maxvalue: 4096 datatype: int}
cmpflags: { value: bondorder|useatomtree|usebondtree description: Comparison flags which will be used in subsequent atom-by-atom matching. Some flags can be used for increasing the filter efficiency enumeration: one:wedge,wedges:charge:stereo:bondorder,bo:terminal:nozwitterioncollapse:nosinglaonaro:nodoubleonaro:isotope:tautomer:arotautomer:matchbondringcount:lazymatchbondringcount:kekule,kekuleodd:strictnomatch:nochainonaro:lazymatchatomringcount:matchatomringcount:bondreaction:pionaro:noaliphaticonaro:relativestereo:fixedframework,fixedframe:nomultibondfg:noarobondfg:noheterofg:useatomtree,atomtree:usebondtree,bondtree:excludesmartsenvironment:openhcount:varbondglobal:varbondindividual:kekuleeven:unsetaromaticisaliphatic:implicitonsingleoraro:nullsubstructureismismatch:nochainonring:atomlistidentity:splitfragments:generalizeheteroatoms:nosuperatomonh:singleattachmentsuperatomsonly:remembercomplexmatches:matchallheavyatoms:fullringsystem:noatomstereook:nobondstereook:multibondorder,singleonany,singleisany:matchfullmolecule,matchfullmol:matchfullensemble,matchfullens:nosmallerrings:noalkyllinks:containedatomlists:chained:no3dcoordinatecomputation,no3dcoordinatescomputation datatype: bitset}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER B_ISAROMATIC A_ISAROMATIC E_ELEMENT_COUNT R_TYPE R_AROMATIC A_HASH A_RING_COUNT B_RING_COUNT atomchange bondchange hadd atom bond ring mod_e_no_hydrogen_query_screen.so
E_NO_HYDROGEN_SCREEN bitvector Screening bits for superstructure search (same as E_SCREEN, but not including any fragments which contain a hydrogen atom)
usevariants: { value: 0 datatype: boolean}
maxvariants: { value: 10 datatype: int}
extended: { value: 2 minvalue: 0 maxvalue: 2 datatype: int}
tauto: { value: 0 datatype: boolean}
ignoreh: { value: 1 datatype: boolean}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange hadd mol mod_e_no_hydrogen_screen.so
E_NRINGS short Total number of rings in ensemble
(builtin) atomchange bondchange merge ring
E_NROTBONDS int Number of bonds which are rotatable and where the rotation has a steric effect
Compiled C module B_ROTATABILITY atomchange bondchange hadd mod_e_nrotbonds.so
E_NSC int NCI Cancer screening database record number
atomchange bondchange
E_NSSSR short Total number of SSSR rings in ensemble
(builtin) R_TYPE atomchange bondchange merge ring
E_NUCLEAR_RECEPTOR_LIGAND_LIKENESS compound Structural likeness to known nucleic receptor agonists or antatonists, computed as highest Tanimoto similarity (on standard similarity property E_SCREEN) to a diverse 1K cpds subset of the NRLiSt BDB (Nuclear Receptors Ligands and Structures Benchmarking Database, http://nrlist.drugdesign.fr/download.php) Lagarde, Nasr, Jeremie, Guillemain, Laville, Labib, Zagury, Montes, J. Med. Chem.. 2014, 57, 3117
similarity byte
structure structure
Tcl script E_SCREEN atomchange bondchange atom bond e_nuclear_receptor_ligand_likeness.xpd
E_NVARIANTS int Estimate of number of structure variant if lists, rgroups, etc. are enumerated. No symmetry analysis!
Tcl script A_TYPE atomchange bondchange merge atom bond e_nvariants.xpd
E_OPENPHACTS_ID int RSC OpenPhacts ID (www.openphacts.org)
Tcl script E_SMILES atomchange bondchange atom bond e_openphacts_id.xpd
E_OPENPHACTS_URL url Data display link for structure data in OpenPHACTS database (openphacts.org).
Tcl script E_OPENPHACTS_ID atomchange bondchange hadd atom bond e_openphacts_url.xpd
E_OPREA_LEADLIKENESS_VIOLATIONS byte Teague, Davis, Leeson, Oprea, Angew. Chem. Int. Ed. 1999, 38, 3743
Tcl script E_WEIGHT E_XLOGP2 E_NROTBONDS atomchange bondchange atom bond e_oprea_leadlikeness_violations.xpd
E_ORGANOBORONS_ID string Database ID in www.organoborons.com
Tcl script atomchange bondchange atom bond e_organoborons_id.xpd
E_ORGANOBORONS_URL url Display URL for entry in www.organoborons.com
Tcl script E_ORGANOBORONS_ID atomchange bondchange atom bond e_organoborons_url.xpd
E_ORIGINAL_STRUCTURE structure Original structure (usually saved as backup property on modified/standardized structure)
Tcl script never e_original_structure.xpd
E_OSDB_ID string Record ID in the OSDB database (osdb.info)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_osdb_id.xpd
E_OSDB_URL url Display URL in the OSDB database (osdb.info)
Tcl script E_OSDB_ID atomchange bondchange stereochange atom bond e_osdb_url.xpd
E_OUTPUTDATE date Output date time stamp for molecule
Tcl script never e_outputdate.xpd
E_OWNER string Owner or contributor of a data record
never
E_PAINS_FILTER compound Compound filtering by the PAINS filters (J. Med. Chem., 2010, 53 (7), pp 2719?2740) by Baell et al.

Filtering is done by means of the original SLN filters from the paper, not the SMARTS approximation which can found on the Internet.

The property has two fields: The filter status (0: no filter match, 1:filter match with pattern from table S6 in original publication with >150 hits, 2: filer match from table S7, 15..150 hits, 3: filter match from table S8, <15 hits in the test dataset used in the paper), and the name of the first matching pattern, as used in the original publication.
J. Med. Chem., 2010, 53 (7), pp 2719–2740
match int
id string
Tcl script atomchange bondchange atom bond e_pains_filter.xpd
E_PARENT_HASH128 uint128 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_hash128.xpd
E_PARENT_HASHY uint64 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_hashy.xpd
E_PARENT_ISOTOPE_HASH128 uint128 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_isotope_hash128.xpd
E_PARENT_ISOTOPE_HASHY uint64 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_isotope_hashy.xpd
E_PARENT_ISOTOPE_STEREO_HASH128 uint128 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_isotope_stereo_hash128.xpd
E_PARENT_ISOTOPE_STEREO_HASHY uint64 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_isotope_stereo_hashy.xpd
E_PARENT_STEREO_HASH128 uint128 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_stereo_hash128.xpd
E_PARENT_STEREO_HASHY uint64 Hashcode of the parent structure
Tcl script E_PARENT_STRUCTURE atomchange bondchange merge e_parent_stereo_hashy.xpd
E_PARENT_STRUCTURE structure Parent structure
saltfile: { value: ions.smi description: Standard counterions datatype: diskfile constraints: readable}
clearisotope: { value: 0 datatype: boolean}
clearatomstereo: { value: 0 datatype: boolean}
clearbondstereo: { value: 0 datatype: boolean}
uniquetautomer: { value: 0 datatype: boolean}
maxtautomers: { value: 250 datatype: int}
pgfile: { value: pg.smi description: Standard protecting group definitions datatype: diskfile constraints: readable}
deprotect: { value: 0 description: If set, try to remove standard protecting groups datatype: boolean}
style: { value: cactvs enumeration: cactvs:pubchem datatype: int}
clearinorganic: { value: 1 datatype: boolean}
clearensprops: { value: 1 datatype: boolean}
cutmetalsalts: { value: 1 datatype: boolean}
cutcomplexbonds: { value: 1 datatype: boolean}
cutmetalbonds: { value: 0 datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange e_parent_structure.xpd
E_PASS_DATA_PA floatvector PASS software Pa value (probability of being an antagonist). This data is for example served by the NCI cancer screening database.
cathepsin_b_inhibitor float
opioid_agonist float
leukotriene_synthesis_inhibitor float
estrogen_receptor_modulator float
antibiotic_oxacephem-like float
dopa_decarboxylase_inhibitor float
bradykinin_antagonist float
factor_xiiia_inhibitor float
gynecological_disorders_treatment float
urinary_incontinence_treatment float
antibiotic_oxazolidinone-like float
antimitotic float
cyclooxygenase_inhibitor float
purinergic_p2_agonist float
cytostatic float
antiallergic float
cyclooxygenase_2_inhibitor float
phosphodiesterase_v_inhibitor float
squalene_epoxidase_inhibitor float
nitric_oxide_synthase_inhibitor float
teratogen float
glutamate_(mglur5)_antagonist float
cardiotoxic float
5_hydroxytryptamine_4_agonist float
geranylgeranyltransferase_inhibitor float
dermatologic float
interleukin_1_antagonist float
acetylcholine_nicotinic_antagonist float
sulfonylureas float
dopamine_antagonist float
adenosine_deaminase_inhibitor float
corneal_wound_healing_stimulator float
non-steroidal_antiinflammatory_agent float
vasopressin_1_antagonist float
interferon_inducer float
growth_hormone_secretion_inhibitor float
hestagen_antagonist float
glucocorticoid_agonist float
vitamin float
retinoid-like float
muscle_relaxant float
excitatory_amino_acid_antagonist float
hiv_protease_inhibitor float
endothelin_antagonist float
antimycobacterial float
5_hydroxytryptamine_3_antagonist float
growth_stimulant float
cholinergic_agonist float
immunomodulator float
hypertermic float
uterine_stimulant float
antibiotic_anthracycline-like float
antiprotozoal float
antibiotic_beta_lactam-like float
endothelin_a_receptor_antagonist float
hiv-1_protease_inhibitor float
spasmolytic float
antibiotic_glycopeptide-like float
spasmogenic float
adenosine_a2_receptor_agonist float
antipsoriatic float
5_hydroxytryptamine_1d_agonist float
antitoxic float
benzodiazepine_agonist float
steroid-like float
immunosuppressant float
antineoplastic float
reverse_transcriptase_inhibitor float
psychotropic float
factor_xa_inhibitor float
histamine_h2_receptor_antagonist float
thrombolytic float
estrone_sulfatase_inhibitor float
trypsin_inhibitor float
antiviral_(hepatitis_c) float
glutamate_(mglur1)_agonist float
antiviral float
oxytocin_agonist float
growth_hormone_release_promoting float
5_hydroxytryptamine_2c_agonist float
purinergic_receptor_antagonist float
nmda_receptor_polyamine_site_activator float
sodium_channel_blocker float
progesterone_antagonist float
antitrypanosomal float
antiinflammatory_intestinal float
antimycoplasmal float
vasopressin_2_antagonist float
dopamine_autoreceptor_agonist float
gaba_receptor_antagonist float
antimigraine float
thyroid_hormone_agonist float
immunosuppressant_cyclosporine-like float
5_hydroxytryptamine_antagonist float
ileal_bile_acid_transport_inhibitor float
kainate_receptor_antagonist float
bronchodilator float
microtubule_formation_inhibitor float
saluretic_reabsorbtion_inhibitor float
acetylcholinesterase_inhibitor float
platelet_antagonist float
5_hydroxytryptamine_2a_antagonist float
complement_inhibitor float
prolactin_inhibitor float
5_hydroxytryptamine_4_antagonist float
anti-helicobacter_pylori float
mydriatic float
glutamate_(mglur5a)_agonist float
opioid_mu_receptor_agonist float
alpha_adrenoreceptor_agonist float
antiglaucomic float
postcoital_contraceptive float
antineoplastic_enhancer float
phospholipase_a2_inhibitor float
adrenaline_antagonist float
atrial_natriuretic_polypeptide_agonist float
histamine_release_stimulant float
antidiuretic_hormone_antagonist float
embryotoxic float
spermicide float
interleukin_1_beta_converting_enzyme_inhibitor float
antibiotic_penicillin-like float
antimalarial float
neutral_endopeptidase_inhibitor float
substance_p_antagonist float
endothelin_b_receptor_antagonist float
beta_adrenoreceptor_antagonist float
antiischemic float
adenosine_kinase_inhibitor float
uterine_relaxant float
antiobesity float
anticerebroischemic float
antibacterial float
mao-a_inhibitor float
hypertensive_ophthalmic float
tryptase_inhibitor float
luteinizing_hormone-releasing_hormone_agonist float
histamine_h3_receptor_agonist float
acetylcholine_release_stimulant float
aldose_reductase_inhibitor float
histamine_h3_receptor_antagonist float
luteinizing_hormone-releasing_hormone_antagonist float
antiinfective_(hiv) float
urokinase_inhibitor float
antidepressant_imipramin-like float
antimetabolite float
gastrin-releasing_peptide_antagonist float
5_hydroxytryptamine_uptake_inhibitor float
antiparkinsonian_tremor_relieving float
antibiotic_trimethoprim-like float
acute_neurologic_disorders_treatment float
5_hydroxytryptamine_2b_antagonist float
inflammatory_bowel_disease_threatment float
glutamate_(mglur5)_agonist float
thymidine_kinase_inhibitor float
5_hydroxytryptamine_1_agonist float
antitussive float
glutamate_(mglur3)_antagonist float
factor_viia_inhibitor float
carbonic_anhydrase_inhibitor float
nmda_receptor_agonist float
anabolic float
photosensitizer float
5_hydroxytryptamine_1a_antagonist float
calcium_regulator float
acetylcholine_antagonist float
antiseptic float
antiinfertility_female float
gaba_aminotransferase_inhibitor float
aromatase_inhibitor float
anesthetic_general float
antiinflammatory float
contraceptive float
glutamate_receptor_antagonist float
uridine_phosphorylase_inhibitor float
diuretic float
topoisomerase_inhibitor float
alcohol_dehydrogenase_inhibitor float
glucagon_receptor_antagonist float
immunostimulant float
ornithine_decarboxylase_inhibitor float
antiosteoporotic float
hypertensive float
rhinitis_treatment float
collagenase_inhibitor float
adenosine_receptor_agonist float
analgesic_non-opioid float
angiotensin_antagonist float
histamine_agonist float
anticataract float
5_hydroxytryptamine_1a_agonist float
antiemphysemic float
tyrosine_kinase_inhibitor float
cholesterol_esterase_inhibitor float
purinergic_receptor_agonist float
phosphodiesterase_iv_inhibitor float
analeptic float
antihelmintic float
chemoprotective float
antihypertensive float
sympatholytic float
beta_1_adrenoreceptor_antagonist float
dihydroorotate_dehydrogenase_inhibitor float
alkylator float
androgen_agonist float
nitric_oxide_donor float
hypoglycemic float
cytokine_modulator float
mutagenic float
5_hydroxytryptamine_2c_antagonist float
antiarthritic float
antipruritic float
quisqualate_antagonist float
cannabinoid_receptor_agonist float
corticosteroid-like float
cocain_dependency_treatment float
antiinflammatory_steroid float
prostaglandin_agonist float
5_alpha_reductase_inhibitor float
adrenergic_transmitter_uptake_inhibitor float
succinic_dehydrogenase_inhibitor float
s-adenosyl-l-methionine_decarboxylase_inhibitor float
alpha_adrenoreceptor_antagonist float
antilipidemic float
glycine_receptor_agonist float
hdl-cholesterol_increasing float
cardiovascular_analeptic float
antibiotic_penem-like float
glutamate_receptor_agonist float
antiinflammatory_pancreatic float
5_hydroxytryptamine_agonist float
glutamate_(mglur2)_antagonist float
kainate_receptor_agonist float
cytosole_dipeptidase_inhibitor float
nasal_decongestant float
selectin_antagonist float
adp_ribosyl_transferase_inhibitor float
ampa_receptor_agonist float
calmodulin_antagonist float
o6-alkylguanine-dna_alkyltransferase_inhibitor float
psychosexual_dysfunction_treatment float
elastase_inhibitor float
choleretic float
glucocorticoid_antagonist float
acetylcholine_m1_receptor_agonist float
glutamate_(mglur2)_agonist float
calcium_agonist float
chemopreventive float
sedative float
cognition_disorders_treatment float
antiamebic float
neuropeptide_y_antagonist float
antibiotic_naphthyridine-like float
protein_kinase_c_inhibitor float
benzodiazepine_antagonist float
beta_3_adrenoreceptor_agonist float
acetylcholine_neuromuscular_blocking_agent float
tumour_necrosis_factor_antagonist float
adenosine_receptor_antagonist float
dipeptidyl_aminopeptidase_iv_inhibitor float
histamine_antagonist float
neurokinin_2_antagonist float
cystic_fibrosis_treatment float
myocardial_ischemia_treatment float
leukopoiesis_inhibitor float
signal_transduction_pathways_inhibitor float
matrix_metalloproteinase_inhibitor float
male_reproductive_disfunction_treatment float
mao_inhibitor float
gaba_b_receptor_agonist float
acetylcholine_muscarinic_agonist float
thromboxane_antagonist float
vasopressor float
beta_2_adrenoreceptor_agonist float
3_hydroxyanthranilate_oxygenase_inhibitor float
progestin_agonist float
myristoyl_transferase_inhibitor float
poly(adp-ribose)synthethase_inhibitor float
23-oxidosqualene-lanosterol_cyclase_inhibitor float
hematopoietic_inhibitor float
antismoking float
sclerosant float
beta_1_adrenoreceptor_agonist float
adrenaline_agonist float
metabolic float
thyrotropin_releasing_hormone_agonist float
alpha_glucosidase_inhibitor float
acetylcholine_nicotinic_agonist float
phospholipase_c_inhibitor float
interleukin_antagonist float
thiol_protease_inhibitor float
cholecystokinin_agonist float
bone_formation_stimulant float
cholecystokinin_a_agonist float
oxytocin_antagonist float
angiotensin_ii_receptor_antagonist float
glutamate_(mglur1)_antagonist float
skeletal_muscle_relaxant float
dopamine_beta_hydroxylase_inhibitor float
antibiotic_isocephem-like float
adenosine_a2a_receptor_antagonist float
glutamate_uptake_inhibitor float
potassium_channel_antagonist float
antibiotic_carbapenem-like float
bisphosphonate float
leukotriene_d4_antagonist float
acetylcholine_m2_receptor_antagonist float
psychostimulant float
anticoccidial float
antimitotic_taxane-like float
5_hydroxytryptamine_2_agonist float
interleukin_6_antagonist float
teratogen_and/or_embryotoxic float
antibiotic_quinolone-like float
reductant float
antibiotic_rifamycin-like float
adenosine_a2a_receptor_agonist float
renin_inhibitor float
opioid_antagonist float
angiogenesis_inhibitor float
insulin_secretagoues float
antidepressant float
neurokinin_3_antagonist float
excitatory_amino_acid_agonist float
analgesic_opioid float
glutamate_(mglur6)_agonist float
radiosensitizer float
glutamate_(mglur)_agonist float
antidiabetic float
nmda_receptor_glycine_site_agonist float
hiv_integrase_inhibitor float
aminopeptidase_microsomal_inhibitor float
adenosine_a1_receptor_agonist float
acetylcholine_muscarinic_antagonist float
anticoagulant float
thrombin_inhibitor float
anxiolytic float
nmda_receptor_antagonist float
xanthine_oxidase_inhibitor float
gaba_receptor_agonist float
thymidylate_synthase_inhibitor float
sigma_receptor_antagonist float
prostaglandin_e2_antagonist float
hepatoprotectant float
5_hydroxytryptamine_1d_antagonist float
antitussive_narcotic float
cardioprotectant float
antiviral_(hepatitis) float
cholecystokinin_a_antagonist float
antineoplastic_alkaloid float
antiarrhythmic float
dopamine_d1_agonist float
protocollagen_prolyl_hydroxylase_inhibitor float
antiviral_(influenza) float
enkephalinase_inhibitor float
alkylphospholipid float
gaba_a_receptor_antagonist float
prolactin_secretion_inhibitor float
5_hydroxytryptamine_1b_agonist float
mucolytic float
angiotensin_at1_receptor_antagonist float
hestagen-like float
antiviral_(hiv) float
respiratory_distress_syndrome_treatment float
bradykinin_b2_receptor_antagonist float
hematopoietic float
thyroid_hormone_antagonist float
catechol_o_methyltransferase_inhibitor float
adenosine_a1_receptor_antagonist float
lymphocytopoiesis_inhibitor float
glutamate_(mglur)_antagonist float
nmda_receptor_glycine_site_antagonist float
topoisomerase_ii_inhibitor float
5_hydroxytryptamine_1f_agonist float
neurotensin_receptor_antagonist float
prostaglandin_antagonist float
antianginal float
neuraminidase_(influenza)_inhibitor float
opioid_kappa_receptor_agonist float
purinergic_p2_antagonist float
somatostatin_agonist float
adenosine_a3_receptor_agonist float
anesthetic_local float
anaphylatoxin_receptor_antagonist float
alpha_1_adrenoreceptor_antagonist float
nootropic float
glucose-6-phosphate_translocase_inhibitor float
endothelin-converting_enzyme_inhibitor float
antihypercholesterolemic float
antibiotic_cephalosporin-like float
antiparkinsonian_rigidity_relieving float
leukotriene_antagonist float
cholinergic_antagonist float
acetylcholine_m3_receptor_antagonist float
antiulcerative float
hcv_ns3-helicase_inhibitor float
antiparkinsonian float
nmda_receptor_polyamine_site_blocker float
bone_resorption_inhibitor float
radioprotector float
cathepsin_l_inhibitor float
cardiodepressant float
renal_disease_treatment float
arrhythmogenic float
glycinamide_ribonucleotide_formyltransferase_inhibitor float
prostate_disorders_treatment float
bombesin_antagonist float
cholecystokinin_b_antagonist float
vasodilator float
ribonucleoside_diphosphate_reductase_inhibitor float
ulcerogenic float
xanthine-like float
phosphodiesterase_inhibitor float
insulin_promoter float
dopamine_d1_antagonist float
keratoses_actinic(solar)_treatment float
antiacne float
platelet_aggregation_inhibitor float
5_hydroxytryptamine_release_stimulant float
restenosis_treatment float
glutamate_(mglur3)_agonist float
alpha_2_adrenoreceptor_antagonist float
gaba_uptake_inhibitor float
peristaltic_stimulant float
phosphodiesterase_iii_inhibitor float
expectorant float
histamine_h2_receptor_agonist float
hmg_coa_reductase_inhibitor float
histidine_decarboxylase_inhibitor float
antibiotic_tetracycline-like float
lipoxygenase_inhibitor float
aldosterone_antagonist float
gaba_b_receptor_antagonist float
gastric_antisecretory float
antifungal float
angiotensin_at2_receptor_antagonist float
interleukin_8_antagonist float
adenosine_a2_receptor_antagonist float
miotic float
cholecystokinin_antagonist float
antibiotic float
antibiotic_aminoglycoside-like float
melatonin_antagonist float
anesthetic_inhalation float
phospholipase_inhibitor float
antibiotic_macrolide-like float
acetylcholine_agonist float
gp_iib/iiia_receptor_antagonist float
hcv_serine_protease_inhibitor float
antiemetic float
potassium_channel_activator float
estrogen_agonist float
respiratory_analeptic float
sodium_channel_blocker_class_ib float
erythropoietin float
leukotriene_b4_antagonist float
hmg_coa_synthase_inhibitor float
liver_fibrosis_treatment float
benzodiazepine_inverse_agonist float
anticonvulsant float
benzodiazepine_agonist_partial float
5_hydroxytryptamine_3_agonist float
antispirochetal float
dopamine_d2_antagonist float
phosphodiesterase_i_inhibitor float
antioxidant float
hypolipemic float
mao-b_inhibitor float
tnf-alpha_release_inhibitor float
vitamin_d-like float
angiotensin_converting_enzyme_inhibitor float
lipid_peroxidase_inhibitor float
purine_nucleoside_phosphorylase_inhibitor float
mineralocorticoid float
neurokinin_antagonist float
alpha_2_adrenoreceptor_agonist float
camp_phosphodiesterase_inhibitor float
keratolytic float
spasmolytic_papaverin-like float
androgen_antagonist float
multiple_sclerosis_treatment float
estrogen_antagonist float
dopamine_d2_agonist float
anesthetic float
chymotrypsin_inhibitor float
alpha_1_adrenoreceptor_agonist float
antipsychotic float
mannosidase_inhibitor float
antidyskinetic float
ampa_receptor_antagonist float
antidiabetic_symptomatic float
septic_shock_treatment float
neuropeptide_antagonist float
pancreatic_disorders_treatment float
carcinogenic float
alzheimer's_disease_treatment float
motilin-like float
adenosine_a3_receptor_antagonist float
cardiotonic float
leukotriene_a4_hydrolase_inhibitor float
parathyroid_hormone_antagonist float
5_hydroxytryptamine_1_antagonist float
antibiotic_carbacephem-like float
platelet_activating_factor_antagonist float
dopamine_d3_antagonist float
antitrichomonal float
dihydrofolate_reductase_inhibitor float
purinergic_p2t_antagonist float
mediator_release_inhibitor float
h+/k+-transporting_atpase_inhibitor float
s-adenosyl-l-homocysteine_hydrolase_inhibitor float
dopamine_uptake_inhibitor float
opioid_delta_receptor_agonist float
interleukin_agonist float
gastrin_inhibitor float
camp_modulator float
neurotrophic_factor float
anorexic float
dopamine_agonist float
farnesyltransferase_inhibitor float
glutamate_(mglur6)_antagonist float
antiasthmatic float
antimitotic_podophyllotoxin-like float
glutamate_(mglur1a)_agonist float
maillard_reaction_inhibitor float
melatonin_agonist float
antineoplastic_antibiotic float
saluretic float
anticholelithogenic float
gaba_a_receptor_agonist float
hypnotic float
coagulant float
opioid_partial_agonist float
beta_lactamase_inhibitor float
treponemicidal float
ribonucleotide_reductase_inhibitor float
uricosuric float
hcv_ns3-4a_protease_inhibitor float
dna_intercalator float
squalene_synthetase_inhibitor float
endothelin_receptor_antagonist float
beta_adrenoreceptor_agonist float
thromboxane_synthase_inhibitor float
antibiotic_tribactam-like float
analgesic float
calpain_inhibitor float
cns_active_muscle_relaxant float
hcv_ns3_protease_inhibitor float
5_hydroxytryptamine_2_antagonist float
protease_inhibitor float
narcotic_antagonist float
ophthalmic_drug float
acetyl_coa_transferase_inhibitor float
hypotermic float
antihistaminic float
dopamine_d4_antagonist float
irritable_bowel_syndrome_therapy float
platelet_adhesion_inhibitor float
spasmolytic_urinary float
atherosclerosis_treatment float
nucleotide_metabolism_regulator float
prolyl_endopeptidase_inhibitor float
hair_growth_promoter float
calcium_channel_antagonist float
histamine_h1_receptor_antagonist float
never
E_PASS_DATA_PI floatvector PASS software Pi value (probability of being an inhibitor). This data is for example served by the NCI cancer screening database.
cathepsin_b_inhibitor float
opioid_agonist float
leukotriene_synthesis_inhibitor float
estrogen_receptor_modulator float
antibiotic_oxacephem-like float
dopa_decarboxylase_inhibitor float
bradykinin_antagonist float
factor_xiiia_inhibitor float
gynecological_disorders_treatment float
urinary_incontinence_treatment float
antibiotic_oxazolidinone-like float
antimitotic float
cyclooxygenase_inhibitor float
purinergic_p2_agonist float
cytostatic float
antiallergic float
cyclooxygenase_2_inhibitor float
phosphodiesterase_v_inhibitor float
squalene_epoxidase_inhibitor float
nitric_oxide_synthase_inhibitor float
teratogen float
glutamate_(mglur5)_antagonist float
cardiotoxic float
5_hydroxytryptamine_4_agonist float
geranylgeranyltransferase_inhibitor float
dermatologic float
interleukin_1_antagonist float
acetylcholine_nicotinic_antagonist float
sulfonylureas float
dopamine_antagonist float
adenosine_deaminase_inhibitor float
corneal_wound_healing_stimulator float
non-steroidal_antiinflammatory_agent float
vasopressin_1_antagonist float
interferon_inducer float
growth_hormone_secretion_inhibitor float
hestagen_antagonist float
glucocorticoid_agonist float
vitamin float
retinoid-like float
muscle_relaxant float
excitatory_amino_acid_antagonist float
hiv_protease_inhibitor float
endothelin_antagonist float
antimycobacterial float
5_hydroxytryptamine_3_antagonist float
growth_stimulant float
cholinergic_agonist float
immunomodulator float
hypertermic float
uterine_stimulant float
antibiotic_anthracycline-like float
antiprotozoal float
antibiotic_beta_lactam-like float
endothelin_a_receptor_antagonist float
hiv-1_protease_inhibitor float
spasmolytic float
antibiotic_glycopeptide-like float
spasmogenic float
adenosine_a2_receptor_agonist float
antipsoriatic float
5_hydroxytryptamine_1d_agonist float
antitoxic float
benzodiazepine_agonist float
steroid-like float
immunosuppressant float
antineoplastic float
reverse_transcriptase_inhibitor float
psychotropic float
factor_xa_inhibitor float
histamine_h2_receptor_antagonist float
thrombolytic float
estrone_sulfatase_inhibitor float
trypsin_inhibitor float
antiviral_(hepatitis_c) float
glutamate_(mglur1)_agonist float
antiviral float
oxytocin_agonist float
growth_hormone_release_promoting float
5_hydroxytryptamine_2c_agonist float
purinergic_receptor_antagonist float
nmda_receptor_polyamine_site_activator float
sodium_channel_blocker float
progesterone_antagonist float
antitrypanosomal float
antiinflammatory_intestinal float
antimycoplasmal float
vasopressin_2_antagonist float
dopamine_autoreceptor_agonist float
gaba_receptor_antagonist float
antimigraine float
thyroid_hormone_agonist float
immunosuppressant_cyclosporine-like float
5_hydroxytryptamine_antagonist float
ileal_bile_acid_transport_inhibitor float
kainate_receptor_antagonist float
bronchodilator float
microtubule_formation_inhibitor float
saluretic_reabsorbtion_inhibitor float
acetylcholinesterase_inhibitor float
platelet_antagonist float
5_hydroxytryptamine_2a_antagonist float
complement_inhibitor float
prolactin_inhibitor float
5_hydroxytryptamine_4_antagonist float
anti-helicobacter_pylori float
mydriatic float
glutamate_(mglur5a)_agonist float
opioid_mu_receptor_agonist float
alpha_adrenoreceptor_agonist float
antiglaucomic float
postcoital_contraceptive float
antineoplastic_enhancer float
phospholipase_a2_inhibitor float
adrenaline_antagonist float
atrial_natriuretic_polypeptide_agonist float
histamine_release_stimulant float
antidiuretic_hormone_antagonist float
embryotoxic float
spermicide float
interleukin_1_beta_converting_enzyme_inhibitor float
antibiotic_penicillin-like float
antimalarial float
neutral_endopeptidase_inhibitor float
substance_p_antagonist float
endothelin_b_receptor_antagonist float
beta_adrenoreceptor_antagonist float
antiischemic float
adenosine_kinase_inhibitor float
uterine_relaxant float
antiobesity float
anticerebroischemic float
antibacterial float
mao-a_inhibitor float
hypertensive_ophthalmic float
tryptase_inhibitor float
luteinizing_hormone-releasing_hormone_agonist float
histamine_h3_receptor_agonist float
acetylcholine_release_stimulant float
aldose_reductase_inhibitor float
histamine_h3_receptor_antagonist float
luteinizing_hormone-releasing_hormone_antagonist float
antiinfective_(hiv) float
urokinase_inhibitor float
antidepressant_imipramin-like float
antimetabolite float
gastrin-releasing_peptide_antagonist float
5_hydroxytryptamine_uptake_inhibitor float
antiparkinsonian_tremor_relieving float
antibiotic_trimethoprim-like float
acute_neurologic_disorders_treatment float
5_hydroxytryptamine_2b_antagonist float
inflammatory_bowel_disease_threatment float
glutamate_(mglur5)_agonist float
thymidine_kinase_inhibitor float
5_hydroxytryptamine_1_agonist float
antitussive float
glutamate_(mglur3)_antagonist float
factor_viia_inhibitor float
carbonic_anhydrase_inhibitor float
nmda_receptor_agonist float
anabolic float
photosensitizer float
5_hydroxytryptamine_1a_antagonist float
calcium_regulator float
acetylcholine_antagonist float
antiseptic float
antiinfertility_female float
gaba_aminotransferase_inhibitor float
aromatase_inhibitor float
anesthetic_general float
antiinflammatory float
contraceptive float
glutamate_receptor_antagonist float
uridine_phosphorylase_inhibitor float
diuretic float
topoisomerase_inhibitor float
alcohol_dehydrogenase_inhibitor float
glucagon_receptor_antagonist float
immunostimulant float
ornithine_decarboxylase_inhibitor float
antiosteoporotic float
hypertensive float
rhinitis_treatment float
collagenase_inhibitor float
adenosine_receptor_agonist float
analgesic_non-opioid float
angiotensin_antagonist float
histamine_agonist float
anticataract float
5_hydroxytryptamine_1a_agonist float
antiemphysemic float
tyrosine_kinase_inhibitor float
cholesterol_esterase_inhibitor float
purinergic_receptor_agonist float
phosphodiesterase_iv_inhibitor float
analeptic float
antihelmintic float
chemoprotective float
antihypertensive float
sympatholytic float
beta_1_adrenoreceptor_antagonist float
dihydroorotate_dehydrogenase_inhibitor float
alkylator float
androgen_agonist float
nitric_oxide_donor float
hypoglycemic float
cytokine_modulator float
mutagenic float
5_hydroxytryptamine_2c_antagonist float
antiarthritic float
antipruritic float
quisqualate_antagonist float
cannabinoid_receptor_agonist float
corticosteroid-like float
cocain_dependency_treatment float
antiinflammatory_steroid float
prostaglandin_agonist float
5_alpha_reductase_inhibitor float
adrenergic_transmitter_uptake_inhibitor float
succinic_dehydrogenase_inhibitor float
s-adenosyl-l-methionine_decarboxylase_inhibitor float
alpha_adrenoreceptor_antagonist float
antilipidemic float
glycine_receptor_agonist float
hdl-cholesterol_increasing float
cardiovascular_analeptic float
antibiotic_penem-like float
glutamate_receptor_agonist float
antiinflammatory_pancreatic float
5_hydroxytryptamine_agonist float
glutamate_(mglur2)_antagonist float
kainate_receptor_agonist float
cytosole_dipeptidase_inhibitor float
nasal_decongestant float
selectin_antagonist float
adp_ribosyl_transferase_inhibitor float
ampa_receptor_agonist float
calmodulin_antagonist float
o6-alkylguanine-dna_alkyltransferase_inhibitor float
psychosexual_dysfunction_treatment float
elastase_inhibitor float
choleretic float
glucocorticoid_antagonist float
acetylcholine_m1_receptor_agonist float
glutamate_(mglur2)_agonist float
calcium_agonist float
chemopreventive float
sedative float
cognition_disorders_treatment float
antiamebic float
neuropeptide_y_antagonist float
antibiotic_naphthyridine-like float
protein_kinase_c_inhibitor float
benzodiazepine_antagonist float
beta_3_adrenoreceptor_agonist float
acetylcholine_neuromuscular_blocking_agent float
tumour_necrosis_factor_antagonist float
adenosine_receptor_antagonist float
dipeptidyl_aminopeptidase_iv_inhibitor float
histamine_antagonist float
neurokinin_2_antagonist float
cystic_fibrosis_treatment float
myocardial_ischemia_treatment float
leukopoiesis_inhibitor float
signal_transduction_pathways_inhibitor float
matrix_metalloproteinase_inhibitor float
male_reproductive_disfunction_treatment float
mao_inhibitor float
gaba_b_receptor_agonist float
acetylcholine_muscarinic_agonist float
thromboxane_antagonist float
vasopressor float
beta_2_adrenoreceptor_agonist float
3_hydroxyanthranilate_oxygenase_inhibitor float
progestin_agonist float
myristoyl_transferase_inhibitor float
poly(adp-ribose)synthethase_inhibitor float
23-oxidosqualene-lanosterol_cyclase_inhibitor float
hematopoietic_inhibitor float
antismoking float
sclerosant float
beta_1_adrenoreceptor_agonist float
adrenaline_agonist float
metabolic float
thyrotropin_releasing_hormone_agonist float
alpha_glucosidase_inhibitor float
acetylcholine_nicotinic_agonist float
phospholipase_c_inhibitor float
interleukin_antagonist float
thiol_protease_inhibitor float
cholecystokinin_agonist float
bone_formation_stimulant float
cholecystokinin_a_agonist float
oxytocin_antagonist float
angiotensin_ii_receptor_antagonist float
glutamate_(mglur1)_antagonist float
skeletal_muscle_relaxant float
dopamine_beta_hydroxylase_inhibitor float
antibiotic_isocephem-like float
adenosine_a2a_receptor_antagonist float
glutamate_uptake_inhibitor float
potassium_channel_antagonist float
antibiotic_carbapenem-like float
bisphosphonate float
leukotriene_d4_antagonist float
acetylcholine_m2_receptor_antagonist float
psychostimulant float
anticoccidial float
antimitotic_taxane-like float
5_hydroxytryptamine_2_agonist float
interleukin_6_antagonist float
teratogen_and/or_embryotoxic float
antibiotic_quinolone-like float
reductant float
antibiotic_rifamycin-like float
adenosine_a2a_receptor_agonist float
renin_inhibitor float
opioid_antagonist float
angiogenesis_inhibitor float
insulin_secretagoues float
antidepressant float
neurokinin_3_antagonist float
excitatory_amino_acid_agonist float
analgesic_opioid float
glutamate_(mglur6)_agonist float
radiosensitizer float
glutamate_(mglur)_agonist float
antidiabetic float
nmda_receptor_glycine_site_agonist float
hiv_integrase_inhibitor float
aminopeptidase_microsomal_inhibitor float
adenosine_a1_receptor_agonist float
acetylcholine_muscarinic_antagonist float
anticoagulant float
thrombin_inhibitor float
anxiolytic float
nmda_receptor_antagonist float
xanthine_oxidase_inhibitor float
gaba_receptor_agonist float
thymidylate_synthase_inhibitor float
sigma_receptor_antagonist float
prostaglandin_e2_antagonist float
hepatoprotectant float
5_hydroxytryptamine_1d_antagonist float
antitussive_narcotic float
cardioprotectant float
antiviral_(hepatitis) float
cholecystokinin_a_antagonist float
antineoplastic_alkaloid float
antiarrhythmic float
dopamine_d1_agonist float
protocollagen_prolyl_hydroxylase_inhibitor float
antiviral_(influenza) float
enkephalinase_inhibitor float
alkylphospholipid float
gaba_a_receptor_antagonist float
prolactin_secretion_inhibitor float
5_hydroxytryptamine_1b_agonist float
mucolytic float
angiotensin_at1_receptor_antagonist float
hestagen-like float
antiviral_(hiv) float
respiratory_distress_syndrome_treatment float
bradykinin_b2_receptor_antagonist float
hematopoietic float
thyroid_hormone_antagonist float
catechol_o_methyltransferase_inhibitor float
adenosine_a1_receptor_antagonist float
lymphocytopoiesis_inhibitor float
glutamate_(mglur)_antagonist float
nmda_receptor_glycine_site_antagonist float
topoisomerase_ii_inhibitor float
5_hydroxytryptamine_1f_agonist float
neurotensin_receptor_antagonist float
prostaglandin_antagonist float
antianginal float
neuraminidase_(influenza)_inhibitor float
opioid_kappa_receptor_agonist float
purinergic_p2_antagonist float
somatostatin_agonist float
adenosine_a3_receptor_agonist float
anesthetic_local float
anaphylatoxin_receptor_antagonist float
alpha_1_adrenoreceptor_antagonist float
nootropic float
glucose-6-phosphate_translocase_inhibitor float
endothelin-converting_enzyme_inhibitor float
antihypercholesterolemic float
antibiotic_cephalosporin-like float
antiparkinsonian_rigidity_relieving float
leukotriene_antagonist float
cholinergic_antagonist float
acetylcholine_m3_receptor_antagonist float
antiulcerative float
hcv_ns3-helicase_inhibitor float
antiparkinsonian float
nmda_receptor_polyamine_site_blocker float
bone_resorption_inhibitor float
radioprotector float
cathepsin_l_inhibitor float
cardiodepressant float
renal_disease_treatment float
arrhythmogenic float
glycinamide_ribonucleotide_formyltransferase_inhibitor float
prostate_disorders_treatment float
bombesin_antagonist float
cholecystokinin_b_antagonist float
vasodilator float
ribonucleoside_diphosphate_reductase_inhibitor float
ulcerogenic float
xanthine-like float
phosphodiesterase_inhibitor float
insulin_promoter float
dopamine_d1_antagonist float
keratoses_actinic(solar)_treatment float
antiacne float
platelet_aggregation_inhibitor float
5_hydroxytryptamine_release_stimulant float
restenosis_treatment float
glutamate_(mglur3)_agonist float
alpha_2_adrenoreceptor_antagonist float
gaba_uptake_inhibitor float
peristaltic_stimulant float
phosphodiesterase_iii_inhibitor float
expectorant float
histamine_h2_receptor_agonist float
hmg_coa_reductase_inhibitor float
histidine_decarboxylase_inhibitor float
antibiotic_tetracycline-like float
lipoxygenase_inhibitor float
aldosterone_antagonist float
gaba_b_receptor_antagonist float
gastric_antisecretory float
antifungal float
angiotensin_at2_receptor_antagonist float
interleukin_8_antagonist float
adenosine_a2_receptor_antagonist float
miotic float
cholecystokinin_antagonist float
antibiotic float
antibiotic_aminoglycoside-like float
melatonin_antagonist float
anesthetic_inhalation float
phospholipase_inhibitor float
antibiotic_macrolide-like float
acetylcholine_agonist float
gp_iib/iiia_receptor_antagonist float
hcv_serine_protease_inhibitor float
antiemetic float
potassium_channel_activator float
estrogen_agonist float
respiratory_analeptic float
sodium_channel_blocker_class_ib float
erythropoietin float
leukotriene_b4_antagonist float
hmg_coa_synthase_inhibitor float
liver_fibrosis_treatment float
benzodiazepine_inverse_agonist float
anticonvulsant float
benzodiazepine_agonist_partial float
5_hydroxytryptamine_3_agonist float
antispirochetal float
dopamine_d2_antagonist float
phosphodiesterase_i_inhibitor float
antioxidant float
hypolipemic float
mao-b_inhibitor float
tnf-alpha_release_inhibitor float
vitamin_d-like float
angiotensin_converting_enzyme_inhibitor float
lipid_peroxidase_inhibitor float
purine_nucleoside_phosphorylase_inhibitor float
mineralocorticoid float
neurokinin_antagonist float
alpha_2_adrenoreceptor_agonist float
camp_phosphodiesterase_inhibitor float
keratolytic float
spasmolytic_papaverin-like float
androgen_antagonist float
multiple_sclerosis_treatment float
estrogen_antagonist float
dopamine_d2_agonist float
anesthetic float
chymotrypsin_inhibitor float
alpha_1_adrenoreceptor_agonist float
antipsychotic float
mannosidase_inhibitor float
antidyskinetic float
ampa_receptor_antagonist float
antidiabetic_symptomatic float
septic_shock_treatment float
neuropeptide_antagonist float
pancreatic_disorders_treatment float
carcinogenic float
alzheimer's_disease_treatment float
motilin-like float
adenosine_a3_receptor_antagonist float
cardiotonic float
leukotriene_a4_hydrolase_inhibitor float
parathyroid_hormone_antagonist float
5_hydroxytryptamine_1_antagonist float
antibiotic_carbacephem-like float
platelet_activating_factor_antagonist float
dopamine_d3_antagonist float
antitrichomonal float
dihydrofolate_reductase_inhibitor float
purinergic_p2t_antagonist float
mediator_release_inhibitor float
h+/k+-transporting_atpase_inhibitor float
s-adenosyl-l-homocysteine_hydrolase_inhibitor float
dopamine_uptake_inhibitor float
opioid_delta_receptor_agonist float
interleukin_agonist float
gastrin_inhibitor float
camp_modulator float
neurotrophic_factor float
anorexic float
dopamine_agonist float
farnesyltransferase_inhibitor float
glutamate_(mglur6)_antagonist float
antiasthmatic float
antimitotic_podophyllotoxin-like float
glutamate_(mglur1a)_agonist float
maillard_reaction_inhibitor float
melatonin_agonist float
antineoplastic_antibiotic float
saluretic float
anticholelithogenic float
gaba_a_receptor_agonist float
hypnotic float
coagulant float
opioid_partial_agonist float
beta_lactamase_inhibitor float
treponemicidal float
ribonucleotide_reductase_inhibitor float
uricosuric float
hcv_ns3-4a_protease_inhibitor float
dna_intercalator float
squalene_synthetase_inhibitor float
endothelin_receptor_antagonist float
beta_adrenoreceptor_agonist float
thromboxane_synthase_inhibitor float
antibiotic_tribactam-like float
analgesic float
calpain_inhibitor float
cns_active_muscle_relaxant float
hcv_ns3_protease_inhibitor float
5_hydroxytryptamine_2_antagonist float
protease_inhibitor float
narcotic_antagonist float
ophthalmic_drug float
acetyl_coa_transferase_inhibitor float
hypotermic float
antihistaminic float
dopamine_d4_antagonist float
irritable_bowel_syndrome_therapy float
platelet_adhesion_inhibitor float
spasmolytic_urinary float
atherosclerosis_treatment float
nucleotide_metabolism_regulator float
prolyl_endopeptidase_inhibitor float
hair_growth_promoter float
calcium_channel_antagonist float
histamine_h1_receptor_antagonist float
never
E_PATENT_LINK_PAGE blob
(switchable between blob diskfile url)
A page with US patent links generated from E_PATENT_SET into the Google patent database.
imgproperty: { value: E_SVG_IMAGE description: Property to use to generate the structure header image datatype: string constraints: property}
imgparameters: { value: {} description: Override attributes for the image computation datatype: dictionary}
filename: { value: {} datatype: string constraints: writeable}
ncols: { value: 4 minvalue: 1 maxvalue: 12 datatype: int}
Tcl script E_PATENT_SET atomchange bondchange atom bond e_patent_link_page.xpd
E_PATENT_SET compoundvector Patent countries and IDs associated with compound, plus s link into Google patents
country string
id string
date date
url url
filterduplicates: { value: 1 description: If set, make patent numbers unique (can be duplicates with SS/SIM queries in E_SCRIPDB_URL) datatype: boolean}
Tcl script E_SCRIPDB_URL atomchange bondchange atom bond e_patent_set.xpd
E_PATHCODE shortvector Path length similiarity code
maxlen: { value: 8 description: Maximum path length to consider datatype: int}
coreligands: { value: 0 description: If set, hetero atom embedded in core (for example, heteroaromats) are counted as substituents datatype: boolean}
xarocore: { value: 0 description: If set, the core includes heteroaromatic rings, not just the carbon skeleton datatype: boolean}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange mod_e_pathcode.so
E_PATH_FINGERPRINT bitvector Hashed fingerprint of paths between subset of structure atoms
size: { value: 256 datatype: int}
minpathlen: { value: 2 datatype: int}
maxpathlen: { value: 5 datatype: int}
pathproperties: { value: A_SYMBOL datatype: string constraints: propertylist}
nbitsperpath: { value: 5 datatype: int}
atomfilter: { value: anormal !hydrogen datatype: string constraints: filterlist}
usebondtype: { value: 0 datatype: boolean}
maxcount: { value: 1 datatype: int}
power: { value: 2 datatype: int}
usesymmetry: { value: 1 datatype: boolean}
useringclosures: { value: 1 datatype: boolean}
maxpathsperatom: { value: -1 datatype: int}
ignorechainch2: { value: 0 datatype: boolean}
pathflags: { value: {} enumeration: none:noringchaincrossing,norccrossing datatype: string}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_RING_COUNT atomchange bondchange ring mod_e_path_fingerprint.so
E_PATRAN_STRING string Query encoded (as far as possible) as a LHASA Patran string
Compiled C module A_QUERY B_QUERY A_ELEMENT B_ORDER atomchange bondchange atom bond mod_e_patran_string.so
E_PDB_LIGAND_EXPO_URL url URL for data in the PDB ligand repository
Tcl script E_PDB_LIGAND_ID atomchange bondchange stereochange atom bond e_pdb_ligand_expo_url.xpd
E_PDB_LIGAND_ID string ID of ligand in PDB database
Tcl script atomchange bondchange stereochange atom bond e_pdb_ligand_id.xpd
E_PDB_LIGAND_URL url URL for data in the PDB ligand repository
Tcl script E_PDB_LIGAND_ID atomchange bondchange stereochange atom bond e_pdb_ligand_url.xpd
E_PDB_STRING string PDB record as a string
Tcl script atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond e_pdb_string.xpd
E_PDF3D_IMAGE diskfile
(switchable between blob diskfile)
3D PDF interactive PDF image
height: { value: 250 datatype: int}
width: { value: 250 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 datatype: int}
frame: { value: 1 datatype: boolean}
title: { value: {} datatype: string}
keywords: { value: {} datatype: string constraints: list}
compression: { value: 0 datatype: boolean}
showtree: { value: 0 datatype: boolean}
showtoolbar: { value: 0 datatype: boolean}
javascriptfile_3d: { value: {} datatype: diskfile constraints: readable}
javascriptfile_doc: { value: {} datatype: diskfile constraints: readable}
previewpngfile: { value: {} datatype: diskfile constraints: readable}
bgcolor: { value: grey20 datatype: color}
message: { value: {} datatype: string}
messagecolor: { value: red datatype: color}
framecolor: { value: black datatype: color}
measure: { value: 0 datatype: boolean}
disclose: { value: 1 datatype: boolean}
ownerpassword: { value: {} datatype: string}
userpassword: { value: {} datatype: string}
downloadfilename: { value: {} datatype: string}
header: { value: {} datatype: string}
headeralignment: { value: center enumeration: left,w:center,c:right,e:topcenter,n:bottomcenter,s:bottomleft,sw:bottomright,se:topright,ne:topleft,nw datatype: string}
footer: { value: {} datatype: string}
footeralignment: { value: center enumeration: left,w:center,c:right,e:topcenter,n:bottomcenter,s:bottomleft,sw:bottomright,se:topright,ne:topleft,nw datatype: string}
footerproperty: { value: {} datatype: string constraints: property}
footercolor: { value: red datatype: color}
headerproperty: { value: {} datatype: string constraints: property}
headercolor: { value: red datatype: color}
font: { value: Helvetica datatype: string}
headerfontsize: { value: 12 datatype: double}
footerfontsize: { value: 12 datatype: double}
fullscreen: { value: 0 datatype: boolean}
Compiled C module E_U3D_MODEL atomchange bondchange stereochange merge 3drelative 3dabsolute hadd mod_e_pdf3d_image.so
E_PDF_IMAGE diskfile
(switchable between string blob diskfile)
A 2D-plot of the structure as PDF image file
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
width: { value: 180 minvalue: 10 maxvalue: 1000 datatype: string}
height: { value: 180 minvalue: 10 maxvalue: 1000 datatype: string}
keywords: { value: {} datatype: string}
frame: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
bgcolor: { value: transparent datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1.0 datatype: double}
linewidth: { value: 1.3 datatype: double}
linespacing: { value: 2.5 datatype: double}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
colormode: { value: gray enumeration: mono,bw,b/w,black,monochrome:gray,grey,grayscale,greyscale:color,colour datatype: int}
wedges: { value: 1 datatype: boolean}
dashes: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
checkintersection: { value: 0 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
showcharge: { value: 1 datatype: boolean}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
showstereogroups: { value: 0 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
border: { value: 12 minvalue: 0 maxvalue: 25 datatype: int}
bonds: { value: 8 minvalue: 3 maxvalue: 25 datatype: int}
symbolfontsize: { value: -1 datatype: int}
annotationfontsize: { value: -1 datatype: double}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
markcolor: { value: blue datatype: color}
highlightcolor: { value: red datatype: color}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
contractgroups: { value: 0 datatype: boolean}
isotopemapping: { value: none datatype: string}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
highlightbonds: { value: {} datatype: intvector}
highlightgroups: { value: {} datatype: intvector}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
font: { value: Helvecica datatype: string}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
annotationcolor: { value: {} datatype: color}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
usesubscripts: { value: 1 datatype: boolean}
downloadfilename: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
uselinecaps: { value: 1 datatype: boolean}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange merge hadd mod_e_pdf_image.so
E_PESTICIDE_COMPENDIUM_URL url Data display link into the Compendium of Pesticide Common Names (http://www.alanwood.net/pesticides)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_pesticide_compendium_url.xpd
E_PHARAO_PHARMACOPHORES compoundvector Pharamcophores as detected by Silicos' pharao program. This is used in the PHAR format I/O module.
AROM:HDON:HACC:LIPO:POSC:NEGC:HYBH:HYBL:EXCL
code int
coords floatvector
spread double
norm boolean
normal floatvector
atomchange bondchange stereochange 3drelative
E_PHASE byte Phase of ensemble
unknown:solid:liquid:gas,gaseous
atomchange bondchange merge
E_PHEROBASE_URL string Data display URL in PheroBase (pherobase.com)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_pherobase_url.xpd
E_PICT_IMAGE diskfile
(switchable between blob diskfile)
PICT format structure drawing, for Apple platforms
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 0 datatype: boolean constraints: property}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.4 datatype: double}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: string}
groupcolor: { value: purple datatype: color}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
usehatch: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 2.0 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 1.5 datatype: double}
checkintersection: { value: 0 datatype: boolean}
showstereogroups: { value: 0 datatype: boolean}
usesubscript: { value: 1 datatype: boolean}
font: { value: Arial datatype: string}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR A_ANNOTATION B_FLAGS A_FLAGS atomchange bondchange stereochange merge hadd mod_e_pict_image.so
E_PLANTCYC_ID string PlantCyc structure ID (http://pmn.plantcyc.org)
Tcl script E_STDINCHI atomchange bondchange stereochange atom bond e_plantcyc_id.xpd
E_PLANTCYC_URL url PlantCyc structure display URL (http://pmn.plantcyc.org)
Tcl script E_PLANTCYC_ID atomchange bondchange stereochange atom bond e_plantcyc_url.xpd
E_PMI floatmatrix Principial moments of inertia, computed on A_XYZ or a custom coordinate property
useh: { value: 1 datatype: boolean}
coordinateproperty: { value: A_XYZ datatype: string constraints: property}
Compiled C module A_XYZ A_TYPE A_WEIGHT E_CENTER A_ELEMENT atomchange bondchange 3drelative hadd atom mod_e_pmi.so
E_POGO_CIDS compoundvector
cid int
score double
obj1 int
obj2 int
maxcids: { value: 50 datatype: int}
mode: { value: none enumeration: none:bond:ringsystemsubsitution:ringsystemresize datatype: string}
label: { value: 0 description: The bond or ringsystem label to operate on datatype: string}
minordirection: { value: 0 description: If set, use the minor (reverse) direction for bond operations datatype: boolean}
database: { value: pogochem datatype: string}
dbtype: { value: mysql datatype: string}
dbuser: { value: {} datatype: string}
dbpassword: { value: {} datatype: string}
dbhost: { value: localhost datatype: string}
dbsocket: { value: /var/run/mysql/mysql.sock datatype: string}
bondscoring: { value: hc enumeration: hc:cc:cl:xc:cx datatype: string}
Tcl script atomchange bondchange atom bond e_pogo_cids.xpd
E_POGO_DISPLAY diskfile
(switchable between blob diskfile xmlstring)
SVG combim image of structures for the Pogochem service
width: { value: 1024 minvalue: 640 maxvalue: 4096 datatype: int}
height: { value: 800 minvalue: 640 maxvalue: 4096 datatype: int}
satelliteclick: { value: {} datatype: url}
bondclick: { value: {} datatype: url}
showaidstats: { value: 0 datatype: boolean}
frame: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
usescoredistance: { value: 1 datatype: boolean}
ringsystemclick: { value: {} datatype: url}
filename: { value: {} datatype: diskfile constraints: writeable}
maxitems: { value: 12 minvalue: 4 maxvalue: 24 datatype: int}
satellitewidth: { value: 150 minvalue: 50 maxvalue: 500 datatype: int}
satelliteheight: { value: 150 minvalue: 50 maxvalue: 500 datatype: int}
centerwidth: { value: 300 minvalue: 50 maxvalue: 500 datatype: int}
centerheight: { value: 300 minvalue: 50 maxvalue: 500 datatype: int}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
Tcl script E_POGO_CIDS atomchange bondchange atom bond e_pogo_display.xpd
E_POLARIZABILITY float Mean Polarizability. Computed indirectly via property E_HEAT_OF_FORMATION
A_XYZ atomchange bondchange
E_POLYLINE_ANNOTATION compound Polyline as structure drawing annotation. This is one of the choice variants of property E_ANNOTATON.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
style bitset
headskip double
tailskip double
headwidth double
tailwidth double
headlength double
taillength double
headflags bitset
tailflags bitset
arcangle double
curved boolean
A_XY never
E_POLYMERSET dataset Expanded polymer structures generated from SGroups
maxexpansion: { value: 35 minvalue: 1 maxvalue: 999 datatype: int}
minexpansion: { value: 0 minvalue: 0 maxvalue: 999 datatype: int}
maxmw: { value: 500 minvalue: 1 maxvalue: 999999 datatype: double}
Tcl script G_SGROUP atomchange bondchange groupchange e_polymerset.xpd
E_POLYMER_HASH uint64
Tcl script E_POLYMERSET never e_polymer_hash.xpd
E_PPI_LIKENESS_VIOLATIONS byte Hamon, Bourgeas, Ducrot, Theret, Xuereb, Basse, Brunel, Combes, Morelli, Roche, J. R. Soc. Interface 2013, 11, 20130860
Tcl script E_WEIGHT E_NRINGS E_NHACCEPTORS atomchange bondchange atom bond e_ppi_likeness_violations.xpd
E_PRICE compound Price per mol for various package sizes
screening currency
lab currency
bulk currency
Tcl script atomchange bondchange stereochange atom bond e_price.xpd
E_PROTECTED_SET dataset Input structure modified by attaching alternate protecting groups to acids, amines, ketones, aldehydes and alcohols. No support yet for other groups with standard protection methodologies (1,2-diols, terminal acetylenes, indoles, sulfonamides, phosphates). These modified structures are intended to be used as alternative query input to find pre-protected starting materials.
testaflags: { value: 0 description: If set, use only groups flagged in A_FLAGS as protected datatype: boolean}
maxtransformproducts: { value: -1 description: Maximum number of transform results to allow for each application of a FG protection transform, -1 for unlimited datatype: int}
includeinputstructure: { value: 1 description: If set, a duplicate of the original input structure is part of the result set datatype: boolean}
maxlevel: { value: 1 description: Maximum obscurity level to apply - more obscure PGs have higher level datatype: int}
groups: { value: acid|amine|carbonyl|hydroxyl description: Types of groups to protect enumeration: none:acid,acids:amine,amines:carbonyl,carbonyls:hydroxyl,hydroxyls,alcohol,alcohols datatype: bitset}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange hadd atom bond e_protected_set.xpd
E_PROTONATIONSET dataset Set of likely protomers, collected in dataset object
maxtotalcharge: { value: 3 datatype: int}
mintotalcharge: { value: -3 datatype: int}
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange merge e_protonationset.xpd
E_PUBCHEMQC_URL string Data URL for the PubchemQC database (http://pubchemqc.riken.jp)
Tcl script E_CID atomchange bondchange stereochange atom bond e_pubchemqc_url.xpd
E_PUBCHEM_3D_IMAGE diskfile 3D structure rendering
never
E_PUBCHEM_3D_THUMBNAIL diskfile 3D structure rendering preview
never
E_PUBCHEM_AID_COUNT intvector PubChem assay screening results. The result is a vector of 4 elements indicating the number of assays where the compound tested, in this order, active, inactive or inconclusive plus the total number of assays the compound was tested in.
active int
inactive int
inconclusive int
total int
Tcl script E_CID atomchange bondchange stereochange merge e_pubchem_aid_count.xpd
E_PUBCHEM_COMPOUND structure Processed PubChem database structure
opseq: { value: hydrogens-made-explicit superatoms-expanded groupV-tetravalent-charged charge-neutralized atoms-verified bonds-verified atomstereo-3d-perceived bondstereo-3d-perceived stereochemistry-verified valence-bond-standardized plot-coordinates-beautified datatype: string}
maxtautomers: { value: 200 datatype: string}
Tcl script never e_pubchem_compound.xpd
E_PUBCHEM_COMPOUND_CANONICALIZED boolean Flag indicating whether compound is canonicalized
atom bond
E_PUBCHEM_COMPOUND_ID compound PUBCHEM compound identifier
deposited:standardized:component:neutralized:mixture:tautomer:pka-state:unset=254:unknown=255 cid=0:sid=1:xid=2:unset=254:unknown=255
type int
idtype int
id int
never
E_PUBCHEM_CONFORMER compoundvector NCBI conformer data, filled by reading PubChem 3D SD files
id uint64
energy double
volume double
selfoverlap double
rmsd double
multipoles doublevector
diverseorder shortvector
shapefingerprint compoundvector
atomchange bondchange stereochange merge 3drelative 3dabsolute mol atom bond
E_PUBCHEM_DEPOSITOR_RECORD_DATE datetime Depositor's record date of a submission
never
E_PUBCHEM_DIFFERENCE_FLAGS uint64 Flags for differences found in structure standardization processing
never
E_PUBCHEM_DIFFERENCE_TIMESTAMP datetime Timestamp for a structure standardization processing difference check
never
E_PUBCHEM_EXT_DATASOURCE_CID int CID from depositor representing the data item
never
E_PUBCHEM_EXT_DATASOURCE_INCHI string InChI string from depositor representing the data item
never
E_PUBCHEM_EXT_DATASOURCE_NAME string Depositor's datasource name
never
E_PUBCHEM_EXT_DATASOURCE_REGID string Depositor's unique external registry ID
never
E_PUBCHEM_EXT_DATASOURCE_SMILES string Kekulized SMILES string from depositor representing the data item
never
E_PUBCHEM_EXT_DATASOURCE_URL url Depositor's external source/database URL
never
E_PUBCHEM_EXT_SUBSTANCE_URL url Depositor's external individual substance URL
never
E_PUBCHEM_GENBANK_GENERIC_ID stringvector NCBI/NLM/NIH GenBank general ID(s)
never
E_PUBCHEM_GENERIC_REGISTRY_NAME stringvector Generic registry name(s)
never
E_PUBCHEM_NCBI_BIOSYSTEM_ID intvector NCBI/NLM/NIH BIOSYSTEM ID(s)
never
E_PUBCHEM_NCBI_MMDB_ID stringvector NCBI/NLM/NIH MMDB ID(s)
never
E_PUBCHEM_NCBI_PROBE_ID intvector NCBI/NLM/NIH PROBE ID(s)
never
E_PUBCHEM_NCBI_TAXONOMY_ID stringvector NLM/NIH Taxonomy ID reference(s)
never
E_PUBCHEM_PATENT_REFERENCES compoundvector User-supplied patent references of compounds registered in PubChem (i.e. with a CID)
patentdate date
patentid string
patenttitle string
patentsubmissiondate date
patentgrantdate date
patenturl url
Tcl script E_CID atomchange bondchange stereochange atom bond e_pubchem_patent_references.xpd
E_PUBCHEM_PATENT_URL url PubChem patent display via CID
Tcl script atomchange bondchange atom bond e_pubchem_patent_url.xpd
E_PUBCHEM_PUBLICATION_DATE datetime Depositor's publication date of journal article associated with compound
never
E_PUBCHEM_PUBMED_ID stringvector NLM/NIH PubMed ID for an article or abstract
never
E_PUBCHEM_PUBMED_REFERENCES compoundvector User-supplied PubMed references of compounds registered in PubChem (i.e. with a CID)
date date
pmid int
title string
journal string
Tcl script E_CID atomchange bondchange stereochange atom bond e_pubchem_pubmed_references.xpd
E_PUBCHEM_REVOKE_SUBSTANCE stringvector Substance revocation comments
never
E_PUBCHEM_SHAPE_FINGERPRINT compoundvector Property holding PubChem 3D fingerprint data
shapecid int
lid int
packedmatrix uint64
atomchange bondchange stereochange merge 3drelative 3dabsolute atom bond
E_PUBCHEM_SID_DATA compoundvector Data on PubChem depositor records
sid int
source string
sourceid string
sourcecategory stringvector
sourcereleasedate date
depositdate date
modifydate date
registrynumber string
dburl url
sburl url
Tcl script E_SIDSET atomchange bondchange stereochange merge e_pubchem_sid_data.xpd
E_PUBCHEM_STANDARDIZED_STRUCTURE structure Structure standardized by the PubChem structure standardization service
transferformat: { value: serialized datatype: string}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT atomchange bondchange stereochange merge mod_e_pubchem_standardized_structure.so
E_PUBCHEM_SUBSTANCE_COMMENT stringvector Substance comments
never
E_PUBCHEM_URL url PubChem compound database URL
Tcl script E_CID atomchange bondchange stereochange merge e_pubchem_url.xpd
E_PUBCHEM_XLOGP3 double Processed PubChem database structure
atom bond
E_PUBCHEM_XREF_EXT_ID stringvector Depositor's external source/database crossreference ID
never
E_PUBMED_IDS intvector PubMed reference IDs for structures found in PubChem
Tcl script E_CID atomchange bondchange atom bond e_pubmed_ids.xpd
E_PUBMED_LINK_PAGE blob
(switchable between blob diskfile url)
A page with links generated from E_PUBCHEM_PUBMED_REFERENCES into the PubMed literature database.
imgproperty: { value: E_SVG_IMAGE description: Property to use to generate the structure header image datatype: string constraints: property}
imgparameters: { value: {} description: Override attributes for the image computation datatype: dictionary}
filename: { value: {} datatype: string constraints: writeable}
ncols: { value: 2 minvalue: 1 maxvalue: 12 datatype: int}
Tcl script E_PUBCHEM_PUBMED_REFERENCES atomchange bondchange atom bond e_pubmed_link_page.xpd
E_PUBMED_URLS urlvector Display links for the PubMed entries identified via E_PUBMED_IDS
Tcl script E_PUBMED_IDS atomchange bondchange atom bond e_pubmed_urls.xpd
E_PYTHON_TEST string Python test function
param1: { value: one datatype: string}
param2: { value: 2 datatype: int}
param3: { value: 3.3 datatype: double}
Python script atomchange bondchange atom bond e_python_test.xpd
E_QUERY compound Ensemble-level search options
none:unwrapped_recursive_smarts undefined:lt:le:eq:ge:gt:ne:in:notin:range:bitset_and {} none:and:or:xor,eor
flags bitset
prefixoperator int
prefixvalue int
chainoperator int
chainsubstructure substructure
never
E_QUERY_SCREEN bitvector Bitvector optimized for standard substructure queries, with focus on ring systems and ring substitutions as well as the capability to generalized heteroatoms and standard element classes (halogens, N/O/S, etc.).
size: { value: 1952 description: Vector size minvalue: 256 maxvalue: 4096 datatype: int}
version: { value: 3 description: Versioning switch to compare evolution of algorithm datatype: int}
power: { value: 2 description: Count step escalation minvalue: 1 maxvalue: 3 datatype: int}
nbitsperpath: { value: 4 description: Bit positions to ser per unique path minvalue: 1 maxvalue: 16 datatype: int}
maxcount: { value: 3 description: Maximum path count to use minvalue: 1 maxvalue: 16 datatype: int}
minpathlen: { value: 2 description: Minimum length of paths fo hash minvalue: 2 maxvalue: 5 datatype: int}
maxpathlen: { value: 5 description: Maximum length of pathes to hash minvalue: 2 maxvalue: 10 datatype: int}
maxpathsperatom: { value: -1 description: Maximum nmber of paths to find per atom, -1 is unlimited minvalue: -1 maxvalue: 9999 datatype: int}
isquery: { value: 0 description: Whether structure is a query sub/superstructure, or a complete structure datatype: boolean}
ignoreh: { value: 0 description: If set, do not create any codes involving hydrogen datatype: boolean}
tauto: { value: 0 description: If set, do not set any bits with H, or involving bond orders in tauo systems datatype: boolean}
debug: { value: 0 description: If set, print found paths datatype: boolean}
useringcombos: { value: 1 description: If set, add ring combo screen bits datatype: boolean}
tracebit: { value: -1 description: Trace which pattern sets this bit position minvalue: -1 maxvalue: 4096 datatype: int}
cmpflags: { value: bondorder|useatomtree|usebondtree description: Comparison flags which will be used in subsequent atom-by-atom matching. Some flags can be used for increasing the filter efficiency enumeration: one:wedge,wedges:charge:stereo:bondorder,bo:terminal:nozwitterioncollapse:nosinglaonaro:nodoubleonaro:isotope:tautomer:arotautomer:matchbondringcount:lazymatchbondringcount:kekule,kekuleodd:strictnomatch:nochainonaro:lazymatchatomringcount:matchatomringcount:bondreaction:pionaro:noaliphaticonaro:relativestereo:fixedframework,fixedframe:nomultibondfg:noarobondfg:noheterofg:useatomtree,atomtree:usebondtree,bondtree:excludesmartsenvironment:openhcount:varbondglobal:varbondindividual:kekuleeven:unsetaromaticisaliphatic:implicitonsingleoraro:nullsubstructureismismatch:nochainonring:atomlistidentity:splitfragments:generalizeheteroatoms:nosuperatomonh:singleattachmentsuperatomsonly:remembercomplexmatches:matchallheavyatoms:fullringsystem:noatomstereook:nobondstereook:multibondorder,singleonany,singleisany:matchfullmolecule,matchfullmol:matchfullensemble,matchfullens:nosmallerrings:noalkyllinks:containedatomlists:chained:no3dcoordinatecomputation,no3dcoordinatescomputation datatype: bitset}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER B_ISAROMATIC A_ISAROMATIC E_ELEMENT_COUNT R_TYPE R_AROMATIC A_HASH A_RING_COUNT B_RING_COUNT atomchange bondchange hadd atom bond ring mod_e_query_screen.so
E_RACEMIC_STEREO_HASH uint64 Ensemble hashcodes for racemic mixtures. These are identical to the minimum molecule stereo hashcod es of the present structure, or its enantiomer. For example, the racemic stereo hashcode for both L-alanine and D-alanine input structures (with known stereochemistry) is, by chance, that of L-alanine, and not that of DL-alanine (with unknown stereochemistry)
Compiled C module M_RACEMIC_STEREO_HASH M_RACEMIC_STEREO_HASH_GROUP atomchange bondchange stereochange merge mod_e_racemic_stereo_hash.so
E_RADIOACTIVE boolean Indicator whether ensemble is radioactive as per atom isotope labelling
Tcl script A_RADIOACTIVE atomchange bondchange atom bond e_radioactive.xpd
E_RAMANIRGIF diskfile IR/RAMAN spectrum as GIF file
width: { value: 660 datatype: int}
height: { value: 300 datatype: int}
filename: { value: {} datatype: string}
type: { value: ir enumeration: ir:raman datatype: string}
multigif: { value: 0 datatype: boolean}
backgrcolor: { value: transparent datatype: color}
axiscolor: { value: black datatype: color}
ircolor: { value: blue datatype: color}
ramancolor: { value: red datatype: color}
legend: { value: 0 datatype: boolean}
interlace: { value: 1 datatype: boolean}
yscalemax: { value: auto datatype: string}
changeyunit: { value: 0 datatype: boolean}
Tcl script E_RAMANSPECTRUM E_IRSPECTRUM atomchange bondchange e_ramanirgif.xpd
E_RAMANSPECTRUM compound Measured or computed Raman spectrum. This is a spectrum type which can be read and written in JCAMP and Galactic SPC format.
experimental boolean
origin string
author string
date date
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum xyvector
peaks floatvector
peakshape stringvector
peakintensity floatvector
peakname stringvector
A_XYZ A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange 3drelative
E_RAMANSPECTRUM_IMAGE diskfile
(switchable between string blob diskfile url)
Raman spectrum rendering
height: { value: 250 datatype: int}
width: { value: 500 datatype: int}
bgcolor: { value: white datatype: color}
title: { value: {} datatype: string}
filename: { value: {} datatype: string constraints: writeable}
format: { value: gif enumeration: png,png24:gif:png8 datatype: string}
titlecolor: { value: black datatype: color}
framecolor: { value: black datatype: color}
signalcolor: { value: #DD0000 datatype: color}
ystyle: { value: transmittance enumeration: transmittance:absorbance datatype: int}
xdirection: { value: reverse enumeration: normal:reverse datatype: int}
xstyle: { value: 1/cm enumeration: 1/cm:um datatype: int}
Tcl script E_RAMANSPECTRUM atomchange bondchange merge mol e_ramanspectrum_image.xpd
E_RAYTRACE_IMAGE diskfile Raytraced image of 3D structure, using the povray raytracer as external application
background: { value: black datatype: color}
height: { value: 250 datatype: int}
width: { value: 250 datatype: int}
quality: { value: 8 datatype: int}
lightx: { value: 60 datatype: int}
lighty: { value: 66 datatype: int}
antialias: { value: 1 datatype: bitset}
preview: { value: 0 datatype: double}
fog: { value: 0 datatype: boolean}
includepath: { value: /usr/local/lib/pov/include datatype: string}
style: { value: ballstick enumeration: wireframe:capped:ball&stick:spacefill datatype: string}
vdwscaling: { value: 25 datatype: double}
bcolor: { value: white datatype: color}
bondradius: { value: 15 datatype: string}
uselabel: { value: 0 datatype: boolean}
usebo: { value: 0 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
atomhighlightcolor: { value: red datatype: color}
bondhighlightcolor: { value: red datatype: color}
transparency: { value: 0 datatype: double}
highlightatoms: { value: {} datatype: intvector}
highlightbonds: { value: {} datatype: intvector}
format: { value: png enumeration: gif:png,png24:ppm:tga datatype: string}
zoom: { value: 100 datatype: double}
ignoreh: { value: 0 datatype: boolean}
Tcl script A_XYZ A_TYPE B_TYPE atomchange bondchange stereochange merge 3drelative 3dabsolute e_raytrace_image.xpd
E_REACTION_ROLE byte Role of ensemble in reaction.
undef,undefined:reagent,educt,reactant,reagents,educts,reactants:product,products:solvent,solvents:catalyst,catalysts:intermediate,intermediates:impurity,impurities:byproduct,byproducts:agent,agents:waste:precursor,precursors:altreagent,altreagents
Compiled C module never mod_e_reaction_role.so
E_RECAP_FRAGMENTS structure Structure fragmented according to the RECAP rules J. Chem. Inf. Comput. Sci. 38, 1998, 511-522
useextratransforms: { value: 0 description: Whether to use extra transforms not in original paper, but in transform library (e.g. aronitrogen-arocarbon cut) datatype: boolean}
useisotopelabels: { value: 0 description: If set, set isotope labels as described in original publication in additon to A_REACP_LINKER_TYPE property datatype: boolean}
patternfile: { value: recap.smirks datatype: diskfile constraints: readable}
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER B_FRAGMENT_CARBON_COUNT atomchange bondchange atom bond ring e_recap_fragments.xpd
E_RECONNECTED_STRUCTURE structure Reconnect structure components by identifying potential complex-bond (carbon monoxide, etc.) and ionic (ion and metal counterion) in metal-centric complex and salt compounds. This is primarily intended to facilitate substructure seach on such compounds.
Tcl script atomchange bondchange stereochange atom bond e_reconnected_structure.xpd
E_RECTANGLE_ANNOTATION compound Rectangle as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
A_XY never
E_REGISTRATION_ID string Registration ID
never
E_REOS_FILTER boolean An implementation template for the Vertex REOS drug-likeness filter Adv. Drug Delivery Reviews 54, 2002, 255-271
minweight: { value: 200 datatype: double}
maxweight: { value: 500 datatype: double}
minlogp: { value: -5 datatype: double}
maxlogp: { value: 5 datatype: double}
minhdonors: { value: 0 datatype: int}
maxhdonors: { value: 5 datatype: int}
minhacceptors: { value: 0 datatype: int}
maxhacceptors: { value: 10 datatype: int}
mincharge: { value: -2 datatype: int}
maxcharge: { value: 2 datatype: int}
minrotbonds: { value: 0 datatype: int}
maxrotbonds: { value: 8 datatype: int}
minheavyatoms: { value: 20 datatype: int}
maxheavyatoms: { value: 50 datatype: int}
patternfile: { value: reos.sma datatype: diskfile constraints: readable}
Tcl script atomchange bondchange atom bond e_reos_filter.xpd
E_REPULSION_ENERGY float Measured or computed Core-Core Repulsion Energy. Computed indirectly via E_HEAT_OF_FORMATION.
A_XYZ A_ELEMENT A_TYPE B_ORDER atomchange bondchange hadd
E_RESONANCE_SET dataset Create a resonance set. Adapted from test suite by Bruno Bienfait of Molecular Networks GmbH
maxens: { value: 1000 datatype: int}
timeout: { value: 0 datatype: int}
Tcl script atomchange bondchange atom bond e_resonance_set.xpd
E_RHEA_IDS stringvector IDs of reactions involving the structure in the RHEA reaction database (www.rhea-db.org)
Tcl script E_CHEBI_ID atomchange bondchange atom bond e_rhea_ids.xpd
E_RHEA_LINK_PAGE blob
(switchable between blob diskfile url)
Page with links to RHEA (www.ebi.ac.uk/rhea) reactions
imgproperty: { value: E_SVG_IMAGE description: Property to use to generate the structure header image datatype: string constraints: property}
imgparameters: { value: {} description: Override attributes for the image computation datatype: dictionary}
filename: { value: {} datatype: string constraints: writeable}
ncols: { value: 5 minvalue: 1 maxvalue: 12 datatype: int}
Tcl script E_RHEA_IDS atomchange bondchange atom bond e_rhea_link_page.xpd
E_RIGID_BOND_COUNT int Number of bonds which are not rotatable because they are in a ring, or have multiple bond order.
Compiled C module B_ROTATABILITY atomchange bondchange hadd mod_e_rigid_bond_count.so
E_RINGSYSTEM_COUNT short Ringsystem count
Compiled C module atomchange bondchange atom bond mod_e_ringsystem_count.so
E_RINGSYSTEM_FRAGMENTS dataset Generate a complete set of fragments, or a set only containing fragments from a single ringsystem, by removing all combinations of ring systems and chain atoms.
singleonly: { value: 0 description: If set, only isolate single ring systems, not combination connected by brdige atoms datatype: boolean}
Tcl script atomchange bondchange atom bond e_ringsystem_fragments.xpd
E_RING_SIZE_COUNT intvector Counts of ring sizes in structure (array element index is size. array size is maximum ring size plus one)
Compiled C module R_SIZE atomchange bondchange mod_e_ring_size_count.so
E_ROSDAL_STRING string Rosdal Line Notation structure representation
atomchange bondchange stereochange merge atom bond
E_ROUNDED_RECTANGLE_ANNOTATION compound Rounded ectangle as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
arcwidth float
archeight float
A_XY never
E_RTECS_NUMBER string CDC RTECS number of structure
Tcl script E_CAS atomchange bondchange atom bond e_rtecs_number.xpd
E_RULE_OF_3_VIOLATIONS byte Carr Rule of 3 violation count (hydrogen donor count, hydrogen acceptor count, logp, weight/100, polar surface area, number of rotatable bonds over 3) Congreve, M., Carr, R., Murray, C. and Jhoti, H. A 'Rule of Three' for fragment-based lead discovery, Drug Discov. Today 2003, 8, 876-877
Tcl script E_NHDONORS E_NHACCEPTORS E_XLOGP E_WEIGHT E_TPSA E_NROTBONDS atomchange bondchange merge atom bond e_rule_of_3_violations.xpd
E_RULE_OF_5_VIOLATIONS byte Count of violated Lipinski Rule of 5 conditions in structure Lipinski CA, Lombardo F, Dominy BW, Feeney PJ, Adv. Drug Deliv. Rev. 46 (1-3): 3–26
uselowermwbound: { value: 0 description: If set, also test for a minimum weight of 150 Dalton datatype: boolean}
Tcl script E_NHDONORS E_NHACCEPTORS E_WEIGHT E_XLOGP2 atomchange bondchange merge atom bond e_rule_of_5_violations.xpd
E_SCAFFOLD_KEYS shortvector Keys for natural scaffold ordering J. Chem. Inf. Model. 2014, 54, 1617-1622
Tcl script A_FRAMEWORK A_TYPE A_ELEMENT A_RING_COUNT R_CONJUGATED atomchange bondchange atom bond ring e_scaffold_keys.xpd
E_SCAFFOLD_TREE_SEQUENCE dataset The order set of subsequent simplifications of the Ertl/Schuffenhauer scaffold tree. J. Chem. Inf. Model. 2007, 47, 47-58
includeoriginal: { value: 0 datatype: boolean}
Tcl script atomchange bondchange mol ring e_scaffold_tree_sequence.xpd
E_SCAFFOLD_TREE_STRUCTURE structure Simplified scaffold structure, as per the Schuffenhauer/Ertl paper. This returns the next step in simplification, or an error if no more simplification is possible. Schuffenhauer et al., J. Chem. Inf. Model. 2007, 47, 47-58
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER Y_AROMATIC R_AROMATIC R_SIZE R_HETEROATOM_COUNT E_NMOLECULES E_RINGSYSTEM_COUNT E_HASHY atomchange bondchange merge atom bond ring e_scaffold_tree_structure.xpd
E_SCALED_SCAFFOLD_KEYS floatvector Keys for natural scaffold ordering, scaled for equal weights (recomputed from 10000 mosty comst commen scaffolds in ChEMBL19 (via F_SCAFFOLD_TABLE) from Cactvs property E_SCAFFOLD_KEYS J. Chem. Inf. Model. 2014, 54, 1617-1622
Tcl script E_SCAFFOLD_KEYS atomchange bondchange atom bond ring e_scaled_scaffold_keys.xpd
E_SCRAMBLED_STRUCTURE structure Ensemble with randomized atom and bond sequence
seed: { value: {} description: A numerical random seed value. If empty, use clock clicks. datatype: string}
scrambleatoms: { value: 1 datatype: boolean}
scramblebonds: { value: 1 datatype: boolean}
scramblewedges: { value: 0 datatype: boolean}
Tcl script A_TYPE B_TYPE B_ORDER A_ELEMENT atomchange bondchange stereochange merge e_scrambled_structure.xpd
E_SCREEN bitvector Screening bits for substructure search
usevariants: { value: 0 datatype: string}
maxvariants: { value: 10 datatype: string}
extended: { value: 2 datatype: string}
tauto: { value: none datatype: string}
ignoreh: { value: 0 datatype: string}
usebo: { value: 1 datatype: string}
(builtin) A_ELEMENT A_TYPE B_TYPE B_ORDER R_TYPE B_ISTAUTOMERIC R_SIZE B_ISAROMATIC atomchange bondchange hadd mol
E_SCRIPDB_URL url Query URL for University of Toronto SCRIBDP IBM patent database interface
startyear: { value: 2001 description: First patent year to query minvalue: 2001 maxvalue: 2099 datatype: int}
endyear: { value: 2020 description: Last patent year to query minvalue: 2001 maxvalue: 2099 datatype: int}
verify: { value: 1 description: If set, check whether there are matches datatype: boolean}
reactionsonly: { value: 0 description: If set, look only for patents containing synthetic procedures datatype: boolean}
threshold: { value: 0.8 description: The threshold for similarity queries minvalue: 0.1 maxvalue: 1.0 datatype: double}
querytype: { value: 0 description: The query type (fullstructure, substructure, similarity) enumeration: fs,fullstructure:ss,substructure:sim,similarity datatype: int}
Tcl script atomchange bondchange atom bond e_scripdb_url.xpd
E_SDBS_ID int Database ID of structure on AIST SDBS (RioDB) spectral database (http://riodb01.ibase.aist.go.jp)
Tcl script E_CAS atomchange bondchange atom bond e_sdbs_id.xpd
E_SDBS_URL url Database URL for display of structure in AIST SDBS (RioDB) spectral database (http://riodb01.ibase.aist.go.jp)
Tcl script E_SDBS_ID atomchange bondchange atom bond e_sdbs_url.xpd
E_SDF_STRING string SDF structure encoding
writelist: { value: {} datatype: string constraints: propertylist}
subformat: { value: 2d enumeration: mol2d,2d,mol,std,standard:mol3d,3d:reaction,rxn,rdf:spectrum:volume:mol0d,0d datatype: int}
eolchars: { value: default enumeration: default:win,windows,crlf:mac,cr:linux,unix,nl datatype: int}
hydrogens: { value: asis enumeration: add:asis:strip:stripall datatype: int}
nitrostyle: { value: asis enumeration: ionic:asis:penta,pentavalent datatype: int}
usev3000: { value: 1 enumeration: ionic:asis:penta,pentavalent datatype: boolean}
writeend: { value: blockend enumeration: blockend:none datatype: int}
Tcl script atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond e_sdf_string.xpd
E_SERIALIZED_JAVA_OBJECT blob Transport container for Java objects. This is used for example in the KNIME native table I/O module for CDKCells.
never
E_SHARC_ACCESS byte Access mode for a record in the SHARC archive
private:groupheader::group,groupfull::header::gradient::::::::everybody,open,full
never
E_SHARC_GROUP string Group of owner or contributor of a data record in the SHARC archive
never
E_SID int PubChem SID structure identifier
Tcl script atomchange bondchange stereochange merge atom bond ring e_sid.xpd
E_SIDSET intvector PubChem SIDs associated with structure identified by its CID
Tcl script E_CID atomchange bondchange stereochange atom bond e_sidset.xpd
E_SIDSET_URL url PubChem substance database URL which displays the collection of SIDs associated with a structure
Tcl script E_SIDSET atomchange bondchange stereochange merge e_sidset_url.xpd
E_SIGMAALDRICH_IDS compoundvector SigmaAldrich catcalog name and catalog ID
catalog string
id string
mfcd string
Tcl script E_SDF_STRING E_SMILES atomchange bondchange stereochange atom bond e_sigmaaldrich_ids.xpd
E_SIGMAALDRICH_URLS urlvector Catalog data display URL for SigmaAldrich
Tcl script E_SIGMAALDRICH_IDS atomchange bondchange stereochange atom bond e_sigmaaldrich_urls.xpd
E_SIMULATION_BOX xyzvector Box for MM simulations (used for example in Gromacs file format). The values are three xyz vectors, defining the box coordinates. Modulo arithmetic is used to map points outside the box back into it.
v1 floatvector
v2 floatvector
v3 floatvector
A_XYZ atomchange bondchange stereochange merge hadd
E_SKETCHER_URL url URL suitable for loading the structure into the Xemistry Web Sketcher (www.xemistry.com/edit)
baseurl: { value: http://www.xemistry.com/edit description: The base URL of the sketcher installation to use datatype: url}
transferformat: { value: blob description: The transfer format to use datatype: string}
Tcl script atomchange bondchange atom bond e_sketcher_url.xpd
E_SLN_STRING string SLN structure encoding
minimal: { value: 0 description: If set, omit compound level property section (>name=xxx<) etc. datatype: boolean}
fold: { value: 0 description: Whether to use multiline format with continuation characters datatype: boolean}
extended: { value: 0 description: Whether to encode extended attributes, such as 2D and 3D coordinates datatype: boolean}
propertylist: { value: {} description: List of ensemble properties to include datatype: string constraints: propertylist}
droplist: { value: {} description: List of ensemble properties to exclude. Overrides inclusion list. datatype: string constraints: propertylist}
computeprops: { value: 0 description: Whether to attempt to compute properties in the inclusion list datatype: boolean}
dimension: { value: -1 description: Coordinate handling. -1: automatic, 0: no coordinates, 2:force 2D, 3: force 3D (both with computation if necessary) minvalue: -1 maxvalue: 3 datatype: int}
usesuperatom: { value: 0 description: Whether to use A_SUPERATOMSTRING for superatoms (default: use unspecified R group symbol) datatype: boolean}
Compiled C module atomchange bondchange stereochange merge hadd atom bond mod_e_sln_string.so
E_SMALLMOLECULES_URL url Structure lookup URL for smallmolecules.com
Tcl script E_CAS atomchange bondchange stereochange atom bond e_smallmolecules_url.xpd
E_SMALLWORLD_NETWORK network Sample implementation of R. Sayles SmallWorld network for accelerated MCSS searching
useelements: { value: 1 datatype: boolean}
usebondorders: { value: 1 datatype: boolean}
addsingleatomfragments: { value: 0 datatype: boolean}
Compiled C module E_HASHY B_HASHGROUP A_ELEMENT A_LABEL B_LABEL A_TYPE B_TYPE B_ISAROMATIC B_RING_COUNT A_SUBSTITUENT_COUNT E_NMOLECULES E_HEAVY_ATOM_COUNT atomchange bondchange atom bond mod_e_smallworld_network.so
E_SMARTS string Encoded structure in SMARTS format J. Chem. Inf. Comput. Sci. 1988, 28, 31-36
usearo: { value: 1 datatype: boolean}
unique: { value: 0 datatype: boolean}
usestereo: { value: 1 datatype: boolean}
usesuperatom: { value: 0 datatype: boolean}
useisotope: { value: 1 datatype: boolean}
usemapping: { value: 1 datatype: boolean}
usestereogroup: { value: 0 datatype: boolean}
smarts: { value: 1 datatype: boolean}
usehcount: { value: 1 datatype: boolean}
useexplicithcount: { value: 0 datatype: boolean}
singleringupdownbond: { value: 1 datatype: boolean}
useexplicith: { value: 1 datatype: boolean}
queryhatoms: { value: {} datatype: intvector}
checkstereo: { value: 1 datatype: boolean}
hideautoh: { value: 1 datatype: boolean}
atomaroproperty: { value: A_ARORING_COUNT datatype: string constraints: property}
Compiled C module A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL atomchange bondchange stereochange merge hadd mod_e_smarts.so
E_SMARTSVIEWER_IMAGE diskfile
(switchable between string blob diskfile mapfile url)
SMARTS query visualization http://smartsview.zbh.uni-hamburg.de/home/auto_retrieving
format: { value: png enumeration: png:pdf:svg label: Image Format: datatype: int}
visualization: { value: complete enumeration: complete:symbols label: Visualization Mode: datatype: int}
legend: { value: both enumeration: none:static:dynamic:both label: Legend: datatype: int}
Tcl script E_SMARTS atomchange bondchange stereochange merge mol e_smartsviewer_image.xpd
E_SMCM float Synthetic and molecular complexity T. K. Allu, T. Oprea, J. Chem. Inf. Model. 2005, 45, 1237-1243
Tcl script A_TYPE B_TYPE B_ORDER A_SYMBOL A_STEREOGENIC B_STEREOGENIC E_ELEMENT_COUNT B_ISAROMATIC E_RING_SIZE_COUNT E_RINGSYSTEM_COUNT atomchange bondchange stereochange e_smcm.xpd
E_SMILES string Encoded structure in SMILES format J. Chem. Inf. Comput. Sci. 1988, 28, 31-36
usearo: { value: 0 datatype: string}
unique: { value: 0 datatype: string}
usestereo: { value: 1 datatype: string}
usesuperatom: { value: 0 datatype: string}
useisotope: { value: 1 datatype: string}
usemapping: { value: 1 datatype: string}
usestereogroup: { value: 0 datatype: string}
smarts: { value: 0 datatype: string}
usehcount: { value: 1 datatype: string}
singleringupdownbond: { value: 1 datatype: string}
useexplicith: { value: 0 datatype: string}
queryhatoms: { value: {} datatype: string}
checkstereo: { value: 1 datatype: string}
hideautoh: { value: 0 datatype: string}
firstatom: { value: -1 datatype: string}
lastatom: { value: -1 datatype: string}
useextrabondtypes: { value: 1 datatype: string}
generalization: { value: none datatype: string}
reuseringlinks: { value: 0 datatype: string}
useexplicithcount: { value: 0 datatype: string}
atomaroproperty: { value: A_ARORING_COUNT datatype: string}
atommapproperty: { value: A_MAPPING datatype: string}
usename: { value: 0 datatype: string}
canonicalizationmethod: { value: cactvs datatype: string}
(builtin) A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL_STEREO B_LABEL_STEREO A_ISOTOPE A_MAPPING A_QUERY B_QUERY atomchange bondchange stereochange merge hadd
E_SMOOTHED_PATHCODE floatvector Smoothed path length similiarity code
Tcl script E_PATHCODE atomchange bondchange e_smoothed_pathcode.xpd
E_SOLUBILITY_URL url Link to predict solubility (showme.physics.drexel.edu/onsc/models/multisolvent.php)
Tcl script atomchange bondchange atom bond e_solubility_url.xpd
E_SORT_FORMULA string Sortable string for sorting E_FORMULA according to C, H, X element rank
useimplicith: { value: 1 description: If set, add implicit Hs to formula datatype: boolean}
Tcl script E_ELEMENT_COUNT atomchange hadd e_sort_formula.xpd
E_SORT_NAME string Sortable string for sorting E_NAME
Tcl script E_NAME never e_sort_name.xpd
E_SOURCE stringvector Source of structure data, in free-form string array format
never
E_SPAN int The maximum of all M_SPAN property values of the ensemble.
Compiled C module M_SPAN atomchange bondchange merge mol atom bond mod_e_span.so
E_SPECIFIC_ROTATION float Specific rotation [alpha]
atomchange bondchange atom bond
E_SPECTRABASE_ID string Record ID in the Spectrabase database (spectrabase.com)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_spectrabase_id.xpd
E_SPECTRABASE_URL url Display URL in the Spectrabase database (spectrabase.com)
Tcl script E_SPECTRABASE_ID atomchange bondchange stereochange atom bond e_spectrabase_url.xpd
E_SPHINX_SCIENTIFIC_ID string ID in Sphinx Scientific catalogue (www.sphinxscientificlab.com)
Tcl script atomchange bondchange atom bond e_sphinx_scientific_id.xpd
E_SPHINX_SCIENTIFIC_URL url Display URL for Sphinx Scientific catalog (www.sphinxscientificlab.com)
Tcl script E_SPHINX_SCIENTIFIC_ID atomchange bondchange atom bond e_sphinx_scientific_url.xpd
E_SRS_ID int Substance ID in the EPA/FDA Substance Registry Services (SRS)
Tcl script E_CAS atomchange bondchange atom bond e_srs_id.xpd
E_SRS_URL url Structure data display page in the EPA/FDA Substance Registry Services (SRS)
Tcl script E_SRS_ID atomchange bondchange atom bond e_srs_url.xpd
E_STANDARDIZED_STRUCTURE structure A collection of structure standardization steps.
nitrostyle: { value: penta enumeration: ignore,asis,default:ionic,charged:pentavalent,penta,uncharged,neutral:xionic,extendedionic,extendedcharged,xcharged:xpentavalent,extendedpentavalent,xpenta,extendedpenty,xneutral,extendedneutral,xuncharged,extendeduncharged datatype: int}
sulfoxidestyle: { value: asis enumeration: ignore,asis,default:ionic,charged:neutral,tetravalent datatype: string}
desalt: { value: 1 datatype: boolean}
clearinorganic: { value: 1 datatype: boolean}
uncharge: { value: 1 datatype: boolean}
chargebalance: { value: 0 datatype: boolean}
saltfile: { value: ions.smi description: Standard counterions datatype: diskfile constraints: readable}
cutmetalsalts: { value: 1 datatype: boolean}
singlefragment: { value: 1 datatype: boolean}
Tcl script A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange stereochange mol atom bond ring e_standardized_structure.xpd
E_STANDARD_ATOM_COUNT int Number of normal (non-query, non-superatom, etc.) atoms in ensemble
Compiled C module A_TYPE atomchange merge hadd mod_e_standard_atom_count.so
E_STDBLE float Standard bond length for plot
(builtin) A_XY never
E_STDINCHI string Standard InChI identifier
options: { value: DONOTADDH description: Set of default option words as defined to standard comment: Many of the option words listed for E_INCHI implicitly switch off standard mode. See INChI lib docs. datatype: string constraints: list}
fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean}
autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean}
stereoperception: { value: 1 datatype: boolean}
stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int}
prefix: { value: 1 datatype: boolean}
stripstereolayer: { value: 0 datatype: boolean}
stripisotopelayer: { value: 0 datatype: boolean}
stripfixedhlayer: { value: 0 datatype: boolean}
stripreconnectlayer: { value: 0 datatype: boolean}
stripchargelayer: { value: 0 datatype: boolean}
Compiled C module B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange merge atom bond mod_e_stdinchi.so
E_STDINCHIKEY string Hash of InChI string
prefix: { value: 1 datatype: boolean}
Compiled C module E_STDINCHI atomchange bondchange stereochange atom bond mod_e_stdinchikey.so
E_STDINCHI_AUXINFO string Standard InChI auxiliary information
B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd atom bond
E_STEREOGENIC intpair Sum of M_STEREOGENIC stereogenic atoms and bond counts
Compiled C module M_STEREOGENIC atomchange bondchange stereochange atom bond mod_e_stereogenic.so
E_STEREOISOMERS dataset Set of stereoisomers from input structure
flipatoms: { value: all description: Select atoms where stereochemistry should be flipped enumeration: undefined:defined:all:none datatype: int}
flipbonds: { value: all description: Select bonds where stereochemistry should be flipped enumeration: undefined:defined:all:none datatype: int}
allowundefinedatoms: { value: 1 description: If not set, result ensembles with undefined atom stereochemistry are deleted datatype: boolean}
allowundefinedbonds: { value: 1 description: If not set, result ensembles with undefined bond stereochemistry are deleted datatype: boolean}
maxisomers: { value: -1 datatype: int}
Tcl script A_LABEL_STEREO B_LABEL_STEREO A_TYPE A_ELEMENT A_STEREOGENIC B_STEREOGENIC atomchange bondchange stereochange 3drelative atom bond e_stereoisomers.xpd
E_STEREOSET dataset
(switchable between diskfile dataset)
Set of stereoisomers and diastereomers (atom and/or bonds) of base compound
coupledbridgeheads: { value: 1 description: iif set, bridgehead atoms are coupled, only synchronous stereo flips allowed datatype: boolean}
filename: { value: {} description: Output file name (only used if datatype is set to diskfile) datatype: string constraints: writeable}
atomsubset: { value: {} description: if set to non-empty set, perform stereo flips only on listed atoms datatype: intvector}
bondsubset: { value: {} description: if set to non-empty set, perform stereo flips only on listed bonds datatype: intvector}
processatoms: { value: 1 description: if set, perform atom inversions datatype: boolean}
processbonds: { value: 0 description: if set, perform double bond flips datatype: boolean}
synthesizeatomstereo: { value: 0 description: if set, assign initial arbitary stereochemistry to stereogenic atoms if no descriptor set datatype: boolean}
synthesizebondstereo: { value: 0 description: if set, assign initial arbitary stereochemistry to stereogenic bonds if no descriptor set datatype: boolean}
nmax: { value: -1 description: maximum number of result structures datatype: int}
feedback: { value: 0 description: if set, print progress info datatype: boolean}
mincouplingringsize: { value: 9 description: minimum size of rings considered coupled via trhe bridgehead criterion datatype: int}
expectduplicates: { value: 1 description: if not set, any stereo duplicate generated is reported datatype: boolean}
Tcl script A_ELEMENT B_TYPE A_TYPE B_ORDER A_LABEL_STEREO B_FLAGS B_LABEL_STEREO atomchange bondchange stereochange merge hadd ring e_stereoset.xpd
E_STEREO_ATOMHASH_COUNT int Number of different stereospecific basic atom hash codes
(builtin) E_HASHGROUP_COUNT_AS atomchange bondchange merge
E_STEREO_COUNT intvector Stereo descriptor counts for atom and bond stereochemistry (potential/set/unset counts for both, as a vector with six elements)
apossible int
adefined int
aundefined int
bpossible int
bdefined int
bundefined int
Compiled C module M_STEREO_COUNT atomchange bondchange stereochange mod_e_stereo_count.so
E_STEREO_DEFINITION intpair Count separately number of set atom and bond stereo descriptors on stereogenic atoms and bonds, stored as an integer pair
(builtin) A_STEREOGENIC B_STEREOGENIC A_DL_STEREO A_CIP_STEREO A_LABEL_STEREO A_HASH_STEREO B_CIP_STEREO B_LABEL_STEREO B_CISTRANS_STEREO B_HASH_STEREO atomchange bondchange stereochange
E_STEREO_HASH128 uint128 Perturbed stereo-sensitive ensemble hashcode, extended to 128 bits
Compiled C module M_STEREO_HASHGROUP128 M_STEREO_HASH128 atomchange bondchange merge hadd mod_e_stereo_hash128.so
E_STEREO_MOLHASH_COUNT int Number of different stereospecific perturbed molecule hash codes
(builtin) E_HASHGROUP_COUNT_MS atomchange bondchange merge hadd
E_STEREO_STATUS byte
n,nostereo:u,undefined:p,partial:d,defined
Compiled C module M_STEREO_STATUS atomchange bondchange stereochange merge mol atom bond mod_e_stereo_status.so
E_STEREO_TAUTO_HASH uint64 Perturbed tautomer-agnostic ensemble stereo hashcode. Only stero infomation outside tautomer systems is used - bond and atom stereochemistry inside tauto systems is assumed to be lost in tautomerization.
maxtautomers: { value: 250 minvalue: 1 maxvalue: 9999 datatype: int}
loghandle: { value: {} description: Tcl molfile handle for writing a log generated structures datatype: string}
scramble: { value: 0 description: If set, scramble hashcodes to move them into new hashcode namespace datatype: int}
setcanonictautomer: { value: 0 description: If set, also set E_CANONIC_TAUTOMER property datatype: boolean}
usekekuleset: { value: 1 description: If set, start from Kekule set of initial structure datatype: boolean}
stereobondmalus: { value: 1 description: If set, downgrade tautomers with bond stereochemistry potential in tauto system datatype: boolean}
restrictedtransforms: { value: 0 description: If set, use smaller transform set datatype: boolean}
setcount: { value: 1 description: If set, also set E_TAUTOMER_COUNT datatype: boolean}
lockringpielectroncount: { value: 0 description: If set, allow only transform results where the pi electroin count of the rings is constant datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASHSY atomchange bondchange stereochange merge mod_e_stereo_tauto_hash.so
E_STEREO_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant ensemble stereo hashcode, 128 bit version
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_STEREO_HASH128 atomchange bondchange stereochange merge mod_e_stereo_tauto_hash128.so
E_STRUCTURE_VARIANTS dataset Generate variants of a structure by inserting or deleting CH2 groups, by substituting them with hetero atoms, or by moving functional groups.
addch2: { value: 1 description: If >0, add CH2 groups in weighted propotion datatype: int}
delch2: { value: 1 description: If >0, remove CH2 groups in weighted proportion datatype: int}
subch2: { value: 1 description: If >0, replace unsubstituted C by hetero atoms in weighted proportion datatype: int}
movegroups: { value: 2 description: If >0, move functional groups in weighted proportion datatype: int}
maxdistance: { value: 2 description: Maximum distance for moved functional groups datatype: int}
minringsize: { value: 4 description: No ring contraction below this size datatype: int}
maxringsize: { value: 8 description: No ring expansion beyond this size datatype: int}
alisubelements: { value: N O S datatype: string constraints: list}
arosubelements: { value: N datatype: string constraints: list}
seed: { value: 0 description: Pseudo-random generator seed datatype: int}
maxvariants: { value: 10 description: Maximum number of variants to generate datatype: int}
maxfailures: { value: 350 description: Maximum allowed number of serially failed attempts to generate new structure datatype: int}
chainmods: { value: 1 description: If set, allow chain modifications datatype: boolean}
ringmods: { value: 1 description: If set, allow ring modifications datatype: boolean}
addoriginal: { value: 0 description: If set, add original structure to set datatype: boolean}
Tcl script B_ISAROMATIC B_ORDER A_FG_SUBSTITUENTS A_FG_PARTICIPATION A_ARORING_COUNT B_RING_SIZE_BITS A_RING_SIZE_BITS atomchange bondchange 3dabsolute atom bond e_structure_variants.xpd
E_SUPRABANK_ID int Structure ID in Suprabank (suprabank.org)
Tcl script atomchange bondchange stereochange atom bond e_suprabank_id.xpd
E_SUPRABANK_URL url Display URL in Suprabank (suprabank.org)
Tcl script atomchange bondchange stereochange atom bond e_suprabank_url.xpd
E_SURECHEMBL_ID string Database ID of structure in the SureChEMBL database (www.surechembl.org)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_surechembl_id.xpd
E_SURECHEMBL_URL url Data display URL for structure in SureChEMBL database (www.surechembl.org)
Tcl script E_SURECHEMBL_ID atomchange bondchange stereochange atom bond e_surechembl_url.xpd
E_SVG_IMAGE diskfile
(switchable between string blob diskfile url xmlstring)
Ensemble image in SVG vector format
width: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int}
height: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 minvalue: 3 maxvalue: 25 datatype: double}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 minvalue: 0 maxvalue: 25 datatype: string}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: string}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
secondarycolor: { value: #00D000 datatype: color}
highlightbonds: { value: {} datatype: intvector}
secondxarybonds: { value: {} datatype: intvector}
highlightatoms: { value: {} datatype: intvector}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.2 datatype: double}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
bondannotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showlabel: { value: 0 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 1.8 datatype: double}
unit: { value: {} datatype: string}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
circleatoms: { value: {} datatype: intvector}
atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Helvetica datatype: string}
usewebfont: { value: 0 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
uselinecaps: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
standalone: { value: 1 datatype: boolean}
xmlheader: { value: 1 datatype: boolean}
id: { value: {} datatype: string}
title: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
showempty: { value: 0 datatype: boolean}
saverendercoordinates: { value: 0 datatype: boolean}
suppressedmols: { value: {} datatype: intvector}
framecolor: { value: black datatype: color}
rawcoordinates: { value: 0 datatype: boolean}
atomclick: { value: {} description: Javascript function to call, substitute %i id, %a atom label, %b bond label, %r ring label, %y ringsystem label datatype: string}
bondclick: { value: {} datatype: string}
ringclick: { value: {} datatype: string}
ringsystemclick: { value: {} datatype: string}
headerclick: { value: {} datatype: string}
footerclick: { value: {} datatype: string}
bgclick: { value: {} datatype: string}
ringclickcolor: { value: {} datatype: color constraints: emptycolor}
ringsystemclickcolor: { value: {} datatype: color constraints: emptycolor}
bondclickcolor: { value: {} datatype: color constraints: emptycolor}
ringhovercolor: { value: {} datatype: color constraints: emptycolor}
ringsystemhovercolor: { value: {} datatype: color constraints: emptycolor}
atomhovercolor: { value: {} datatype: color constraints: emptycolor}
bondhovercolor: { value: {} datatype: color constraints: emptycolor}
activehbonds: { value: 0 description: If set, undrawn bonds to H become active on hovering and are clickable if a bond click action has been set datatype: boolean}
style: { value: default description: General plot style. Can either be default, or patran for Patran-style atom and bond annotations enumeration: default:patran datatype: int}
maxannotationlength: { value: -1 description: Maximum character length of atom and bond annotations. If an annotation is longer, the plotted value is abbreviated, and a SVG title attribute with the full string added datatype: int}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
extrabondannotationproperty: { value: {} datatype: string constraints: property}
Compiled C module A_TYPE A_ELEMENT A_XY A_HSPECIAL A_CSPECIAL B_TYPE B_ORDER A_ANNOTATION B_ANNOTATION B_FLAGS A_FLAGS A_QUERY B_QUERY atomchange bondchange stereochange merge atom bond mod_e_svg_image.so
E_SYMMETRY string Molecular Point Group
A_XYZ atomchange bondchange stereochange hadd
E_SYNTHETIC_ACCESSIBILITY double Estimation of synthetic acessibility by the Ertl/Schuffenhauer algorithm Ertl, Schuffenhauer, J. Cheminf. 2009, 1:8
fragfile: { value: echash_toheavy_usebo.db datatype: diskfile constraints: readable}
defaultscore: { value: -6.047372 description: value to use if encountering an unknown sphere hash, corresponds to score of singleton in hash db datatype: double}
scale: { value: -0.801403346304195 description: experimental parameter to scale result between range 1(simplest) to 10(most complex) datatype: double}
offset: { value: 6.1171206468215455 description: experimental parameter to scale result between range 1(simplest) to 10(most complex) datatype: double}
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER A_EC_HASH atomchange bondchange atom bond e_synthetic_accessibility.xpd
E_SYNTHONIX_ID string
Tcl script E_CAS atomchange bondchange stereochange atom bond e_synthonix_id.xpd
E_SYNTHONIX_URL url
Tcl script E_SYNTHONIX_ID atomchange bondchange stereochange atom bond e_synthonix_url.xpd
E_T3DB_ID string Toxin and Toxin Target Database (T3DB) structure ID (http://www.t3db.ca)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_t3db_id.xpd
E_T3DB_URL url Toxin and Toxin Target Database (T3DB) structure display URL (http://www.t3db.ca)
Tcl script E_T3DB_ID atomchange bondchange stereochange atom bond e_t3db_url.xpd
E_TAUTOMER_COUNT int Number of tautomers found for compound
A_TYPE B_TYPE B_ORDER A_ELEMENT atomchange merge atom bond
E_TAUTOMER_NETWORK network The network of tautomers, with V_STRUCTURE nodes containing the structures and C_NAME indicating the transform which generated it
storeimages: { value: 0 description: If set, store an image of the structures in the nodes in property V_GRAPHICS datatype: boolean}
maxtautomers: { value: 1000 description: The maximum number of unique tautmer structures generated minvalue: 0 datatype: int}
usekekuleset: { value: 1 description: Whether to start with a Kekule form set (recommended) datatype: boolean}
restricted: { value: 0 description: Whether to use a restricted transform set datatype: boolean}
maxtransforms: { value: -1 description: If not negative, the maximum number of transforms to apply minvalue: -1 datatype: int}
preservegroups: { value: 0 description: Whether to preserve group information on the tautomers datatype: boolean}
imgparameters: { value: width 100 height 100 bgcolor grey80 atomcolor black bondcolor black format png frame 0 bonds 6 description: Image parameters datatype: dictionary}
transformfile: { value: {} description: If set, read transform set from specified file datatype: diskfile constraints: readable autodatapath}
Compiled C module atomchange bondchange atom bond mod_e_tautomer_network.so
E_TAUTOMER_SCORE int Scoring function for tautomers
stereobondmalus: { value: 1 description: If set, give malus to stereogenic bonds (which may appear stereochemically defined, but are not really) datatype: boolean}
explain: { value: 0 description: If set, print the score components datatype: boolean}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT B_ISAROMATIC R_TYPE R_AROMATIC A_FORMAL_CHARGE atomchange bondchange atom bond ring mod_e_tautomer_score.so
E_TAUTOSET dataset Set of structure tautomers generated by application of a standard set of tautomer SMIRKS transforms
maxtautomers: { value: 1000 description: Maximum number of tautomers to create datatype: int}
usekekuleset: { value: 1 description: Generate a Kekule set as first step, and then apply tuatomer transforms on this set datatype: boolean}
restricted: { value: 0 description: If set, use smaller set of transforms datatype: boolean}
nametransforms: { value: 0 description: If set, set E_NAME of result molecules to transform sequence datatype: boolean}
maxtransforms: { value: -1 description: Maximum number of transform applications datatype: int}
preservegroups: { value: 0 description: If set, lock ensemble group subobjects datatype: boolean}
sorted: { value: 0 description: If set, sort entries according to sortproperty parameter, using the hash code for tie breaking, with the top-rated structure first in the dataset datatype: boolean}
hashcode: { value: E_HASHY description: The hashcode to use for duplicate checks datatype: string constraints: property}
sortproperty: { value: E_TAUTOMER_SCORE description: The property to use for dataset element comparisons if the sort flag is set datatype: string constraints: property}
transformfile: { value: {} description: If set, read transform set from specified file datatype: diskfile constraints: readable autodatapath}
Compiled C module A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange merge atom bond mod_e_tautoset.so
E_TAUTO_HASH uint64 Perturbed tautomer-tolerant ensemble hashcode, independent of isotope labelling and stereochemistry
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
stereobondmalus: { value: 0 datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASHY atomchange bondchange merge mod_e_tauto_hash.so
E_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant ensemble hashcode, 128 bit version
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASH128 atomchange bondchange stereochange merge mod_e_tauto_hash128.so
E_TCM_TAIWAN_ID int Compound ID for TCL@Taiwan Traditional Chinese Medicine database (tcm.cmu.edu.tw)
Tcl script atomchange bondchange atom bond e_tcm_taiwan_id.xpd
E_TCM_TAIWAN_URL url URL for display of compound in TCL@Taiwan Traditional Chinese Medicine database (tcm.cmu.edu.tw)
Tcl script E_TCM_TAIWAN_ID atomchange bondchange atom bond e_tcm_taiwan_url.xpd
E_TEXT_ANNOTATION compound Annotation string for a structure drawing. It is one possiblöe type of the property-class data values of choice vector property E_ANNOTATION. This data is for example read from and written to CDX/CDXML files.
{} {} {} center:left:right center:top:bottom {} {} ^none:bold:italic:underline:outline:shadow:subscript:superscript:formula
coords floatpair
text stringvector
color color
align int
valign int
font string
fontsize float
style bitset
charset string
width double
height double
autosize boolean
autoresize boolean
autoalign boolean
preferredwidth double
A_XY never
E_TEX_IMAGE diskfile
(switchable between blob diskfile)
Structure drawing representation for the chemfig Tex macro packge (http://www.ctan.org/pkg/chemfig/) by Christian Tellechea
filename: { value: {} datatype: string constraints: writeable}
downloadfilename: { value: {} datatype: string}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
showstereo: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showcharge: { value: 1 datatype: boolean}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
showstereogroups: { value: 0 datatype: boolean}
footer: { value: {} datatype: string}
footerproperty: { value: {} datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
usesubscripts: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
wedges: { value: 1 datatype: boolean}
dashes: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
highlightgroups: { value: {} datatype: intvector}
eolchars: { value: {} description: Empty string is platform default datatype: string}
fulldocument: { value: 0 description: If set, create a complete minimal text document. By default. only include file is created datatype: boolean}
Compiled C module atomchange bondchange stereochange merge mol atom bond mod_e_tex_image.so
E_TGI compound TGI tumor screen data in the NCI cancer screening database
concunit shortstring
lcconc float
panel shortstring
cell string
panelnumber short
cellnumber short
nlog_tgi float
ntest_this short
ntest_max short
atomchange bondchange merge
E_TIMESTAMP datetime Timestamp
Tcl script atomchange bondchange stereochange merge e_timestamp.xpd
E_TITLE string Title string in free format
never
E_TOTAL_ENERGY float Measured or computed singlepoint energies
Tcl script E_ELECTRONIC_ENERGY E_REPULSION_ENERGY atomchange bondchange 3drelative 3dabsolute e_total_energy.xpd
E_TOTAL_SUBSTRUCTURE_COUNT int Total number of connected substructures in the molecule. This includes topological duplicates. By default, the snip path count from E_SMALLWORLD_NETWORK is used, not the real substructure count, which is usually not exactly the same.
usessmatch: { value: 0 description: If set, do explicit counted substructure matching instead of snap path counts datatype: boolean}
Compiled C module E_SMALLWORLD_NETWORK atomchange bondchange atom bond mod_e_total_substructure_count.so
E_TOTAL_WALK_COUNT double Sum of M_TOTAL_WALK_COUNT values J. Chem. Inf. Comput. Sci. 2000, 40, 99-106
Compiled C module M_TOTAL_WALK_COUNT atomchange bondchange mol atom bond mod_e_total_walk_count.so
E_TOXICOPHORE_COUNT intpair Count of toxicophores Kazius, McGuire, Bursi, J. Med. Chem. 2005, 48, 321-320
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange merge ring e_toxicophore_count.xpd
E_TPSA float Computed topological polar surface area P. Ertl, B. Rohde, P. Selzer, J. Med. Chem. 43, 3714-3717, 2000
usechemaxonextensions: { value: 1 datatype: boolean}
trace: { value: 0 datatype: boolean}
pentavalentnitrogroups: { value: 1 datatype: boolean}
Tcl script A_ELEMENT A_VB_NEIGHBOR_COUNT A_HCOUNT R_SIZE B_ISAROMATIC B_ORDER A_FORMAL_CHARGE B_ORDER B_ORDER atomchange bondchange hadd e_tpsa.xpd
E_TRAFO_ARO uint64 Hash code transformation (isolated aromatic core)
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_aro.xpd
E_TRAFO_AROCSKEL uint64 Hash code transformation - aromatic systems and carbon skeleton
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_arocskel.xpd
E_TRAFO_AROCSKEL_ALPHA uint64 Hash code transformation - aromatic systems plus carbon skeleton plus alpha atoms
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_arocskel_alpha.xpd
E_TRAFO_AROCSKEL_ALPHA_OXO uint64 Hash code transformation (C skeleton plus aromatic ring plus alpha atoms, then oxidation)
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE A_IUPAC_GROUP A_FREE_ELECTRONS atomchange bondchange merge atom bond e_trafo_arocskel_alpha_oxo.xpd
E_TRAFO_AROCSKEL_SUB uint64 Hash code transformation (aromatic and carbon skeleton, followed by generalization of substituents)
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_arocskel_sub.xpd
E_TRAFO_ARO_ALPHA uint64 Hash code transformation (aromatic system plus alpha atom, then h-addition)
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE E_CANONIC_TAUTOMER atomchange bondchange merge atom bond e_trafo_aro_alpha.xpd
E_TRAFO_ARO_ALPHA_OXO uint64 Hash code transformation - aromatic system and alpha atoms, followed by oxidation
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE A_IUPAC_GROUP E_CANONIC_TAUTOMER A_FREE_ELECTRONS atomchange bondchange merge atom bond e_trafo_aro_alpha_oxo.xpd
E_TRAFO_ARO_SUB uint64 Hash code transformation - aromatic system and generalized substituents
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_aro_sub.xpd
E_TRAFO_CSKEL uint64 Hash code transformation - isolate carbon skeleton
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_cskel.xpd
E_TRAFO_CSKEL_ALPHA uint64 Hash code transformation - carbon skeleton plus alpha atoms
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: string constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_cskel_alpha.xpd
E_TRAFO_CSKEL_ALPHA_OXO uint64 Hash code transformation - isolate carbon skeleton and alpha atoms, followed by oxidation
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_cskel_alpha_oxo.xpd
E_TRAFO_CSKEL_SUB uint64 Hash code transformation - isolate carbon skeleton and mark substitution points
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_cskel_sub.xpd
E_TRAFO_FRAME uint64 Hash code transformation: Isolate the framework, i.e. replace all non-H non-carbon atoms with carbon.
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_frame.xpd
E_TRAFO_OXIDATION uint64 Hash code transformation - standard oxidation
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_oxidation.xpd
E_TRAFO_REDUCTION uint64 Hash code transformation - standard reduction
log: { value: 0 datatype: string}
logfile: { value: trafolog.cbin datatype: string}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_reduction.xpd
E_TRAFO_RING uint64 Hash code transformation - isolate ring system
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ring.xpd
E_TRAFO_RINGCSKEL uint64 Hash code transformation - isolate rings and carbon skeleton
log: { value: 0 datatype: int}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ringcskel.xpd
E_TRAFO_RINGCSKEL_ALPHA uint64 Hash code transformation - rings and carbon skeleton and alpha atom
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ringcskel_alpha.xpd
E_TRAFO_RINGCSKEL_ALPHA_OXO uint64 Hash code transformation - isolate rings and carbon skeleton plus alpha atoms, then oxidize
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ringcskel_alpha_oxo.xpd
E_TRAFO_RINGCSKEL_SUB uint64 Hash code transformation- isolate ring and carbon skeleton, then mark substition points
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ringcskel_sub.xpd
E_TRAFO_RING_ALPHA uint64 Hash code transformation - isolate ring system and alpha atoms
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ring_alpha.xpd
E_TRAFO_RING_ALPHA_OXO uint64 Hash code transformation - isolate ring syetem and alpha atoms, then oxidation
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ring_alpha_oxo.xpd
E_TRAFO_RING_SUB uint64 Hash code transformation - isolate ring system with generalized substituent site markers
log: { value: 0 datatype: boolean}
logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable}
Tcl script A_ELEMENT B_TYPE B_ORDER A_TYPE atomchange bondchange merge atom bond e_trafo_ring_sub.xpd
E_U3D_MODEL diskfile 3D structure model in Intel U3D format, converted from the IDTF representation (E_IDTF_MODEL). This is used for inclusion of interactive 3D PDF file (property E_PDF3D_IMAGE)
filename: { value: {} datatype: diskfile constraints: writeable}
debug: { value: 0 datatype: boolean}
excludenormals: { value: 0 datatype: boolean}
removezerofaces: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: diskfile}
checklibs: { value: 0 datatype: boolean}
Compiled C module E_IDTF_MODEL atomchange bondchange stereochange merge 3drelative 3dabsolute hadd mod_e_u3d_model.so
E_UNICHEM_URL url EBI Unichem link page for the structure (www.ebi.ac.uk)
Tcl script E_STDINCHIKEY atomchange bondchange atom bond e_unichem_url.xpd
E_UNII stringvector FDA Unique Ingredient Identifier (UNII)
Tcl script E_CID atomchange bondchange stereochange atom bond e_unii.xpd
E_UNIPROT_URL url Data display URL in Uniprot database (www.uniprot.org)
Tcl script E_CHEBI_ID atomchange bondchange stereochange atom bond e_uniprot_url.xpd
E_UNIQUE_SUBSTRUCTURE_COUNT int Unqiue number of connected substructures in the molecule. This includes duplicates - e.g. butane has one butane, one propane, one ethane and one methane substructures.
Compiled C module E_SMALLWORLD_NETWORK atomchange bondchange atom bond mod_e_unique_substructure_count.so
E_UNIT_CELL floatvector Crystallographic unit cell., in a/b/c/alpha/beta/gamma sequence. Used in the CIF file format I/O module.
a float
b float
c float
alpha float
beta float
gamma float
atomchange bondchange stereochange merge 3drelative 3dabsolute
E_UNSPECIFIED_AIDSET intvector Set of PubChem assay IDs testing this compound as unspecified
Tcl script E_CID atomchange bondchange stereochange e_unspecified_aidset.xpd
E_URL url URL of molecular data file
never
E_UUUTS_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: uuuTS datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
forcemagic: { value: 0 datatype: string}
useisotope: { value: 0 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_UUUTS_STRUCTURE datatype: string}
secondarytag: { value: 01-xx datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 0 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
csbasehash: { value: E_HASHSY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_uuuts_id.xpd
E_UUUTS_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_UUUTU_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: uuuTu datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
forcemagic: { value: 0 datatype: string}
useisotope: { value: 0 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_UUUTU_STRUCTURE datatype: string}
secondarytag: { value: 01-xx datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 0 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
csbasehash: { value: E_HASHY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_uuutu_id.xpd
E_UUUTU_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_UUUUS_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: uuuuS datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
forcemagic: { value: 0 datatype: string}
useisotope: { value: 0 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_UUUUS_STRUCTURE datatype: string}
secondarytag: { value: 01-xx datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 1 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
csbasehash: { value: E_HASHSY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_uuuus_id.xpd
E_UUUUS_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_UUUUU_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: uuuuu datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
forcemagic: { value: 0 datatype: string}
useisotope: { value: 0 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_UUUUU_STRUCTURE datatype: string}
secondarytag: { value: 01-xx datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 1 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
csbasehash: { value: E_HASHY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_uuuuu_id.xpd
E_UUUUU_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_UUUXX_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: uuuxx datatype: string}
scope: { value: private datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
forcemagic: { value: 0 datatype: string}
useisotope: { value: 0 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_UUUXX_STRUCTURE datatype: string}
secondarytag: { value: 01-xx datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 0 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
csbasehash: { value: E_HASHY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_uuuxx_id.xpd
E_UUUXX_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_UVSPECTRUM compound UV/Vis spectrum, usually read from JCAMP files. This property is also computable via a look-up in the NIST WebBook.
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum floatvector
Tcl script atomchange bondchange e_uvspectrum.xpd
E_UVSPECTRUM_IMAGE diskfile
(switchable between string blob diskfile url)
UV/Vis spectrum rendering
height: { value: 250 datatype: int}
width: { value: 500 datatype: int}
bgcolor: { value: white datatype: color}
title: { value: {} datatype: string}
filename: { value: {} datatype: string constraints: writeable}
format: { value: gif enumeration: gif:png,png24:png8 datatype: string}
titlecolor: { value: black datatype: color}
framecolor: { value: black datatype: color}
signalcolor: { value: #DD0000 datatype: color}
Tcl script E_UVSPECTRUM atomchange bondchange merge mol e_uvspectrum_image.xpd
E_VEBER_BIOAVAILABILITY_FLAG boolean Veber bioavailability flag (E_TPSA<=140 && E_NROTBONDS<=10) Journal of Medicinal Chemistry, Vol. 45, pp. 2615-2623, 2002
Compiled C module E_NROTBONDS E_TPSA atomchange bondchange atom bond mod_e_veber_bioavailability_flag.so
E_VIBRATION_VRML diskfile VRML scene of the normal vibrations of the molecule(s)
vibscale: { value: 0.5 datatype: string}
index: { value: 0 datatype: string}
filename: { value: {} datatype: string}
nframes: { value: 10 datatype: string}
stdinterval: { value: 1.0 datatype: string}
bcolor: { value: white datatype: string}
usebo: { value: 1 datatype: string}
step: { value: 0 datatype: string}
usefreq: { value: 0 datatype: string}
Tcl script A_XYZ A_ELEMENT A_TYPE B_TYPE B_ORDER A_NORMAL_VIBRATIONS atomchange bondchange stereochange merge 3dabsolute e_vibration_vrml.xpd
E_VRML diskfile
(switchable between blob diskfile url)
VRML scene of molecular ensemble
style: { value: ballstick enumeration: ballstick:capped:wireframe:spacefill:all datatype: string}
vdwscaling: { value: 25 datatype: double}
bondcolor: { value: atomsplit datatype: string}
bondradius: { value: 15 datatype: double}
annotationsize: { value: 15 datatype: double}
labelsize: { value: 15 datatype: double}
showlabel: { value: 0 datatype: boolean}
labelcolor: { value: purple datatype: color}
annotationcolor: { value: cyan datatype: color}
annotationproperty: { value: A_SHIELDING datatype: string constraints: property}
showbondorder: { value: 0 datatype: boolean}
showproperty: { value: 0 datatype: boolean}
useabsolute: { value: 0 datatype: boolean}
suppress: { value: none enumeration: none:neg:neg0:pos:pos0:zero:nonzero:all datatype: string}
nicsgrid: { value: 0 datatype: boolean}
colorcode: { value: 0 datatype: boolean}
positivecolor: { value: red datatype: color}
neutralcolor: { value: white datatype: color}
negativecolor: { value: green datatype: color}
transform: { value: none enumeration: none:log:loglog:root2:root3:pow2:pow3 datatype: string}
mincubesize: { value: 4 datatype: double}
maxcubesize: { value: 40 datatype: double}
glossfactor: { value: 75 datatype: double}
scaling: { value: auto datatype: string}
transparency: { value: 0 datatype: double}
structure: { value: 0 datatype: boolean}
filename: { value: {} datatype: string constraints: writeable}
geometry: { value: 0 datatype: boolean}
atomhighlightcolor: { value: red datatype: color}
highlightatoms: { value: {} datatype: intvector}
bondhighlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
animation: { value: 0 datatype: boolean}
cycletime: { value: 1 datatype: double}
playoption: { value: 0 datatype: boolean}
httpheader: { value: 0 datatype: int}
ignoreh: { value: 0 datatype: boolean}
setviewpoint: { value: 1 datatype: boolean}
downloadfilename: { value: {} datatype: string}
Compiled C module A_XYZ A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange merge mod_e_vrml.so
E_WEB_STRUCTURE_QUERY_URL url Perform various structure queries on Internet databases and return a URL which can be used to display the results. Depending on the database contacted, this URL may either just display results, with the query already having been executed, or perform the actual query without prior job submission.
database: { value: pcstructure enumeration: pcstructure:pcsubstance:chebi:hmdb:chembl:chemspider datatype: string}
querytype: { value: fullstructure enumeration: fullstructure,fs:identity,id:substructure,ss,sub:superstructure,su,super:similarity,sim:formula,form,frm datatype: int}
trace: { value: 0 datatype: boolean}
threshold: { value: 95 description: Minimum required similarity value in percent datatype: int}
stereomode: { value: absolute enumeration: ignore:absolute:relative:nonconflicting datatype: int}
isotopemode: { value: ignore enumeration: ignore:isotope datatype: int}
tautomode: { value: ignore enumeration: ignore:tautomer datatype: int}
maxhits: { value: 500 minvalue: -1 maxvalue: 999999 datatype: int}
maxurllength: { value: 2048 minvalue: -1 maxvalue: 999999 datatype: int}
Tcl script atomchange bondchange atom bond e_web_structure_query_url.xpd
E_WEIGHT float Molecular weight of ensemble
allisotopes: { value: 0 datatype: string}
useimplicith: { value: 1 datatype: string}
(builtin) A_WEIGHT atomchange merge
E_WIKIPEDIA_CHEMBOX diskfile
(switchable between string blob diskfile)
Text to use by editors in Wikipedia chembox, as defined in http://en.wikipedia.org/wiki/Template:Chembox
trycas: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
verifycas: { value: 1 datatype: boolean}
threaded: { value: 0 description: If set, computed with multiple threads datatype: boolean}
Tcl script E_CID E_CHEMSPIDER_ID E_DRUGBANK_ID E_CHEBI_ID E_EINECS_ID E_UNII E_EC_NUMBER E_RTECS_NUMBER E_IUPHAR_ID E_CHEMBL_ID atomchange bondchange stereochange merge hadd e_wikipedia_chembox.xpd
E_WIKIPEDIA_DRUGBOX diskfile
(switchable between string blob diskfile)
Text suitable for use by editors in Wikipedia drugbox template, pre-filled with standard attributes computed by Internet lookup
filename: { value: {} datatype: diskfile constraints: writeable}
threaded: { value: 0 datatype: boolean}
trycas: { value: 1 datatype: boolean}
verifycas: { value: 1 datatype: boolean}
Tcl script E_IUPAC_PREFERRED_NAME E_CID E_CHEMSPIDER_ID E_DRUGBANK_ID E_CHEBI_ID E_CAS E_CHEMBL_ID E_IUPHAR_ID E_UNII atomchange bondchange stereochange merge hadd e_wikipedia_drugbox.xpd
E_WIKIPEDIA_URL url Wikipedia compound id URL. Lookup is performed by CAS number, PubChem CID, InChI, StdInChI in that order
language: { value: en enumeration: en:de:es:fr:ru:ja comment: language set selected to contain reasonable chemistry content, e.g. a pyrdine entry datatype: string}
trycas: { value: 1 datatype: string}
trycid: { value: 1 datatype: string}
tryinchi: { value: 1 datatype: string}
trystdinchi: { value: 1 datatype: string}
trycomputedcas: { value: 0 datatype: string}
Tcl script E_CID E_CAS E_INCHI E_STDINCHI atomchange bondchange stereochange merge e_wikipedia_url.xpd
E_WILEY_URL url URL to display references in Wiley/VCH literature (www.compoundsearch.com)
Tcl script E_STDINCHIKEY atomchange bondchange atom bond e_wiley_url.xpd
E_WLN_STRING string Wisswesser Line Notation structure representation. The computation function only identifies a WLN string in the names in E_NAMESET (which ususally comes from the NCI resolver). It.does not algorithmically compute the name.
Tcl script E_NAMESET atomchange bondchange stereochange merge atom bond e_wln_string.xpd
E_WOLFRAMALPHA_URL url Link into the WolframAlpha database (wolframalpha.com)
Tcl script atomchange bondchange atom bond e_wolframalpha_url.xpd
E_WOODHEAD_FRAGMENTLIKENESS_VIOLATIONS byte This is a stricter verion of E_JHOTI_FRAGMENTLIKENESS_VIOLATIONS Congreve, Chessari, Tisi, Woodhead, J. Med. Chem. 2008, 51, 3661
Tcl script E_WEIGHT E_NHDONORS E_NHACCEPTORS E_XLOGP2 E_NROTBONDS E_TPSA atomchange bondchange atom bond e_woodhead_fragmentlikeness_violations.xpd
E_XLOGP float Calculating the XLOGP value according to the algorithm published in R. Wang, Y. Fu, L.Lai J. Chem. Inf. Comput. Sci. 37, 1997, 615-621 R. Wang, Y. Fu, L.Lai J. Chem. Inf. Comput. Sci. 37, 1997, 615-621
Tcl script A_ELEMENT A_TYPE atomchange bondchange e_xlogp.xpd
E_XLOGP2 float Calculating the XLOGP value (version 2) R. Wang, Y. Gao, L. Lai, Persp. Drug Disc. Design 19, 2000, 47-66
logcomputation: { value: 0 datatype: boolean}
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange e_xlogp2.xpd
E_XSCREEN bitvector Extended path-based screening bit set. Superceded by E_QUERY_SCREEN.
length: { value: 1024 datatype: int}
space: { value: 4096 datatype: int}
depth: { value: 3 datatype: int}
nohdepth: { value: 1 datatype: int}
tauto: { value: 0 datatype: boolean}
usech: { value: 1 datatype: boolean}
nobranchdepth: { value: 3 datatype: int}
traceatom: { value: -1 datatype: int}
tracebit: { value: -1 datatype: int}
maxatoms: { value: 8 datatype: int}
tracefile: { value: {} datatype: diskfile constraints: writeable}
maxfork: { value: 3 datatype: int}
maxnfork: { value: 2 datatype: int}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange atom bond mod_e_xscreen.so
E_XYEXTENT floatvector 2D display coordinate bounding box
xmin double
xmax double
ymin double
ymax double
(builtin) A_XY A_FLAGS atomchange merge hadd
E_XYZEXTENT floatvector 3D coordinate bounding box
xmin double
xmax double
ymin double
ymax double
zmin double
zmax double
coordinateproperty: { value: A_XYZ datatype: string}
(builtin) A_XYZ atomchange merge 3drelative 3dabsolute hadd
E_YEAST_SCREEN compound NCI yeast screen data (used as a field in the NCI database browser)
concentration float
strain string
diff_inhibit float
avg_inhibit float
atomchange bondchange merge
E_YMDB_ID string Yeast metabolome structure ID (http://www.ymdb.ca)
Tcl script atomchange bondchange stereochange atom bond e_ymdb_id.xpd
E_YMDB_URL url Yeast metabolome structure display URL (http://www.ymdb.ca)
Tcl script E_YMDB_ID atomchange bondchange stereochange atom bond e_ymdb_url.xpd
E_ZEROPOINT_ENERGY float Computed zeropoint energy. This can be indireclty obtained via E_HEAT_OF_FORMATION with a VAMP computation in the standard set-up.
A_XYZ atomchange bondchange 3dabsolute
E_ZINC_ID string zinc.docking.org ID
Tcl script E_STDINCHI atomchange bondchange stereochange merge e_zinc_id.xpd
E_ZINC_URL url zinc.docking.org URL
Tcl script E_ZINC_ID atomchange bondchange stereochange merge e_zinc_url.xpd
E_ZMATRIX compoundvector Z matrix of structure. This is for example used in the I/O modules for Gaussian Archive, Mopac Input and Ouptut. and Gaussian Input.
distance double
angle double
torsion double
atom1 int
atom2 int
atom3 int
atomchange bondchange stereochange merge 3drelative 3dabsolute shuffle hadd
F_AUTHOR compound Structure or reaction file author data, computation copies these from the internal object author fields
name string
author string
email string
phone string
orcid string
authorurl url
date date
version string
affiliation string
affiliationurl url
affiliationduns string
doi string
infourl url
street string
city string
zip string
state string
country string
literature string
keywords string
comment string
license string
licenseurl url
category string
repopath string
baseuuid string
versionuuid string
Tcl script never f_author.xpd
F_AVERAGE_ATOM_COUNT double Average atom count of compounds in file
Tcl script never f_average_atom_count.xpd
F_AVERAGE_RING_COUNT double Average ESSSR ring count of compounds in file
Tcl script never f_average_ring_count.xpd
F_AVERAGE_WEIGHT double Average molecular weight of compounds in file
Tcl script never f_average_weight.xpd
F_COMMENT string Free comment attached to file
never
F_DATE date File creation date
atomchange bondchange atom bond
F_DIVERSITY_SET dataset Select a diverse subset from the source dataset.
property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property}
query: { value: all description: Structure filter query expression datatype: string}
feedback: { value: 0 description: Output a dot to stderr for every n structures added to the set - 0 for no feedback datatype: int}
size: { value: 50 description: Target size minvalue: 1 datatype: int}
startindex: { value: -1 description: First structure source index, -1 is random. This is an index into the eligible records, not directly a file record number. datatype: int}
minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int}
Tcl script atomchange bondchange atom bond f_diversity_set.xpd
F_GAUSSIAN_JOB_PARAMS compound Parameters for a Gaussian job. These are intergrated into the output of structure files in Gaussian Input file format, and filled when reading Gaussian input structure files.
link0 stringvector
route stringvector
title stringvector
charge_spin intpair
redundant stringvector
never
F_IDENT string Ident string of structure file
Tcl script atomchange bondchange atom bond f_ident.xpd
F_MARVIN typeddictionary Marvin GUI Props
never
F_QUERY compound Statistics on last query executed on the file. Set by "molfile scan" command.
ens,structure:enslist,elist,structures:record,rec:recordlist,reclist:bitvector,bit:count,cnt:delete,del:property,prop:propertylist,proplist:file,molfile:filelist:table,qtable,hitlist:reaction:reactionlist,xlist,reactions:array,tclarray,pythonarray:vrecord,vrec:vrecordlist,vreclist:custom:customlist:ensblob:reactionblob:exists:tablecollection:vertex:vertexlist:row,index:rowlist,indexlist
mode int
query string
retrieve string
timeout int
maxhits int
date datetime
startpos int
endpos int
nhits int
nexamined int
querytime int
eof boolean
comment string
displayquery string
never
F_QUERY_GIF diskfile
(switchable between string blob diskfile url)
Depiction of last query executed on file
width: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int}
height: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int}
bgcolor: { value: transparent datatype: color}
suppressnodes: { value: E_LIVE_IN_ENTREZ datatype: string}
frame: { value: 0 datatype: int}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int}
crop: { value: 2 minvalue: -1 datatype: int}
format: { value: gif datatype: string}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
fixiepngsize: { value: 1 datatype: boolean}
molimgwidth: { value: 75 minvalue: 25 maxvalue: 500 datatype: int}
molimgheight: { value: 75 minvalue: 25 maxvalue: 500 datatype: int}
font: { value: arialn datatype: string}
fontsize: { value: 8 datatype: string}
interlace: { value: 1 datatype: string}
suppressedproperties: { value: {} datatype: string constraints: propertylist}
downloadfilename: { value: {} datatype: string}
Compiled C module F_QUERY never mod_f_query_gif.so
F_SCAFFOLD_TABLE table A list of Ertl-type scaffolds extracted from a file. The table contains the counts and SMILES strings as columns, plus row-attached structures.
maxrecs: { value: -1 description: The maximum number of records to process, -1 is infinite datatype: int}
maxscaffolds: { value: -1 description: The maximum number of scaffolds to record, -1 is infinite datatype: int}
maxsimplification: { value: 1 description: The maximum number of scaffolds simplification steps to perform, -1 is infinite datatype: int}
compoundfilter: { value: all description: A compound filter expression (see 'ens scan' command) scaffolds must match datatype: string}
Tcl script E_SMILES E_SCAFFOLD_TREE_STRUCTURE atomchange bondchange stereochange atom bond f_scaffold_table.xpd
F_SCAFFOLD_TREE datatree The scaffolds of the structures in the dataset in sorted, hierarchical order. The first node a an empty root node, and its children are the irreducible scaffolds. The individual scaffold nodes of the tree contain SMILES strings as value and the (non-stereo/non-isotope) ensemble hashcode as name, followed by all more complex scaffolds which are reduced to the current scaffold by one simplification step.
maxlevel: { value: -1 description: Maximum tree depth to generate, -1 for unlimited datatype: int}
includeoriginals: { value: 0 description: If set, include the base structures. By default, only the scaffolds are included datatype: boolean}
hashcode: { value: E_HASHY description: The hashcode property to be used to check structure identity datatype: string constraints: property}
nodenameproperty: { value: E_HASHY description: Instance values of this property are stored as node names. datatype: string constraints: property}
auxproperties: { value: {} description: Instance data of these properties is appended to the right of the SMILES data in the nodes datatype: string constraints: propertylist}
Tcl script atomchange bondchange atom bond f_scaffold_tree.xpd
F_TREE_DATA_GIF diskfile
(switchable between string blob diskfile url)
Rendering of tree-style property data (must be of property datatype "datatree") as a GIF/PNG image using a modified Reingold-Tilford tree layout algorithm.
property: { value: F_SCAFFOLD_TREE description: Property to read rendered data from datatype: string constraints: property}
treeindex: { value: 0 datatype: string}
maxlevel: { value: -1 datatype: int}
boxwidth: { value: 100 datatype: int}
boxheight: { value: 100 datatype: int}
treedistance: { value: 10 description: Minimum horizontal distance between boxes on a level which do not have the same parent datatype: int}
siblingdistance: { value: 5 description: Minimum horizontal distance between boxes on a level which do have the same parent datatype: int}
leveldistance: { value: 25 description: Distance between lower box Y of parent level and upper box Y of child level datatype: int}
border: { value: 5 description: Unused pixels around tree datatype: int}
decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean}
showname: { value: 0 description: If set, include the node name in rendering datatype: boolean}
showcount: { value: 0 description: If set, include non-negative count node fields in rendering datatype: boolean}
interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean}
alignstructures: { value: 1 description: If structures are rendered, align them hierarchically datatype: boolean}
excluderoot: { value: 0 description: If set, do not render root node datatype: boolean}
framewidth: { value: 0 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
linecolor: { value: red datatype: color}
boxframecolor: { value: blue datatype: color}
boxbgcolor: { value: grey90 datatype: color}
format: { value: png enumeration: gif:png,png24:png8 datatype: string}
font: { value: arialn datatype: string}
fontsize: { value: 8.0 datatype: double}
filename: { value: {} description: Output file name, if data type is diskfile. If empty, generate /tmp file datatype: diskfile constraints: writeable}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
Compiled C module atomchange bondchange atom bond mod_f_tree_data_gif.so
F_VECTOR_SUM intvector
property: { value: E_SCREEN datatype: string constraints: property}
filter: { value: all datatype: string}
Compiled C module atomchange bondchange atom bond mod_f_vector_sum.so
G_AROMATIC short Group aromaticity status, indicating whether none, some or all atoms in the group are aromatic.
no,none:some,partially:full,all
Compiled C module B_ISAROMATIC B_TYPE atomchange bondchange groupchange atom bond ring group mod_g_aromatic.so
G_ATOMS intvector Atoms in each group, extracted as labels from the internal group object. Group objects which are not atoms are skipped.
Compiled C module G_TYPE A_LABEL atomchange bondchange groupchange atom bond group mod_g_atoms.so
G_AUTODOCK4_BRANCH compound Autodock 4 torsion branch data. Used by the Autodock PDBQT file I/O module. This property is also computable from general geometric principles.
level int
linkatom1 int
linkatom2 int
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT B_ROTATABILITY A_AUTODOCK4_TYPE atomchange bondchange groupchange merge atom bond ring group mod_g_autodock4_branch.so
G_BGCOLOR color If set to a real color, use it is as background rendered square behind the group atoms
never
G_BONDS intvector Labels of bonds linking atoms within the group, or explicit group bond set, if the group has bond elements. Impplicit bonds are the same as containment bonds in MDL nomenclature
filters: { value: {} description: Set of filters the returned bonds need to pass datatype: string constraints: filterlist}
Tcl script B_LABEL atomchange bondchange atom bond group
G_CONSTRAINT compound Constraints for 3D searching, mirroring the MDL 3D query standards
none:point_distance,distance:point_angle,angle:point_torsion,torsion:centroid:sphere:linepoint_abs,linepoint_absolute:linepoint_rel,linepoint_relative:plane:line:point_line_distance:point_plane_distance:line_line_angle:plane_plane_angle:linepoint_vector:line_from_plane:plane_from_line
type int
range floatpair
name string
color string
comment string
flag boolean
alist intvector
never
G_ELEMENT_COUNT shortvector Count of element types of atoms of group
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
Compiled C module A_ELEMENT A_TYPE atomchange groupchange merge hadd group mod_g_element_count.so
G_FG_COUNT shortvector Count of functional groups in group
^cf:cx:ccdb:cctb
groupindex: { value: -1 datatype: int}
add_h_on_c: { value: 0 datatype: boolean}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange groupchange group mod_g_fg_count.so
G_FORMAL_CHARGE short Sum of the formal atom charges in the group
Compiled C module A_TYPE A_FORMAL_CHARGE atomchange groupchange atom group mod_g_formal_charge.so
G_FORMULA string Elemental formula of the group
usecharges: { value: 0 datatype: boolean}
format: { value: ascii enumeration: ascii:html datatype: int}
useimplicith: { value: 0 datatype: boolean}
usequeryatoms: { value: 0 datatype: boolean}
Compiled C module G_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_QUERY A_ISOTOPE A_FORMAL_CHARGE atomchange groupchange atom group mod_g_formula.so
G_HACCEPTOR_COUNT int Number hydrogen acceptors in group
Tcl script A_HYDROGEN_BONDING atomchange bondchange groupchange group g_hacceptor_count.xpd
G_HASHGROUP_COUNT intvector Group-oriented population of basic atom hash groups
Compiled C module A_EXTENDED_GROUPHASH A_GROUP_NUMBER atomchange bondchange groupchange merge hadd group mod_g_hashgroup_count.so
G_HASHY uint64 Perturbed group hashcode
usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
Compiled C module atomchange bondchange groupchange hadd group mod_g_hashy.so
G_HDONORS_COUNT int Number of hydrogen donors in group
Tcl script A_HYDROGEN_BONDING atomchange bondchange groupchange group g_hdonor_count.xpd
G_LABEL int Arbitrary group label
(builtin) never
G_MOL_NUMBER short Number of molecule (A_MOL_NUMBER) group belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge group
G_NAME string Name of a group
never
G_PI_ELECTRON_COUNT short Number of pi electrons in group
Compiled C module A_FREE_ELECTRONS A_TYPE B_TYPE B_ORDER B_ISAROMATIC ring mod_g_pi_electron_count.so
G_QUERY compound Query attributes for matched substructure groups
^none:aromatic,fullyaromatic:aliphatic,fullyaromatic:saturated:unsaturated,insaturated:carbocyclic:heterocyclic:monocyclic:polycyclic:mixed,mixedaromaticaliphatic:partiallyaromatic:partiallyaliphatic:topoequivalent,fullytopoequivalent:topodistinct,fullytopodistinct:mixedtopoequivalent:partiallytopoequivalent:partiallytopodistinct
flags bitset
formula formulamatch
substituentcount bitset
valencecount bitset
neighborcount bitset
hydrogencount bitset
heterosubstituentcount bitset
ringbondcount bitset
pielectroncount bitset
query querytree
alphaformula formulamatch
topodistance bitset
atomchange bondchange atom bond
G_RING_COUNT int Number of ESSR rings intersecting with group atoms
Tcl script R_TYPE bondchange groupchange ring group g_ring_count.xpd
G_SGROUP compound MDL SGroup Data
none,non:superatom,sup:multigroup,mul:sru:monomer,mon:mer:copolymer,cop:crosslink,cro:modification,mod:graft,gra:component,com:mixture,mix:formulation,for:datagroup,dat:anypolymer,any:generic,gen:stereo,ste:query,que:match,mat:fgroup,fg none:alt:ran:blo none:hh:ht:eu {} {} {} {} {} F:N:T
type int
subtype int
connectivity int
label int
text string
bracket1 xyvector
bracket2 xyvector
name string
fieldtype int
units string
data stringvector
coords floatpair
class string
minmultiplier int
maxmultiplier int
Compiled C module never mod_g_sgroup.so
G_SIZE int Size of groups, measured in number of objects in each group. There is no discrimination between atoms, bonds or groups as objects in the count.
Compiled C module groupchange group mod_g_size.so
G_STANDARD_GROUP_NAME string Detection of functional groups and abbreviated strings
groupsubstructures: { value: {C(=O)[OH] COOH} {[NH2] NH2} {N([CH3])[CH3] NMe2} {N([CH2][CH3])[CH2][CH3] NEt2} {C(=O)O[CH2][CH3] COOEt} {C(=O)O[CH3] COOMe} {N(=O)O NO2} {S(=O)(=O)[OH] SO3H} {S(=O)(=O)O[Na] SO3Na} {O[CH2][CH3] OEt} {[CH]=O CHO} {O[CH2][CH2][CH3] OPr} {O[CH]([CH3])[CH3] OiPr} {[OH] OH} {C#N CN} {[Si]([CH3])([CH3])[CH3] TMS} datatype: string}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange groupchange hadd ring group g_standard_group_name.xpd
G_SURFACEINFO compound Data on surface sections, as read from files in the the IFF/RIFF/VEGA file formats
{} {} dotted:mesh:solid {} {} ^visible:alpha
id int
name string
type int
alpha int
dotsize int
flags bitset
never
G_TITRATION byte Create an atom group set which describes standard functional groups as protonable or deprotonable.
deprotonation=-1:neutral=0:protonation=1
deprotfgs: { value: [H]O[S,P,Se,Te,As,Sb,Cl,Br,I](=O) [H]OC=O [H]O[C;a] [H]C(C=O)C=O [H]OC=CC=O description: Standard SMARTS substructures of groups which can be deprotonated datatype: string}
protfgs: { value: [N;A;+0;!$(N-C=O);!$(N=O)] description: Standard SMARTS substructures of groups which can be protonated datatype: string}
Tcl script atomchange bondchange groupchange merge hadd atom bond group g_titration.xpd
G_TOPO_EQUIVALENCE short Group topological equivalence status, indicating whether none, some or all atoms in the group are in the same topological class, as defined by an atom hashcode
no,none:some,partially:full,all
topoproperty: { value: A_ISOTOPE_STEREO_HASH description: Atom property used to determined topological atom class datatype: string constraints: property}
Compiled C module A_ISOTOPE_STEREO_HASH atomchange bondchange stereochange groupchange atom bond ring group mod_g_topo_equivalence.so
G_TYPE int Group classifiction, following the MDL Molfile convention.

Computation is performed indirectly via G_SGROUP, which contains the same information has first element in compound datastructure.
none,non:superatom,sup:multigroup,mul:sru:monomer,mon:mer:copolymer,cop:crosslink,cro:modification,mod:graft,gra:component,com:mixture,mix:formulation,for:datagroup,dat:anypolymer,any:generic,gen:stereo,ste:query,que:match,mat:fgroup,fg
never
G_XBONDS intvector Labels of bonds linking group atoms to non-group atoms (crossing bonds in MDL nomenclature)
filters: { value: {} description: Filter set the returned bonds must pass datatype: string constraints: filterlist}
Tcl script B_LABEL atomchange bondchange groupchange group
G_XYEXTENT floatvector Bounding box of group elements, computed from A_XY
Compiled C module A_XY A_FLAGS groupchange merge group mod_g_xyextent.so
G_XYZ floatvector Group 3D coordinates (may be planes, vectors)
(builtin) A_XYZ atomchange bondchange merge 3drelative 3dabsolute group
H_IDENT string Free-form ID of the hierarchy
Tcl script never h_ident.xpd
H_LEVEL short Level of the hierarchy object within a hierarchy. The hierarchy root is level 0.
Compiled C module never mod_h_level.so
H_NAME string Free-form name of the hierarchy
never
I_ID compound Bioitem (biologics component) item class (class identifier and element number or index into superatom or fragment table)
undefined=-1:none:element,atom:fragment,biofragment:superatom
class int
fragmentid int
never
I_LABEL int Bioitem (biologics component) label
Compiled C module never mod_i_label.so
I_SYMBOL shortstring Bioitem (biologics component) item symbol (i.e. amino acid abbreviation, superatom symbol, element symbol, etc.)
Compiled C module never mod_i_symbol.so
J_LABEL int Biolink (biologics component join) label
Compiled C module never mod_j_label.so
J_LINK compound Biolink (biologics component join) item link data
undefined=-1:none:simple:amide:disulfide:ester:ether
bondclass int
label1 int
label2 int
bondtype int
order short
never
K_LABEL int Arbitrary label for bond angle objects
(builtin) never
K_MOL_NUMBER short Number of molecule (A_MOL_NUMBER) bondangle object belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge bondangle
L_1DPATTERN_SVG_IMAGE diskfile
(switchable between string blob diskfile url xmlstring)
SVG depiction of the 1D patterns applicable to the currently loaded transform
boxwidth: { value: 250 datatype: int}
boxheight: { value: 250 datatype: int}
Tcl script E_SVG_IMAGE never l_1dpattern_svg_image.xpd
L_2DPATTERN_SVG_IMAGE diskfile
(switchable between string blob diskfile url xmlstring)
SVG depiction of the 2D patterns applicable to the currently loaded transform
boxwidth: { value: 250 datatype: int}
boxheight: { value: 250 datatype: int}
Tcl script E_SVG_IMAGE never l_2dpattern_svg_image.xpd
L_CODE_COVERAGE intpairvector Accumulated bytecode execution coverage, as a per-line (accumulated across libraries) integer pair vector. First element value 0: Not executed, 2: executed, 1: partially executed, i.e. there are multiple bytecodes generated from a single source line and some, but not all of them were executed. The second element holds the source file index.
Compiled C module never mod_l_code_coverage.so
L_NEW1DPATTERN_SVG_IMAGE diskfile
(switchable between string blob diskfile url xmlstring)
SVG depiction of the NEW1D patterns applicable to the currently loaded transform
boxwidth: { value: 250 datatype: int}
boxheight: { value: 250 datatype: int}
Tcl script E_SVG_IMAGE never l_new1dpattern_svg_image.xpd
M_3DSIZE floatvector Various 3D size measures for molecules, computed from property A_XYZ and the geometrical molecule center in M_CENTER. The property is a float vector, fields:

index 0: diameter (maximum 3D atom distance in molecule)
index 1: radius (maximum atom distance from molecule center in smae molecule)
index 2: radius of gyration (squared atom distances from center divided by number of atoms in molecule)
index 3: separation (sum of intramolecular atom distances divided by number of atoms in molecule)

diameter float
radius float
radiusofgyration float
separation float
Compiled C module A_XYZ M_CENTER A_MOL_LABEL atomchange bondchange stereochange 3drelative mol atom bond mod_m_3dsize.so
M_AMINO_ACID_SEQUENCE string Amino acid sequence in 1- or 3-letter letter code. Can be computed from molecular structure with standard amino acid set.
nomenclature: { value: a description: Whether to use single-letter amino acid codes (a) or 3-letter codes (aaa) enumeration: a,letter1=1:aaa,letter3=3 datatype: int}
encodeterminals: { value: 0 description: If set, include H- and -OH terminal encodings datatype: boolean}
encodebridges: { value: 0 description: If set, encode SS disulfide bridges in (x) format datatype: boolean}
separator: { value: {} description: Separator character between AA encodings (can be empty) datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange mol atom bond mod_m_amino_acid_sequence.so
M_AMOUNT double
atomchange bondchange mol atom bond
M_ASCII_IMAGE string
(switchable between string unicode)
ASCII (or Unicode) rendering of a chemical structure.

Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the alst line.
width: { value: 40 minvalue: 25 maxvalue: 256 datatype: int}
height: { value: 30 minvalue: 25 maxvalue: 256 datatype: int}
showcharge: { value: 0 datatype: boolean}
useunicode: { value: 1 datatype: boolean}
bonds: { value: 10 minvalue: 3 maxvalue: 25 datatype: double}
usecolor: { value: 0 datatype: boolean}
usefontstyle: { value: 0 datatype: boolean}
showradical: { value: 0 datatype: boolean}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,exten ded,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,y es datatype: int}
csymbol: { value: all enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: white datatype: color}
highlightcolor: { value: red datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
frame: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
crop: { value: left|right|top|bottom enumeration: ^none:left:right:top:bottom datatype: bitset}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
usealtcharset: { value: 0 datatype: boolean}
leadnewline: { value: 0 datatype: boolean}
tailnewline: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
hcolor: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
unicodeforringbonds: { value: macrocycles enumeration: no,never:macrocycles,largerings:yes,always datatype: int}
badunicodechars: { value: 0x2571 0x2572 0x2573 0x2afd description: Codes of Unicode chars which should not be used, for example because they are missing in the terminal font comment:
0x2afd: double slash, 0x244a: double backslash,
0x2500: horizontal single line, 0x2501: horizontal bold single line, 0x2502: vertical single line,
0x2504: vertical bold single line, 0x2504: horizontal dotted line, 0x2506: vertical dotted line,
0x250c: corner lower right, 0x2510: corner lower left, 0x2514: corner upper right, 0x2518: corner upper left,
0x2550: horizontal double line, 0x2551: vertical double line, 0x2554: double corner lower right,
0x2557: double corner lower left, 0x255A: double corner upper right, 0x255D: double corner upper left,
0x2571: diagonal lower left to upper right, 0x2572: diagonal upper left to lower right, 0x2573: cross,
0x2630: horizontal triple line
datatype: string constraints: list}
lineprefix: { value: {} description: Characters to add to the 2nd and later lines, for example to compensate for database table formatting datatype: string}
Compiled C module A_TYPE A_ELEMENT A_FLAGS B_FLAGS A_QUERY B_QUERY A_FORMAL_CHARGE A_RESIDUE A_SYMBOL A_XSYMBOL A_XY A_HSPECIAL A_CSPECIAL A_COLOR A_ANNOTATION B_TYPE B_LABEL B_ORDER B_COLOR R_TYPE atomchange bondchange stereochange merge mol atom bond mod_m_ascii_image.so
M_ATOM_RANGE intpair Ids of first and last atom of molecule
(builtin) M_STANDARD_ATOM_COUNT atomchange bondchange merge shuffle hadd
M_BENZENOID_INDEX double The count of benzene ESSSR rings divided by the total number of aromatic ESSSR rings. Zero in case there are no aromatic rings. Roughley and Jordan, J. Med. Chem. 2011, 54, 3451-3479
Compiled C module R_TYPE R_AROMATIC R_HETEROATOM_COUNT R_MOL_NUMBER atomchange bondchange mol atom bond mod_m_benzenoid_index.so
M_BP floatpair Boiling point in Kelvin, with optional temperature range
value float
range float
pressure: { value: 760 datatype: double}
pressureunit: { value: Torr datatype: string}
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE atomchange bondchange mol
M_CARBON_COUNT int Number of carbon atoms in fragment - the same as M_ELEMENT_COUNT(6)
Compiled C module A_TYPE A_ELEMENT A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_carbon_count.so
M_CAS string Chemical Abstracts registry number for ensemble
useresolver: { value: 1 datatype: boolean}
usepubchem: { value: 1 datatype: boolean}
uselookchem: { value: 0 datatype: boolean}
Tcl script M_HASHISY M_CID atomchange bondchange stereochange groupchange merge 3drelative 3dabsolute shuffle hadd dup mol atom bond ring sigma pi group reaction dataset file table network vertex edge surface ringsystem bondangle torsion hierarchy biological bioitem biolink 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 m_cas.xpd
M_CENTER compound Box, geometric and mass-weighted molecule centers
box floatvector
geo floatvector
mass floatvector
coordinateproperty: { value: A_XYZ datatype: string}
useh: { value: 1 datatype: string}
(builtin) E_XYZEXTENT A_WEIGHT A_XYZ A_MOL_NUMBER atomchange bondchange 3drelative 3dabsolute mol
M_CHARACTER byte Classification of 3D molecular structure (minimum,transition,etc)
unknown,u,?:minimum,n,m,nu,mu:transition,t:fixed,f,x
A_XYZ atomchange bondchange stereochange 3drelative hadd mol
M_CHARGE short Sum of charges in the molecules
(builtin) A_FORMAL_CHARGE A_MOL_NUMBER atomchange mol
M_CHARGED_ATOM_COUNT int Number of atoms in the molecule which are formally charged and not direclty adjacent to an atom of opposite formal charge (such as in ionic nitro groups).
Compiled C module A_TYPE A_FORMAL_CHARGE B_TYPE A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_charged_atom_count.so
M_CHARGED_GROUP_COUNTS intpair Counts of groups charged positively or negatively under neutral conditions in protic solvents. This is a simple guestimate from A_HYDROGEN_BONDING, using acidic and basic groups as starting points and combining close centers (i.e. a P(=O)(OH)2 group with 2 acidic protons only gets a single positive charge count).
positive int
negative int
Compiled C module A_TYPE A_ELEMENT A_HYDROGEN_BONDING B_TYPE A_ARORING_COUNT A_UNSATURATION A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_charged_group_counts.so
M_CHIRALITY byte Stereo status or potential of molecule
none:meso:unspecified:chiral:contradictory
Compiled C module A_LABEL A_STEREOGENIC A_MOL_NUMBER E_NMOLECULES A_HASH A_ALLENE A_HASH_STEREO B_HASH_STEREO A_LABEL_STEREO atomchange bondchange stereochange 3drelative mol atom bond mod_m_chirality.so
M_CID int PubChem CID structure identifier
Tcl script E_SMILES E_STDINCHIKEY atomchange bondchange stereochange merge hadd m_cid.xpd
M_COLOR color Background color to use in plots
never
M_COMPLEXITY float Molecular complexity according to modified Bertz/Hendrickson algorithm W. D. Ihlenfeldt, Ph.D. Thesis, TU Munich 1991
Compiled C module A_ELEMENT B_TYPE B_ORDER B_HASH atomchange bondchange merge mol mod_m_complexity.so
M_CONVENTION string Description of structure encoding convention. This is for example used in CML files, where you can legally encode your data in any way you please, without regard to capabilities of software inputting that data again.
never
M_DENSITY float Density of molecule at room temperature in kg/L
Tcl script A_ELEMENT A_ISOTOPE atomchange bondchange mol m_density.xpd
M_ELEMENT_COUNT shortvector Count of element types of atoms of molecules
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
(builtin) A_MOL_NUMBER A_ELEMENT A_TYPE atomchange bondchange merge shuffle hadd mol
M_EMF_IMAGE diskfile
(switchable between blob diskfile url)
A 2D-plot of the structure as a WMF or EMF file
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: smiles datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.4 datatype: double}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
usehatch: { value: 0 datatype: boolean}
format: { value: wmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int}
frame: { value: 1 datatype: int}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 1.5 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
crop: { value: -1 datatype: int}
showstereogroups: { value: 0 datatype: int}
font: { value: Arial datatype: string}
usesubscripts: { value: 1 datatype: boolean}
usereactionscaling: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange merge hadd mol mod_m_emf_image.so
M_EXACT_MASS floatpair Exact mass of most abundant compound isotope combination, assuming natural abundance
weight double
abundance double
useimplicith: { value: 1 description: Whether to include implicit hydrogens datatype: boolean}
Compiled C module A_TYPE A_ELEMENT A_ISOTOPE atomchange merge mol atom mod_m_exact_mass.so
M_FG_COUNT shortvector Count of functional groups in molecule
^cf:cx:ccdb:cctb
groupindex: { value: -1 datatype: int}
add_h_on_c: { value: 0 datatype: boolean}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange mol mod_m_fg_count.so
M_FORMULA string Molecular formula of molecules
usecharges: { value: 0 datatype: string}
format: { value: ascii datatype: string}
useimplicith: { value: 1 datatype: string}
usequeryatoms: { value: 0 datatype: string}
(builtin) A_ISOTOPE A_MOL_NUMBER atomchange merge mol
M_FSP3 double Carbon flatness score - the ratio of SP3 hybridized carbon atoms to total carbon atom count Lovering, F. et al., J.Med.Chem. 2009, 52, 6752-6756
Compiled C module A_TYPE A_ELEMENT A_HYBRIDIZATION A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_fsp3.so
M_GIF diskfile
(switchable between string blob diskfile url)
A 2D-plot of the structure as a GIF or PNG file
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black description: A color name, the magic value "atomsplit", or a bond color property. In case of an empty string, use B_COLOR comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
footer: { value: {} datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: string}
interlace: { value: 1 datatype: boolean}
commenttype: { value: property enumeration: none:text:property,prop datatype: string}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
highlightbonds2: { value: {} datatype: intvector}
highlightatoms: { value: {} datatype: intvector}
explicithydrogens: { value: {} datatype: intvector}
linkatoms: { value: {} description: Atom pairs between which a dotted line should be drawn datatype: intpairvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
crop: { value: -1 datatype: int}
wedges: { value: 1 datatype: boolean}
saverendercoordinates: { value: 0 description: If set, try to set A_RENDER_XY to indicate the atom image coordinates datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
format: { value: gif datatype: string}
markcolor: { value: blue datatype: diskfile}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
font: { value: arialn datatype: string}
symbolfontsize: { value: -1 datatype: int}
annotationfontsize: { value: -1 datatype: double}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
showisotope: { value: 1 datatype: boolean}
isotopemapping: { value: none datatype: string}
showstereoh: { value: 1 datatype: boolean}
suppressedmols: { value: {} datatype: intvector}
linewidth: { value: 1.4 datatype: double}
showempty: { value: 0 datatype: boolean}
voronoicolorproperty: { value: {} datatype: color constraints: emptycolor}
voronoifilter: { value: {} datatype: string constraints: filtername}
showmapping: { value: 0 datatype: boolean}
showstereogroups: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
frame: { value: 0 datatype: int}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: int}
footerfontsize: { value: -1 datatype: int}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circleatoms: { value: {} datatype: intvector}
atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 2.0 datatype: double}
fixiepngsize: { value: 1 datatype: boolean}
rawcoordinates: { value: 0 datatype: boolean}
checkintersection: { value: 0 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
usereactionscaling: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange merge hadd mol mod_m_gif.so
M_HALIDE_FRACTION double Fraction of molecular weight of the fragment contributed by halogen atoms
Compiled C module A_TYPE A_ELEMENT A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_halide_fraction.so
M_HASH uint64 Basic molecule hashcode
(builtin) A_HASHGROUP A_MOL_NUMBER A_HASH atomchange bondchange
M_HASH128 uint128 Perturbed molecule hashcode, extended to 128 bits
Compiled C module A_HASH A_HASHGROUP M_HASHGROUP_COUNT atomchange bondchange hadd mol mod_m_hash128.so
M_HASHGROUP index Hash group id index for basic molecule hash code
(builtin) M_HASH atomchange bondchange merge
M_HASHGROUP128 index Hash group id index for perturbated molecule hash code, based on M_HASH128
Compiled C module M_HASH128 atomchange bondchange merge mol mod_m_hashgroup128.so
M_HASHGROUP_COUNT intvector Molecule-oriented population of basic atom hash groups
(builtin) A_HASH atomchange bondchange merge hadd mol
M_HASHGROUP_Y index Hash group id index for perturbated molecule hash code
(builtin) M_HASHY atomchange bondchange merge
M_HASHISY uint64 Isotopic stereospecific perturbed molecule hashcode
(builtin) A_ISOTOPE_STEREO_HASHGROUP A_ISOTOPE_STEREO_HASH A_MOL_NUMBER atomchange bondchange stereochange merge hadd
M_HASHIY uint64 Perturbed molecule hashcode with isotopes
(builtin) A_ISOTOPE_HASHGROUP A_ISOTOPE_HASH M_ISOTOPE_HASHGROUP_COUNT atomchange bondchange merge hadd
M_HASHS uint64 Stereospecific basic molecule hashcode
(builtin) A_STEREO_HASHGROUP A_STEREO_HASH A_MOL_NUMBER atomchange bondchange stereochange merge hadd
M_HASHSY uint64 Perturbed stereospecific molecule hashcode
useisotope: { value: 0 datatype: string}
(builtin) A_STEREO_HASH A_STEREO_HASHGROUP M_STEREO_HASHGROUP_COUNT atomchange bondchange hadd
M_HASHY uint64 Perturbed molecule hashcode
useisotope: { value: 0 datatype: string}
(builtin) A_HASH A_HASHGROUP M_HASHGROUP_COUNT atomchange bondchange hadd
M_HEAVY_ATOM_COUNT int Number of non-hydrogen atoms in the molecule
Compiled C module A_MOL_NUMBER A_ELEMENT A_TYPE atomchange bondchange mol atom bond mod_m_heavy_atom_count.so
M_HETEROATOM_CARBON_RATIO double Number of hetero atoms devided by number of carbon atoms
Compiled C module A_TYPE A_ELEMENT A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_heteroatom_carbon_ratio.so
M_HETEROATOM_COUNT int Number of hetero (not C or H) atoms in the molecules/fragments
Compiled C module A_TYPE A_ELEMENT atomchange bondchange mol atom bond mod_m_heteroatom_count.so
M_HYDROGEN_COMPLETE boolean Boolean flag indicating whether there are no open hydrogen sites
Compiled C module A_HYDROGENS_NEEDED A_MOL_NUMBER atomchange bondchange hadd mol atom bond mod_m_hydrogen_complete.so
M_IDENT string Freeform molecule ID
Tcl script never m_ident.xpd
M_INCHI string Fragment-level InChI string
options: { value: DONOTADDH FIXEDH RECMET NOWARNINGS description: Set of option words as used in the original NIST software comment: Supported option words: NOLABELS SAVEOPT AUXNONE MISMATCHISERROR OUTERRINCHI Key XHash1 XHash2 SNON NEWPSOFF DONOTADDH LooseTSACheck SREL ChiralFlagOFF SUU SLUUD FIXEDH RECMET KET 15T PT_22_00 PT_16_00 PT_06_00 PT_39_00 LargeMolecules Polymers Polymers105 NPZz NoWarnings MergeHash NoInChI FoldCRU FoldSRU FrameShift: NoFrameShift NoEdits SATZZ FNUDOFF FixSp3bugOFF FBOFF FB2OFF SPXYZOFF SASXYZOFF Polymers105+. Record processing options INPAUX START: END: RECORD: have no effect. datatype: string constraints: list}
fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean}
stereoperception: { value: 1 description: If set, perceive stereochemistry, if no, use what is presently set on the structure datatype: boolean}
stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int}
autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean}
prefix: { value: 1 description: If set, include InChI= prefix in output datatype: boolean}
stripstereolayer: { value: 0 datatype: boolean}
stripisotopelayer: { value: 0 datatype: boolean}
stripfixedhlayer: { value: 0 datatype: boolean}
stripreconnectlayer: { value: 0 datatype: boolean}
stripchargelayer: { value: 0 datatype: boolean}
Compiled C module B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd mol atom bond mod_m_inchi.so
M_INCHI_AUXINFO string InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting M_INCHI
B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd mol atom bond
M_ISOTOPE_COUNT int Number of isotopically labelled atoms in molecule
Compiled C module A_TYPE A_ISOTOPE A_MOL_NUMBER atomchange merge mol atom bond mod_m_isotope_count.so
M_ISOTOPE_HASH128 uint128 Perturbed molecule hashcode, extended to 128 bits, with isotopes
Compiled C module A_ISOTOPE_HASH A_ISOTOPE_HASHGROUP M_ISOTOPE_HASHGROUP_COUNT atomchange bondchange hadd mol mod_m_isotope_hash128.so
M_ISOTOPE_HASHGROUP128 index Hash group id index for perturbated molecule hash code, based on M_ISOTOPE_HASH128
Compiled C module M_ISOTOPE_HASH128 atomchange bondchange merge mol mod_m_isotope_hashgroup128.so
M_ISOTOPE_HASHGROUP_COUNT intvector Molecule-oriented population of isotope atom hash groups
(builtin) A_ISOTOPE_HASH atomchange bondchange merge hadd mol
M_ISOTOPE_HASHGROUP_Y index Hash group id index for perturbed isotopic molecule hash code
(builtin) M_HASHIY atomchange bondchange merge hadd
M_ISOTOPE_STEREO_HASH128 uint128 Perturbed molecule hashcode, extended to 128 bits, with stereochemistry and isotopes
Compiled C module A_STEREO_HASH A_STEREO_HASHGROUP M_STEREO_HASHGROUP_COUNT atomchange bondchange hadd mol mod_m_isotope_stereo_hash128.so
M_ISOTOPE_STEREO_HASHGROUP128 index Hash group id index for perturbated molecule hash code, based on M_ISOTOPE_STEREO_HASH128
Compiled C module M_ISOTOPE_STEREO_HASH128 atomchange bondchange merge mol mod_m_isotope_stereo_hashgroup128.so
M_ISOTOPE_STEREO_HASHGROUP_COUNT intvector Molecule-oriented population of isotope stereo atom hash groups
(builtin) A_ISOTOPE_STEREO_HASH atomchange bondchange merge hadd mol
M_ISOTOPE_STEREO_HASHGROUP_Y index Hash group id index for isotopic stereospecific perturbed molecule hash code
(builtin) M_HASHISY atomchange bondchange merge hadd
M_ISOTOPE_STEREO_TAUTO_HASH uint64 Perturbed tautomer-tolerant molecule isotope stereo hashcode
M_HASHISY E_HASHISY E_ISOTOPE_STEREO_TAUTO_HASH atomchange bondchange mol
M_ISOTOPE_STEREO_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant molecule isotope stereo hashcode, 128 bit version
M_ISOTOPE_STEREO_HASH128 E_ISOTOPE_STEREO_HASH128 E_ISOTOPE_STEREO_TAUTO_HASH128 atomchange bondchange mol
M_ISOTOPE_TAUTO_HASH uint64 Perturbed tautomer-tolerant molecule hashcode, without stereochemistry but with isotope labelling
M_HASHIY E_HASHIY E_ISOTOPE_TAUTO_HASH atomchange bondchange mol
M_ISOTOPE_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant molecule isotope hashcode, 128 bit version
M_ISOTOPE_HASH128 E_ISOTOPE_HASH128 E_ISOTOPE_TAUTO_HASH128 atomchange bondchange mol
M_LABEL int Arbitrary molecule label
(builtin) never
M_LIPINSKI_ACCEPTOR_COUNT int Number of hydrogens on N and O atoms - H-bond acceptors according to simple Lipinski definition.
For a more refined definition, use property E_NHACCEPTORS.
Compiled C module A_TYPE A_ELEMENT A_MOL_NUMBER A_FREE_ELECTRONS atomchange bondchange mol atom bond mod_m_lipinski_acceptor_count.so
M_LIPINSKI_DONOR_COUNT int Number of oxygen and nitrogen atoms according to really simple Lipinski definition. For a more refined definition, use E_NHDONORS.
Compiled C module A_TYPE A_ELEMENT A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_lipinski_donor_count.so
M_MAX_CHAIN_FRAGMENT_SIZE int The maximum value of A_CHAIN_LENGTH in the molecule, i.e. the size of the largest fragment of connected non-ring non-hydrogen atoms.
Compiled C module A_CHAIN_LENGTH A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_max_chain_fragment_size.so
M_MAX_CONJUGATED_SYSTEM_SIZE int The maximum size of a conjugated system in the fragment according to the Shoichet definition (see literature reference). J. Med. Chem. 2003, 46, 4477-4486
Compiled C module A_CONJUGATED_SYSTEM_SIZE atomchange bondchange mol atom bond mod_m_max_conjugated_system_size.so
M_MAX_LINEAR_CHAIN_FRAGMENT_SIZE int The maximum value of A_LINEAR_CHAIN_LENGTH in the molecule, i.e. the size of the largest fragment of connected non-ring non-branching non-hydrogen atoms.
Compiled C module A_LINEAR_CHAIN_LENGTH A_MOL_NUMBER atomchange bondchange mol atom bond mod_m_max_linear_chain_fragment_size.so
M_MESO boolean Flag indicating that the molecule is mesomeric (i.e. all stereogenic sites are defined, and the enantiomer of the molecule is the same compound (example: R.S. and S.R tartric acid, but not the R.R. or S.S. variants.
Tcl script A_STEREOGENIC A_HASH_STEREO E_ENANTIOMER atomchange bondchange stereochange atom bond m_meso.xpd
M_METADATA dictionary Dublin Core metadata for structure fragment
never
M_MOLNAME string Molecule name(s)
atomchange bondchange
M_MOL_NUMBER short Number of molecule
(builtin) atomchange bondchange merge shuffle mol
M_MONOISOTOPIC_MASS float Mass computed with most abundant isotope only, not natural abundance
useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
Compiled C module A_ELEMENT A_TYPE A_ISOTOPE atomchange mol mod_m_monoisotopic_mass.so
M_MP floatpair Melting Point in Kelvin, with optional range
value float
range float
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE atomchange bondchange mol
M_NAME string Free-form molecule name
Tcl script never m_name.xpd
M_NATOMS int Number of atoms in molecule
(builtin) A_MOL_NUMBER A_TYPE atomchange bondchange hadd mol
M_NBONDS int Number of bonds in molecule
(builtin) B_MOL_NUMBER bondchange mol
M_NCBI_STANDARDIZER_HASH uint64 NCBI standardization hashcode (no h, no charges, bond order)
A_ELEMENT B_ORDER B_TYPE A_TYPE atomchange bondchange merge
M_NCOLLISIONS int Number of atomic close contacts
Compiled C module A_XYZ A_ELEMENT A_TYPE atomchange 3drelative mol mod_m_ncollisions.so
M_NRINGS int Number of rings in molecule
Compiled C module A_MOL_NUMBER R_SIZE M_LABEL bondchange mol bond ring mod_m_nrings.so
M_ORGANIC byte Flag indicating whether molecule is organic (i.e. contains carbon, and is not one of a small set of simple compounds like carbon monoxide, carbon dioxide, a cyanide, etc.). Value: 0: no, 1:yes, -1:undecidable
undefined=-1:inorganic=0:organic=1
Compiled C module A_TYPE A_ELEMENT A_MOL_NUMBER B_TYPE atomchange bondchange mol mod_m_organic.so
M_PMI floatmatrix Principial moments of inertia, computed on A_XYZ or a custom coordinate property
useh: { value: 1 datatype: boolean}
coordinateproperty: { value: A_XYZ datatype: string constraints: property}
Compiled C module A_XYZ A_TYPE A_WEIGHT A_MOL_NUMBER A_ELEMENT atomchange 3drelative hadd mol atom mod_m_pmi.so
M_POINTGROUP shortstring Point group of molecule. Read for example from SHARC files.
atomchange bondchange stereochange 3drelative hadd mol
M_RACEMIC_STEREO_HASH uint64 Molecule hashcodes for racemic mixtures. These are identical to the minimum molecule stereo hashcodes of the present structure, or its enantiomer. For example, the racemic stereo hashcode for both L-alanine and D-alanine input structures (with known stereochemistry) is, by chance, that of L-alanine, and not that of DL-alanine (with unknown stereochemistry)
Compiled C module A_STEREO_HASH M_HASHSY atomchange bondchange stereochange mol mod_m_racemic_stereo_hash.so
M_RACEMIC_STEREO_HASH_GROUP index Group memberships of the racemic molecule stereo hash codes
Compiled C module M_RACEMIC_STEREO_HASH atomchange bondchange stereochange mol mod_m_racemic_stereo_hash_group.so
M_RADIALCODE floatvector Gasteiger radial distribution function structure encoding
B: { value: 400 datatype: int}
rmax: { value: 6.4 datatype: double}
codelen: { value: 128 datatype: int}
normalize: { value: 0 datatype: boolean}
Compiled C module A_TYPE A_ELEMENT A_XYZ atomchange bondchange 3drelative mol mod_m_radialcode.so
M_REACTION_LABEL int Section number of reaction component in MDL RXN/RDF files
Tcl script atomchange bondchange atom bond
M_REACTION_ROLE int Role of molecule in reaction. More fine-grained than E_REACTION_ROLE
undef,undefined:reagent,educt,reactant:product:solvent:catalyst:intermediate:impurity:byproduct:agent:waste
Tcl script atomchange bondchange atom bond
M_RIGID_BOND_COUNT int Number of bonds which are not rotatable because they are in a ring, or have multiple bond order.
Compiled C module B_ROTATABILITY A_MOL_NUMBER atomchange bondchange hadd mol mod_m_rigid_bond_count.so
M_RINGSYSTEM_COUNT short Ringsystem count
Compiled C module atomchange bondchange mol atom bond mod_m_ringsystem_count.so
M_ROTATABLE_BOND_COUNT int Number of bonds which are rotatable and where the rotation has a steric effect
Compiled C module B_ROTATABILITY atomchange bondchange hadd mol mod_m_rotatable_bond_count.so
M_SMILES string SMILES strings of individual molecules/fragments in an ensemble.
useexplicithcount: { value: 0 datatype: string}
generalization: { value: none datatype: string}
usehcount: { value: 1 datatype: string}
firstatom: { value: -1 datatype: string}
lastatom: { value: -1 datatype: string}
checkstereo: { value: 1 datatype: string}
reuseringlinks: { value: 0 datatype: string}
usestereogroup: { value: 0 datatype: string}
hideautoh: { value: 0 datatype: string}
usestereo: { value: 1 datatype: string}
unique: { value: 0 datatype: string}
singleringupdownbond: { value: 1 datatype: string}
usesuperatom: { value: 0 datatype: string}
atomaroproperty: { value: A_ARORING_COUNT datatype: string}
useexplicith: { value: 0 datatype: string}
queryhatoms: { value: {} datatype: string}
usemapping: { value: 1 datatype: string}
smarts: { value: 0 datatype: string}
usearo: { value: 0 datatype: string}
useisotope: { value: 1 datatype: string}
useextrabondtypes: { value: 1 datatype: string}
usename: { value: 0 description: If set, append M_NAME to the SMILES after a blank datatype: boolean}
Tcl script E_SMILES atomchange bondchange stereochange hadd mol atom bond m_smiles.xpd
M_SPAN int Largest distance in bonds between any two atoms in molecule
Compiled C module B_TYPE A_TOPO_DISTANCE atomchange bondchange hadd mol atom bond mod_m_span.so
M_STANDARD_ATOM_COUNT int Number of traditional atoms in molecule
(builtin) A_MOL_NUMBER A_TYPE atomchange bondchange hadd mol
M_STATE byte Molecule state (as used for example in a reaction)
unknown:solid:liquid:gas,gaseous:plasma:oil
temperature: { value: 298.15 minvalue: 0 datatype: double}
Tcl script M_BP M_MP atomchange bondchange mol atom bond m_state.xpd
M_STDINCHI string Standard InChI identifier of molecular fragments in ensemble
options: { value: DONOTADDH description: Set of default option words as defined to standard comment: Many of the option words listed for E_INCHI implicitly switch off standard mode. See INChI lib docs. datatype: string constraints: list}
fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean}
autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean}
stereoperception: { value: 1 datatype: boolean}
stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int}
prefix: { value: 1 datatype: boolean}
stripstereolayer: { value: 0 datatype: boolean}
stripisotopelayer: { value: 0 datatype: boolean}
stripfixedhlayer: { value: 0 datatype: boolean}
stripreconnectlayer: { value: 0 datatype: boolean}
stripchargelayer: { value: 0 datatype: boolean}
Compiled C module B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd atom bond mod_m_stdinchi.so
M_STDINCHIKEY string Hash of InChI string
prefix: { value: 1 datatype: boolean}
Compiled C module E_STDINCHI atomchange bondchange stereochange mol atom bond mod_m_stdinchikey.so
M_STDINCHI_AUXINFO string InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting M_STDINCHI
B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd mol atom bond
M_STEREOGENIC intpair Flags whether tthe molecule is stereogenic in the atom or bond set
Compiled C module A_STEREOGENIC B_STEREOGENIC A_MOL_NUMBER atomchange bondchange stereochange atom bond mod_m_stereogenic.so
M_STEREO_COUNT intvector Stereo counts
apossible int
adefined int
aundefined int
bpossible int
bdefined int
bundefined int
Compiled C module A_LABEL_STEREO B_LABEL_STEREO A_STEREOGENIC B_STEREOGENIC A_MOL_LABEL B_MOL_LABEL atomchange bondchange stereochange mol mod_m_stereo_count.so
M_STEREO_HASH128 uint128 Perturbed molecule hashcode, extended to 128 bits, with stereochemistry
Compiled C module A_STEREO_HASH A_STEREO_HASHGROUP M_STEREO_HASHGROUP_COUNT atomchange bondchange hadd mol mod_m_stereo_hash128.so
M_STEREO_HASHGROUP index Hash group id index for stereospecific basic molecule hash code
(builtin) M_HASHS atomchange bondchange merge
M_STEREO_HASHGROUP128 index Hash group id index for perturbated molecule hash code, based on M_STEREO_HASH128
Compiled C module M_STEREO_HASH128 atomchange bondchange merge mol mod_m_stereo_hashgroup128.so
M_STEREO_HASHGROUP_COUNT intvector Molecule-oriented population of stereo atom hash groups
(builtin) A_STEREO_HASH atomchange bondchange merge hadd mol
M_STEREO_HASHGROUP_Y index Hash group id index for stereospecific perturbated molecule hash code
(builtin) M_HASHSY atomchange bondchange stereochange merge
M_STEREO_STATUS byte Check stereogenic atoms/bonds vs. stereo definition status, set overall status flag
n,nostereo:u,undefined:p,partial:d,defined
Compiled C module A_LABEL_STEREO B_LABEL_STEREO A_STEREOGENIC B_STEREOGENIC A_MOL_NUMBER A_STEREO_GROUP atomchange bondchange stereochange atom bond mod_m_stereo_status.so
M_STEREO_TAUTO_HASH uint64 Perturbed tautomer-tolerant molecule stereo hashcode
M_HASHSY E_HASHSY E_STEREO_TAUTO_HASH atomchange bondchange mol
M_STEREO_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant molecule stereo hashcode, 128 bit version
M_STEREO_HASH128 E_STEREO_HASH128 E_STEREO_TAUTO_HASH128 atomchange bondchange mol
M_SVG_IMAGE diskfile
(switchable between string blob diskfile url xmlstring)
Molecule images in SVG vector format
width: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int}
height: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 minvalue: 3 maxvalue: 25 datatype: double}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 minvalue: 0 maxvalue: 25 datatype: string}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: string}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
secondarycolor: { value: #00D000 datatype: color}
highlightbonds: { value: {} datatype: intvector}
secondarybonds: { value: {} datatype: intvector}
highlightatoms: { value: {} datatype: intvector}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.2 datatype: double}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
bondannotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showlabel: { value: 0 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 1.8 datatype: double}
unit: { value: {} datatype: string}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
circleatoms: { value: {} datatype: intvector}
atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int}
circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Helvetica datatype: string}
usewebfont: { value: 0 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
usereactionscaling: { value: 0 datatype: boolean}
uselinecaps: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
standalone: { value: 1 datatype: boolean}
xmlheader: { value: 1 datatype: boolean}
id: { value: {} datatype: string}
title: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
showempty: { value: 0 datatype: boolean}
saverendercoordinates: { value: 0 description: If set, try to set A_RENDER_XY to indicate the atom image coordinates datatype: boolean}
suppressedmols: { value: {} datatype: intvector}
framecolor: { value: black datatype: color}
rawcoordinates: { value: 0 datatype: boolean}
atomclick: { value: {} description: Javascript function to call, substitute %i id, %a atom label, %b bond label, %r ring label, %y ringsystem label datatype: string}
bondclick: { value: {} datatype: string}
ringclick: { value: {} datatype: string}
ringsystemclick: { value: {} datatype: string}
headerclick: { value: {} datatype: string}
footerclick: { value: {} datatype: string}
bgclick: { value: {} datatype: string}
ringclickcolor: { value: {} datatype: color}
ringsystemclickcolor: { value: {} datatype: color}
bondclickcolor: { value: {} datatype: color}
ringhovercolor: { value: {} datatype: color}
ringsystemhovercolor: { value: {} datatype: color}
atomhovercolor: { value: {} datatype: color}
bondhovercolor: { value: {} datatype: color}
activehbonds: { value: 0 description: If set, undrawn bonds to H become active on hovering and are clickable if a bond click action has been set datatype: boolean}
style: { value: default description: General plot style. Can either be default, or patran for Patran-style atom and bond annotations enumeration: default:patran datatype: int}
maxannotationlength: { value: -1 description: Maximum character length of atom and bond annotations. If an annotation is longer, the plotted value is abbreviated, and a SVG title attribute with the full string added datatype: int}
forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean}
extrabondannotationproperty: { value: {} datatype: string constraints: property}
Compiled C module A_TYPE A_ELEMENT A_XY A_HSPECIAL A_CSPECIAL B_TYPE B_ORDER A_ANNOTATION B_ANNOTATION B_FLAGS A_FLAGS A_QUERY B_QUERY atomchange bondchange stereochange merge mol atom bond mod_m_svg_image.so
M_TAUTOMER_SCORE int Scoring function for tautomers
stereobondmalus: { value: 1 description: If set, give malus to stereogenic bonds (which may appear stereochemically defined, but are not really) datatype: boolean}
explain: { value: 0 description: If set, print the score components datatype: boolean}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT B_ISAROMATIC R_TYPE R_AROMATIC A_FORMAL_CHARGE atomchange bondchange atom bond ring mod_m_tautomer_score.so
M_TAUTO_HASH uint64 Perturbed tautomer-tolerant molecule hashcode, without stereochemistry and isotope labelling
M_HASHY E_HASHY E_TAUTO_HASH atomchange bondchange mol atom bond
M_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant molecule hashcode, 128 bit version
M_HASH128 E_HASH128 E_TAUTO_HASH128 atomchange bondchange mol
M_TITLE string Molecule title string
Tcl script M_NAME never m_title.xpd
M_TOTAL_WALK_COUNT double Total molecule walk count (as defined by Rücker and Rücker) J. Chem. Inf. Comput. Sci. 2000, 40, 99-106
excludebonds: { value: {} datatype: intvector}
usexatoms: { value: 1 description: If set, use heteroatom vs. carbon for additional differentiation. By default, non-hydrogen atoms are anonymous datatype: boolean}
usebo: { value: 1 description: If set, use bond order for additional walks datatype: boolean}
Compiled C module M_HEAVY_ATOM_COUNT B_TYPE B_ORDER B_ISAROMATIC A_TYPE A_ELEMENT atomchange bondchange mol atom bond mod_m_total_walk_count.so
M_VDW_VOLUME double Van der Waals molecular volume Zhao, Abraham, Zissimos, J. Org. Chem. 2003, 68, 7368-7373
Tcl script A_TYPE A_ELEMENT atomchange bondchange mol m_vdw_volume.xpd
M_WEIGHT float Molecular weight of molecules
useimplicith: { value: 1 datatype: string}
(builtin) A_MOL_NUMBER A_WEIGHT atomchange merge mol
M_XYEXTENT floatvector 2D display coordinate bounding box
(builtin) A_XY A_MOL_NUMBER A_FLAGS atomchange merge hadd
M_XYZEXTENT floatvector 3D coordinate bounding box for molecules
(builtin) A_XYZ atomchange merge 3drelative 3dabsolute hadd
N_AUTHOR compound Network author data, computation copies these from the internal object author fields
name string
author string
email string
phone string
orcid string
authorurl url
date date
version string
affiliation string
affiliationurl url
affiliationduns string
doi string
infourl url
street string
city string
zip string
state string
country string
literature string
keywords string
comment string
license string
licenseurl url
category string
repopath string
baseuuid string
versionuuid string
Tcl script never n_author.xpd
N_COMMENT string Network object comment in free format
never
N_CONNECTION_COUNT int Connection count (number of connection objects in network)
Tcl script never n_connection_count.xpd
N_CREATOR string Network creator information
never
N_DIRECTED boolean Flag indicating whether a network is directed
never
N_GIF diskfile
(switchable between string blob diskfile url)
Network renderer
filename: { value: {} datatype: diskfile constraints: writeable}
format: { value: png enumeration: png:png8:gif datatype: string}
nodeproperty: { value: {} datatype: string constraints: property}
boxwidth: { value: 100 datatype: int}
boxheight: { value: 100 datatype: int}
boxgap: { value: 50 datatype: int}
interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean}
framewidth: { value: 0 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
linecolor: { value: red datatype: color}
boxframecolor: { value: blue datatype: color}
boxbgcolor: { value: grey90 datatype: color}
font: { value: arialn datatype: string}
fontsize: { value: 8.0 datatype: double}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean}
Compiled C module V_XY V_GRAPHICS atomchange bondchange atom bond vertex edge mod_n_gif.so
N_GRAPHICS compound Global network graphics
none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon
type int
attributes dictionary
never
N_IDENT string Network identifier
Tcl script never n_ident.xpd
N_IMAGE_URL url Network rendering reference URL
atomchange bondchange atom bond
N_LABEL_GRAPHICS compound Global network label graphics
none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon
type int
attributes dictionary
never
N_NAME string Network name string in free form
never
N_ONTOLOGY_HEADER dictionary ODO Ontology header data
never
N_ORGANISM string Organism identifier for the network
atomchange bondchange atom bond
N_SIZE intpair Counts of vertices(nodes) and connections(edges)
vertices int
connections int
Compiled C module vertex edge mod_n_size.so
N_TEXT string Network text label
never
N_URL url Network reference URL
atomchange bondchange atom bond
N_VERTEX_COUNT string Vertex count of network
Tcl script never n_vertex_count.xpd
N_XYEXTENT floatvector 2D display coordinate bounding box
xmin double
xmax double
ymin double
ymax double
Compiled C module V_XY atomchange merge hadd mod_n_xyextent.so
O_AREA double Area of surface patch or other graphical object
O_XYZ never
O_AREACHARGE double Partial charge associatd with a surface patch
O_XYZ O_CHARGE O_AREA never
O_CHARGE double Surface patch partial charge. Read for example from COSMO output files (filex_cosmo).
O_XYZ never
O_COLOR colorvector Color of surface area or point
atomchange bondchange 3drelative atom bond
O_DATA double Unclassified property data attached to surface elements
atomchange bondchange 3drelative atom bond
O_ID int Surface patch ID
atomchange bondchange 3drelative atom bond
O_IS_POINTVALUE boolean indicatesy whether O_DATA surface patch value belongs to O_POINTS (True) or to Triangles in O_TRIANGLE (False)
atomchange bondchange 3drelative atom bond
O_LABEL int Arbitrary label for surface elements and other graphics objects
(builtin) never
O_MOL_NUMBER int Number of molecule (A_MOL_NUMBER) surface element belongs to
(builtin) A_MOL_NUMBER atomchange bondchange 3drelative 3dabsolute
O_NORMALVECTOR floatvector Normal vectors for surface patches
O_XYZ atomchange bondchange 3drelative atom bond
O_POINT xyzvector like O_XYZ but contains a list of coordinates (vertex points) for bigger surface patches. If required, a surface computation can be performed with the VAMP program.
filename: { value: {} datatype: string constraints: writeable}
prgpath: { value: /usr/local/bin/vamp datatype: string}
method: { value: AM1 datatype: string}
Tcl script A_XYZ never o_point.xpd
O_POINTINDEX intvector Indices of surface points (O_POINT) which make up a geometric shape (triangle or triangle patch)
O_XYZ O_TYPE atomchange bondchange 3drelative atom bond
O_POTENTIAL double Surface patch potential potential (of undefined physical nature)
O_XYZ A_XYZ never
O_TRIANGLE xyzvector Triangle point coordinates of surface element
O_XYZ atomchange bondchange 3drelative atom bond
O_TYPE byte Type of surface patch
none:point:triangle:surface
atomchange bondchange 3drelative atom bond
O_VALUE doublevector like O_DATA but contains a vector of values for bigger surface patches
O_POINT atomchange bondchange 3drelative atom bond
O_XYZ floatvector Surface or other graphical object coordinates
A_XYZ never
P_ATOMS intvector Labels of atoms in pi system
Tcl script A_LABEL atomchange bondchange stereochange groupchange merge 3drelative 3dabsolute shuffle hadd dup mol atom bond ring sigma pi group reaction dataset file table network vertex edge surface ringsystem bondangle torsion hierarchy biological bioitem biolink 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 p_atoms.xpd
P_CLASS short Classification of pi systems
none:primary:orthogonal
pi
P_ELECTRON_COUNT int Number of pi electrons in the pi system.
Compiled C module A_FREE_ELECTRONS B_TYPE B_ORDER atomchange bondchange atom bond pi mod_p_electron_count.so
P_ELEMENT_COUNT shortvector Count of element types of atoms of pi system
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
Compiled C module A_ELEMENT A_TYPE atomchange merge hadd ring mod_p_element_count.so
P_EXCESS_ELECTRONS short Electron count in excess to electron pair and bond electrons in set. Used in (now abandonded) Beilstein XML format (bxml)
A_FORMAL_CHARGE B_TYPE B_ORDER A_FREE_ELECTRONS atomchange bondchange hadd atom bond
P_FORMULA string Elemental formula of the pi system
usecharges: { value: 0 datatype: boolean}
format: { value: ascii enumeration: ascii:html datatype: int}
useimplicith: { value: 0 datatype: boolean}
usequeryatoms: { value: 0 datatype: boolean}
Compiled C module P_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_ISOTOPE A_FORMAL_CHARGE A_QUERY atomchange atom pi mod_p_formula.so
P_HUCKEL_ENERGIES doublevector Pi system energies computed with a plain connectivity-only (not extended) Huckel model. Energies are in arbitrary beta units, with higher values corresponding to lower MO energies.
trace: { value: 0 description: If set, print matrices datatype: boolean}
hyperconjugation: { value: 1 description: If set, include alkyl substituents according to heteroatom hyperconjugation model datatype: boolean}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER P_ELECTRON_COUNT atomchange bondchange atom bond pi mod_p_huckel_energies.so
P_HUCKEL_HOMO_ENERGY double HOMO pi system energy, computed via plain Huckel approximation
atomchange bondchange atom bond pi
P_HUCKEL_LUMO_ENERGY double LUMO pi system energy, computed via plain Huckel approximation
atomchange bondchange atom bond pi
P_HUCKEL_MO_OCCUPANCY bytevector MO occupancy (electron count) according to plain Huckel model
P_HUCKEL_ENERGIES atomchange bondchange atom bond pi
P_LABEL int Arbitrary pi system label
(builtin) never
P_MOL_NUMBER short Number of molecule (A_MOL_NUMBER) pi system belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge pi
P_NATOMS int Size of pi system
(builtin) atomchange bondchange merge mol atom pi
Q_FILE compound Info about the file the biologics was read from
filename string
startrecord int
endrecord int
line int
format string
offset int64
length int
atomchange bondchange stereochange merge
Q_NAME string Free-text ID of biologics item
never
Q_URL url URL of molecular data file
never
R_AROMATIC byte Flags for aromatic (1) and antiaromatic (-1) rings
antiaromatic=-1:no=0:aromatic=1
strict: { value: 0 datatype: string}
exodb1pe: { value: 0 datatype: string}
(builtin) A_PICENTER A_FREE_ELECTRONS A_FORMAL_CHARGE B_TYPE B_ORDER atomchange bondchange ring
R_ATOMS intvector Labels of the atoms in the ring
(builtin) A_LABEL atomchange bondchange merge ring
R_BONDS intvector Labels of the bonds in the ring
(builtin) B_LABEL B_TYPE atomchange bondchange ring
R_CONJUGATED boolean Flag indicating a ring where all bonds are conjugated, as per the Ertl definition J. Chem. Inf. Model. 2014, 54, 1617-1622
Tcl script atomchange bondchange atom bond r_conjugated.xpd
R_DAYLIGHT_AROMATIC byte Flags for aromatic (1) and anti-aromatic (-1) rings, according to the Daylight aromaticity definition. It is a companion to standard property R_AROMATIC, which uses the switchable global aromaticity model. This property is for example used for Daylight-style structure matching without altering the global aromaticity model.
@antiaromatic:no:aromatic
strict: { value: 0 description: If set, always refuse aromaticity for rings where an atom partipicates in multiple multi-binds datatype: boolean}
exodb1pe: { value: 0 description: If set, an exo DB is assumed to contribute one pi electron, not zero. This interpretation matches some Daylight tools. datatype: boolean}
Compiled C module A_PICENTER A_FREE_ELECTRONS A_FORMAL_CHARGE B_TYPE B_ORDER atomchange bondchange ring mod_r_daylight_aromatic.so
R_ELEMENT_COUNT shortvector Count of element types of atoms of ring
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
Compiled C module A_ELEMENT A_TYPE atomchange merge hadd ring mod_r_element_count.so
R_FORMULA string Elemental formula of the ring
usecharges: { value: 0 datatype: boolean}
format: { value: ascii enumeration: ascii:html datatype: int}
useimplicith: { value: 0 datatype: boolean}
usequeryatoms: { value: 0 datatype: boolean}
Compiled C module R_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_QUERY A_ISOTOPE A_FORMAL_CHARGE atomchange atom mod_r_formula.so
R_FUSED_RING_COUNT int Number of rings this ring is fused to (fused means that two rings share a common bond)
Compiled C module R_TYPE atomchange bondchange atom bond mod_r_fused_ring_count.so
R_HASHGROUP_COUNT intvector Ring-oriented population of basic atom hash groups
Compiled C module A_EXTENDED_RINGHASH A_RINGSYSTEM_NUMBER atomchange bondchange merge hadd ring mod_r_hashgroup_count.so
R_HCOUNT short Number of hydrogen ligands on ring
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange hadd atom bond ring mod_r_hcount.so
R_HETEROATOM_COUNT byte Number of hetero atoms in the ring
(builtin) E_NRINGS A_ELEMENT A_TYPE atomchange bondchange ring
R_HETERO_SUBSTITUENT_COUNT short Number of non-hydrogen, non-carbon substituents outside ring bonded via valence or complex bond
Compiled C module A_TYPE B_TYPE A_ELEMENT atomchange bondchange atom bond ring mod_r_hetero_substituent_count.so
R_LABEL int Arbitrary ring label
(builtin) atomchange bondchange
R_MOL_NUMBER short Number of molecule ring belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge ring
R_NAME string Free-form user-defined ring name
atomchange bondchange stereochange ring
R_PI_ELECTRON_COUNT short Number of pi electrons in ring
Compiled C module A_FREE_ELECTRONS A_TYPE B_TYPE B_ORDER B_ISAROMATIC ring mod_r_pi_electron_count.so
R_QUERY compound Query attributes for matched substructure rings
^none:aromatic:aliphatic:saturated:unsaturated,insaturated:carbocyclic:heterocyclic:monocyclic:polycyclic
flags bitset
formula formulamatch
substituentcount bitset
valencecount bitset
neighborcount bitset
hydrogencount bitset
heterosubstituentcount bitset
ringbondcount bitset
pielectroncount bitset
query querytree
alphaformula formulamatch
atomchange bondchange atom bond
R_SIZE short Sizes of rings
(builtin) atomchange bondchange ring
R_SUBSTITUENT_COUNT short Number of non-hydrogen substituents outside ring bonded via valence or complex bond
Compiled C module A_TYPE B_TYPE A_ELEMENT atomchange bondchange atom bond ring mod_r_substituent_count.so
R_SYSTEM short Number of ring system the ring is part of, beginning with 1
(builtin) R_TYPE atomchange bondchange ring
R_TYPE bitset Ring classification
^none:sssr:esssr,triple:k,usssr:envelope
(builtin) atomchange bondchange ring
R_UNSATURATED short Number of classical multiple bonds in the ring
(builtin) B_TYPE B_ORDER atomchange bondchange ring
R_UNSATURATION short Overall unsaturation of ring (every non-aromatic multiple bond counts as n-1)
countarobonds: { value: 0 description: If set, aro bonds are counted with their Kekule bond order datatype: boolean}
Compiled C module B_TYPE B_ORDER B_ARORING_COUNT atomchange bondchange atom bond ring mod_r_unsaturation.so
R_VB_NEIGHBOR_COUNT short Number of ligands on ring
Compiled C module B_TYPE A_TYPE atomchange bondchange atom bond ring mod_r_vb_neighbor_count.so
S_LABEL int Arbitrary sigma system label
(builtin) never
S_MOL_NUMBER short Number of molecule (A_MOL_NUMBER) sigma system belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge sigma
T_AID int PubChem AID assay identifier
Tcl script never t_aid.xpd
T_ANNOTATED_MAP diskfile
(switchable between string blob diskfile url)
Image where data in table has been plotted into
imagefile: { value: kinmap1.png datatype: diskfile constraints: readable}
imagewidth: { value: 1275 datatype: int}
imageheight: { value: 1650 datatype: int}
coordsfile: { value: kinmap.tab datatype: diskfile constraints: readable}
xfactor: { value: 0.735 datatype: double}
yfactor: { value: -0.735 datatype: double}
xoffset: { value: 115 datatype: double}
yoffset: { value: 1550 datatype: double}
annotationfontsize: { value: 10 datatype: double}
annotationfont: { value: Arial datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
tagcolumn: { value: {} datatype: string}
namecolumn: { value: {} datatype: string}
shapecolumn: { value: {} datatype: string}
sizecolumn: { value: {} datatype: string}
outlinecolorcolumn: { value: {} datatype: string}
fillcolorcolumn: { value: {} datatype: string}
textcolorcolumn: { value: {} datatype: string}
headercolumn: { value: {} datatype: string}
footercolumn: { value: {} datatype: string}
datacolumn1: { value: {} datatype: string}
datacolumn2: { value: {} datatype: string}
datacolumn3: { value: {} datatype: string}
datacolumn4: { value: {} datatype: string}
datacolumn5: { value: {} datatype: string}
httpheader: { value: 0 datatype: int}
id: { value: {} datatype: string}
onmouseover: { value: {} datatype: string}
onmouseout: { value: {} datatype: string}
onclick: { value: {} datatype: string}
taglocations: { value: 0 datatype: boolean}
markedtaglocations: { value: {} datatype: string constraints: list}
markedtagcolor: { value: orange datatype: color}
markedtaglocations2: { value: {} datatype: string constraints: list}
markedtagcolor2: { value: red datatype: color}
imgonmousedown: { value: {} datatype: string}
imgonmouseup: { value: {} datatype: string}
imgonmousemove: { value: {} datatype: string}
taglocationonclick: { value: {} datatype: string}
dragobj: { value: 0 datatype: boolean}
shownamelegend: { value: 0 datatype: boolean}
showsizelegend: { value: 0 datatype: boolean}
tagsizelegend: { value: 25 5 50 10 75 15 100 20 comment: value/tagsize combos for legend datatype: string}
Tcl script atomchange bondchange stereochange atom bond t_annotated_map.xpd
T_AUTHOR compound Table author data, computation copies these from the internal object author fields
name string
author string
email string
phone string
orcid string
authorurl url
date date
version string
affiliation string
affiliationurl url
affiliationduns string
doi string
infourl url
street string
city string
zip string
state string
country string
literature string
keywords string
comment string
license string
licenseurl url
category string
repopath string
baseuuid string
versionuuid string
Tcl script never t_author.xpd
T_COMMENT stringvector FCree-form table comment strings
never
T_DIVERSITY_SET table Select a diverse subset from the source dataset.
property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property}
structurecolumn: { value: -1 description: Column with decodable structure data or a structure cell object which is used to perform the structure filter query on, or to compute the similarity bitvector if it is not taken from a table column. Value -1 uses the row ensemble. datatype: int}
query: { value: all description: Structure filter query expression datatype: string}
size: { value: 50 description: Target size minvalue: 1 datatype: int}
startrow: { value: -1 description: First structure source row, -1 is random datatype: int}
minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int}
Tcl script atomchange bondchange atom bond t_diversity_set.xpd
T_EXTJS_VISUALIZATION blob
(switchable between blob diskfile)
Interface to standard Web visualizations using the ExtJS JavaScript library
style: { value: barchart description: Graphics style enumeration: barchart datatype: int}
height: { value: 300 description: Canvas width minvalue: 50 maxvalue: 5000 datatype: int}
width: { value: 400 description: Canvas height minvalue: 50 maxvalue: 5000 datatype: string}
xcolumn: { value: 0 datatype: string}
ycolumn: { value: 1 datatype: string}
font: { value: sans-serif datatype: string}
fontsize: { value: 10 minvalue: 5 maxvalue: 32 datatype: int}
barcolor: { value: #4682B4 datatype: string}
margin: { value: 25 minvalue: 0 maxvalue: 100 datatype: int}
ylabel: { value: {} datatype: string}
xlabel: { value: {} datatype: string}
filename: { value: {} datatype: string}
htmlpage: { value: 0 description: If set, write complete HTML page, otherwise write only ExtJS generator statements. datatype: boolean}
title: { value: {} description: Graph title datatype: string}
rendertarget: { value: {} description: DOM id of object to render to (empty is default body) datatype: string}
extjspath: { value: . description: path to ExtJS installation datatype: string}
graphvar: { value: graph description: JavaScript variable to hold the graph root object reference. If empty, do not set a var. datatype: string}
valuelabels: { value: 1 description: if set, add point/bar value labels datatype: boolean}
Tcl script atomchange bondchange atom bond t_extjs_visualization.xpd
T_HISTOGRAM blob
(switchable between blob diskfile)
Histogram plot of a table column as a GIF or PNG image. Also computes image map T_HISTOGRAM_IMAGE_MAP for Web applications.
width: { value: 200 datatype: int}
height: { value: 200 datatype: int}
nbins: { value: 5 datatype: int}
datacolumn: { value: 0 datatype: string}
bgcolor: { value: white datatype: color}
barcolor1: { value: grey datatype: color}
barcolor2: { value: black datatype: color}
format: { value: png enumeration: gif:png,png24:png8 datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
axiscolor: { value: black datatype: color}
border: { value: 5 datatype: int}
spacing: { value: 3 datatype: int}
axisfont: { value: arialn datatype: string}
axisfontsize: { value: 8 datatype: double}
tickwidth: { value: 3 datatype: int}
nticks: { value: 5 datatype: int}
showxname: { value: 1 datatype: boolean}
showxrange: { value: 1 datatype: boolean}
Tcl script never t_histogram.xpd
T_HISTOGRAM_IMAGEMAP string Image map associated with table column histogram T_HISTOGRAM
name: { value: {} datatype: string}
target: { value: {} datatype: string}
url: { value: {} datatype: url}
title: { value: {} datatype: string}
mapcolumn: { value: {} datatype: string}
T_HISTOGRAM never
T_HISTORY compoundvector Table data record processing history
program string
version string
patchlevel string
pgmdate date
user string
date date
machine string
never
T_IDENT string Table ID
Tcl script atomchange bondchange atom bond t_ident.xpd
T_NAME string Table name
atomchange bondchange atom bond
T_NCBI_ASSAY_ANNOTATED_XREFS compoundvector NCBI annotated assay reference
{} {} undefined:pcit=1:pgene=2
xref choice
comment string
type int
never
T_NCBI_ASSAY_CONCENTRATION compound NCBI assay concentration item
0 {mm=4:um=5:nm=6:pm=7:fm=8:mgml=9:ugml=10:ngml=11:pgml=12:fgml=13:m=14:unspecified=254} -1
concentration double
unit int
dr-id int
never
T_NCBI_ASSAY_COUNTS intvector Activity counts for a PubChem assay
sid_total int
sid_active int
sid_inactive int
sid_inconclusive int
sid_unspecified int
sid_probe int
cid_total int
cid_active int
cid_inactive int
cid_inconclusive int
cid_unspecified int
cid_probe int
Compiled C module never mod_t_ncbi_assay_counts.so
T_NCBI_ASSAY_DESCRIPTION compound NCBI assay description data
{} {} {} {} {} {} {} {} {} {} {} other:screening:confirmatory:summary {} smallmolecule=1:nucleotide=2:other=255 {} mlscn=1:mlpcn=2:mlscn-ap=3:mlpcn-ap=4:journal-article=5:assay-vendor=6:literature-extracted=7:literature-author=8:literature-publisher=9:rnaigi=10:other=255
aid compound
source choice
name string
description stringvector
protocol stringvector
comment stringvector
xrefs compoundvector
results compoundvector
pub choicevector
revision int
targets compoundvector
activity-outcome-method int
doseresponses compoundvector
substance-type int
grant-number stringvector
project-category int
is-panel boolean
assay-group stringvector
panel-info compound
is-mlp-late-stage boolean
categorized-comment dictionary
Compiled C module never mod_t_ncbi_assay_description.so
T_NCBI_ASSAY_DOSE_RESPONSE_ATTRIBUTIONS compoundvector NCBI assay dose/response attribution
id int
description string
dn string
rn string
type int
never
T_NCBI_ASSAY_ID compound NCBI assay identifier
aid int
version int
Tcl script never t_ncbi_assay_id.xpd
T_NCBI_ASSAY_PANEL compound Info on assay panels (combined assays)
name string
description string
members compoundvector
never
T_NCBI_ASSAY_PANEL_MEMBERS compoundvector Info on assay panel members
{} {} {} {} {} {} {} other:screening:confirmatory:summary
mid int
name string
description string
protocol stringvector
comment stringvector
targets compoundvector
xrefs compoundvector
activity-outcome-method int
doseresponses compoundvector
categorized-comment dictionary
never
T_NCBI_ASSAY_PANEL_TEST_RESULT intpair Assay panel test result data
{} regular=1:outcome=2:score=3:ac=4
never
T_NCBI_ASSAY_RESULT_CONSTRAINTS choice NCBI assay result column constraints
fset floatvector
fmin double
fmax double
frange floatpair
iset intvector
imin int
imax int
irange intpair
sset stringvector
never
T_NCBI_ASSAY_RESULT_TYPES compoundvector NCBI assay result (column) definitions
{} {} {} float=1:int=2:bool=3:string=4 {} ppt=1:ppm=2:ppb=3:mm=4:um=5:nm=6:pm=7:fm=8:mg/ml,mgml=9:ug/ml,ugml=10:ng/ml,ngml=11:pg/ml,pgml=12:fm/ml,fmml=13:m=14:percent=15:ratio=16:sec=17:rsec=18:min=19:rmin=20:day=21:rday=22:ml/min/kg,ml-min-kg,mlminkg=23:l/kg,l-kg,lkg=24:hr*ng/ml,hr-ng-ml,hrngml=25:cm/sec,cm-sec,cmsec=26:mg/kg,mg-kg,mgkg=27:none=254:unspecified=255 {} linear=1:ln=2:log=3:reciprocal=4:negative=5:nlog=6:nln=7 {} {} {} {} none:pmid:mmdb:url:protein-gi:nucleotide-gi:taxonomy:mim:gene:probe:aid:sid:cid:protein-target-gi:nucleotide-target-gi:target-name:target-descr:target-tax-id:gene-target-id
tid int
name string
description stringvector
type int
constraints choice
unit int
sunit string
transform int
stransform string
tc compound
ac boolean
panelinfo intpair
annotation int
never
T_NCBI_ASSAY_SUBMIT choice NCBI assay submission data
aid int
source choice
description compound
aidversion intpair
never
T_NCBI_ASSAY_TARGETS compoundvector NCBI assay target data
{} {} {unknown=0:protein=1:dna=2:rna=3:other-biopolymer=4}
name string
mol-id int
molecule-type int
organism compound
description string
comment stringvector
never
T_NCBI_ASSAY_XREF choice NCBI assay crossreference data
regid string
rn string
mesh string
pmid int
gi int
mmdb int
sid int
cid int
dburl url
sburl url
asurl url
protein-gi int
nucleotide-gi int
taxonomy int
aid int
mim int
gene int
probe int
biosystem int
geogse int
geogsm int
patent string
never
T_NCBI_BIBLIO_AFFILIATION choice NCBI author affiliation
str string
std compound
never
T_NCBI_BIBLIO_ARTICLE_FROM choice Article container reference
journal compound
book compound
proc compound
never
T_NCBI_BIBLIO_ARTICLE_ID_SET choicevector Article reference ID set
pubmed int
medline int
doi string
pii string
pmcid int
pmcpid string
pmpid string
other compound
never
T_NCBI_BIBLIO_AUTHORS choice NCBI author reference
std compoundvector
ml stringvector
str stringvector
never
T_NCBI_BIBLIO_AUTHOR_LIST compound NCBI author reference
names choice
affil choice
never
T_NCBI_BIBLIO_FULL_AUTHOR_SET compoundvector NCBI author reference
{} primary=1:secondary=2 compiler=1:editor=2:patent-assignee=3:translator=4
name choice
level int
role int
affil choice
is-corr boolean
never
T_NCBI_BIBLIO_IMPRINT compound Document imprint data
{} {} {} {} {} {} {} {} {} published:submitted:in-press:other=255 {} {} none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255
date date
volume string
issue string
pages string
section string
pub choice
cprt date
part-sup string
language string
prepub int
part-supi string
retract compound
pubstatus int
history compoundvector
never
T_NCBI_BIBLIO_MEETING compound Meeting reference
number string
date date
place choice
never
T_NCBI_BIBLIO_PATENT_ID choice Patent ID reference
number string
app-number string
never
T_NCBI_BIBLIO_PATENT_PRIORITY compoundvector Patent priorities
country string
number string
date date
never
T_NCBI_BIBLIO_PUBSTATUS_HISTORY compoundvector Publication status history
none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255
pubstatus int
date date
never
T_NCBI_BIBLIO_RETRACTION compound Document retraction information
none:retracted:notice:in-error:erratum
type int
exp string
never
T_NCBI_BIBLIO_STD_AFFILIATION compound NCBI structured affiliation
affil string
div string
city string
sub string
country string
street string
email string
fax string
phone string
postal-code string
never
T_NCBI_BIBLIO_TITLE choicevector NCBI bibliographic title reference
name string
tsub string
trans string
jta string
iso-jta string
ml-jta string
coden string
issn string
abr string
isdn string
never
T_NCBI_BIOSOURCE compound NCBI assay target organism
{unknown:genomic:chloroplast:chromoplast:kinetoplast:mitochondrion:plastid:macronuclear:extrachrom:plasmid:transposon:insertion-seq:cyanelle:proviral:virion:nucleomorph:apicoplast:leucoplast:proplastid:endogenous-virus:hydrogenosome:chromosome} {unknown:natural:natmut:mut:artificial:synthetic:other=255}
genome int
origin int
organism compound
never
T_NCBI_DBTAG compound Structured data to identify a database entry
db string
tag string
never
T_NCBI_DBTAGS compoundvector Structured data to identify a database entry
db string
tag string
never
T_NCBI_DBTRACKING compound NCBI assy db source data
name string
source-id string
date date
description string
pub choice
never
T_NCBI_MMDB compound MMDB source information
mmdb-id int
molecule-id int
molecule-name stringvector
residue-id int
residue-name string
atom-id int
atom-name string
never
T_NCBI_ORGANISM compound NCBI organism descriptor
taxname string
common string
mod stringvector
db compoundvector
syn stringvector
never
T_NCBI_PERSON_ID choice NCBI person reference
dbtag compound
name compound
str string
consortium string
never
T_NCBI_PUBLICATION choice Publication in PubMed style
gen compound
sub compound
medline compound
muid int
article compound
journal compound
book compound
proc compound
patent compound
pat-id compound
man compound
equiv choicevector
pmid int
never
T_NCBI_PUBLICATION_ARTICLE compound Article reference
title choicevector
authors compound
from choice
ids choicevector
never
T_NCBI_PUBLICATION_BOOK compound Book reference
title choicevector
coll choicevector
authors compound
imp compound
never
T_NCBI_PUBLICATION_GENERAL compound General publication reference
cit string
authors compound
muid int
journal choicevector
volume string
issue string
pages string
date date
serial-number int
title string
pmid int
never
T_NCBI_PUBLICATION_JOURNAL compound Journal reference
title choicevector
imp compound
never
T_NCBI_PUBLICATION_MANUSCRIPT compound Manuscript reference
{} {} unknown:manuscript:letter:thesis
cit compound
man-id string
type int
never
T_NCBI_PUBLICATION_MEDLINE compound Medline reference
{} {} {} {} {} {} {} {} {} {} {} {} publisher:premedline:medline
uid int
em date
cit compound
abstract string
mesh compoundvector
substance compoundvector
xref compoundvector
idnum stringvector
gene stringvector
pmid int
pub-type stringvector
mlfield compoundvector
status int
never
T_NCBI_PUBLICATION_MEDLINE_FIELD_DOCREF_SET compoundvector Docrefs of NCBI medline field of publication
none:medline:pubmed:ncbigi
type int
uid int
never
T_NCBI_PUBLICATION_MEDLINE_FIELD_SET compoundvector NCBI medline field of publication
other:comment:erratum
type int
str string
ids compoundvector
never
T_NCBI_PUBLICATION_MEDLINE_MESH_QUALIFIER_SET compoundvector Medline mesh term qualifiers
mp boolean
subh string
never
T_NCBI_PUBLICATION_MEDLINE_MESH_SET compoundvector Medline mesh references
mp boolean
term string
qual compoundvector
never
T_NCBI_PUBLICATION_MEDLINE_RN_SET compoundvector Medline substance references
nameonly:cas:rc
type int
cit string
name string
never
T_NCBI_PUBLICATION_MEDLINE_SI_SET compoundvector Medline crossreferences
none:ddbj:carbbank:embl:hdb:genbank:hgml:mim:msd:pdb:pir:prfseqdb:psd:swissprot:gdb
type int
cit string
never
T_NCBI_PUBLICATION_PATENT compound Patent reference
title string
authors compound
country string
doc-type string
number string
date-issue date
class stringvector
app-number string
app-date date
applicants compound
assignees compound
priority compoundvector
abstract string
never
T_NCBI_PUBLICATION_PATENT_ID compound Patent ID reference
country string
id choice
doc-type string
never
T_NCBI_PUBLICATION_PROCEEDINGS compound Proceedings reference
book compound
meeting compound
never
T_NCBI_PUBLICATION_SET choicevector Publication in PubMed style
gen compound
sub compound
medline compound
muid int
article compound
journal compound
book compound
proc compound
patent compound
pat-id compound
man compound
equiv string
pmid int
never
T_NCBI_PUBLICATION_SUBMISSION compound Submission reference
{} {} unknown:paper:tape:floppy:email:other=255
authors compound
imp compound
medium int
date date
descr string
never
T_NCBI_SOURCE choice NCBI assay source data
individual choice
db compound
mmdb compound
Tcl script never t_ncbi_source.xpd
T_NCBI_STD_NAME compound NCBI standardized name reference
last string
first string
middle string
full string
initials string
suffix string
title string
never
T_PUBCHEM_URL url PubChem assay id data display URL
Tcl script T_AID atomchange bondchange stereochange merge t_pubchem_url.xpd
T_QUERY compound Structured information about query used to generate this table.
ens,structure:enslist,elist,structures:record,rec:recordlist,reclist:bitvector,bit:count,cnt:delete,del:property,prop:propertylist,proplist:file,molfile:filelist:table,qtable,hitlist:reaction:reactionlist,xlist,reactions:array,tclarray,pythonarray:vrecord,vrec:vrecordlist,vreclist:custom:customlist:ensblob:reactionblob:exists:tablecollection:vertex:vertexlist:row,index:rowlist,indexlist
mode int
query string
retrieve string
timeout int
maxhits int
date datetime
startpos int
endpos int
nhits int
nexamined int
querytime int
eof boolean
comment string
displayquery string
file string
parameters string
webenv string
extid int
extdb string
never
T_QUERY_GIF diskfile
(switchable between string blob diskfile url)
Depiction of query used to generate a table
width: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int}
height: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int}
bgcolor: { value: transparent datatype: color}
suppressnodes: { value: E_LIVE_IN_ENTREZ datatype: string}
frame: { value: 0 datatype: int}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int}
crop: { value: 2 minvalue: -1 datatype: int}
format: { value: gif datatype: string}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
fixiepngsize: { value: 1 datatype: boolean}
molimgwidth: { value: 75 minvalue: 25 maxvalue: 500 datatype: int}
molimgheight: { value: 75 minvalue: 25 maxvalue: 500 datatype: int}
font: { value: arialn datatype: string}
fontsize: { value: 8 datatype: string}
interlace: { value: 1 datatype: string}
suppressedproperties: { value: {} datatype: string constraints: propertylist}
downloadfilename: { value: {} datatype: string}
Compiled C module T_QUERY never mod_t_query_gif.so
T_TIMESTAMP datetime Table timestamp
Tcl script never t_timestamp.xpd
T_XYPLOT blob
(switchable between blob diskfile)
XY plot of two table columns
width: { value: 200 datatype: int}
height: { value: 200 datatype: int}
xdatacolumn: { value: 0 datatype: string}
ydatacolumn: { value: 1 datatype: string}
bgcolor: { value: white datatype: color}
format: { value: gif datatype: string}
filename: { value: {} datatype: string constraints: writeable}
axiscolor: { value: black datatype: color}
border: { value: 5 datatype: int}
spacing: { value: 3 datatype: int}
axisfont: { value: arialn datatype: string}
axisfontsize: { value: 8 datatype: int}
tickwidth: { value: 3 datatype: int}
xnticks: { value: 5 datatype: int}
ynticks: { value: 5 datatype: int}
markercolor: { value: black datatype: color}
markerstyle: { value: cross enumeration: cross:box:diamond:circle:dot datatype: string}
markersize: { value: 5 datatype: int}
showxname: { value: 1 datatype: boolean}
showyname: { value: 1 datatype: boolean}
xaxisstart: { value: auto datatype: string}
yaxisstart: { value: auto datatype: string}
Tcl script never t_xyplot.xpd
T_XYPLOT_IMAGEMAP string Image map associated with xyplot
name: { value: {} datatype: string}
target: { value: {} datatype: string}
url: { value: {} datatype: string}
title: { value: {} datatype: string}
mapcolumn: { value: {} datatype: string}
T_XYPLOT never
U_LABEL int Arbitrary label for torsion objects
(builtin) never
U_MOL_NUMBER short Number of molecule (A_MOL_NUMBER) torsion belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge torsion
V_COMMENT string Vertex (node) comment in free format
never
V_GRAPHICS compoundvector Vertex (node) graphics
none:arc:bitmap:image:line:oval,ellipse,ellipsis:polygon:rectangle,rect:text:box:circle:rhombus,diamond:ver_ellipsis:hor_ellipsis:triangle:pentagon:hexagon:octagon:roundedrectangle,roundrectangle,roundrect,roundedrect
type int
attributes dictionary
imgproperty: { value: E_GIF description: Property to use as image data datatype: string constraints: property}
directory: { value: img description: Image directory datatype: string constraints: directory}
imgparameters: { value: crop 4 bonds 6 frame 0 bgcolor white height 120 width 120 bondcolor black atomcolor black asymbol xsymbol description: Override attributes for the image computation datatype: dictionary}
Tcl script V_STRUCTURE never v_graphics.xpd
V_HASHY uint64 Vertex node structure hash, without stereochemistry or isotope labelling (usually copied from E_HASHY structure values)
atomchange bondchange atom bond
V_IDENT string Vertex ident string
Compiled C module never mod_v_ident.so
V_LABEL int Vertex (node) label in network objects
Compiled C module never mod_v_label.so
V_LABELSET intvector Vertex (node) full label set (primary and alternative). This is for example used in the OBO network format I/O module.
never
V_LABEL_GRAPHICS compound Vertex (node) label graphics
none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon
type int
attributes dictionary
never
V_LEVEL short Distance of vertex to root
Compiled C module never mod_v_level.so
V_NAME string Vertex (node) name in free format
never
V_ONTOLOGY_DBXREFS compoundvector Ontology database cross references
db string
record string
description string
never
V_ONTOLOGY_TERM compound Ontology term. Used for example in the OBO network data I/O module
id string
name string
definition compound
synonyms compoundvector
dbxrefs compoundvector
substructure structure
structurehash uint64
altids stringvector
obsolete boolean
comment string
never
V_ONTOLOGY_TERM_DEFINITION compound Ontology term definition with references to database entries defining these
definition string
dbxrefs compoundvector
never
V_ONTOLOGY_TERM_SYNONYMS compoundvector Ontology term synonyms, with classification of the synonym relationship and database references thereof
{} default:exact:broad:narrow:related
text string
scope int
type string
dbxrefs compoundvector
never
V_PARTITION int Partition code for vertices (nodes). If a symbolic name is available, I/O modules modify the enumeration field of the property.
atomchange bondchange atom bond
V_RECORD int Reference record number (1-based) for a vertex data item
atomchange bondchange atom bond
V_SMALLWORLD_DATA compound Vertex data for a fragment network modelled after R. Sayles SmallWorld approach
record int
smiles string
count int
atomchange bondchange atom bond
V_STRUCTURE structure A structure associated with a network vertex/node
never
V_TEXT string Vertex (node) text label
never
V_TYPE string Vertex type identifier (free form)
atomchange bondchange atom bond
V_URL url Vertex reference URL
atomchange bondchange atom bond
V_WEIGHT double Graph vertex (node) weight
Compiled C module never mod_v_weight.so
V_XY floatpair Vertex (node) graph coordinates
x float
y float
layouter: { value: neato enumeration: dot:neato:twopi:circle:fdp:sfdp:patchwork datatype: string}
Compiled C module never mod_v_xy.so
X_ANNOTATION choicevector Graphical annotation objects for reaction renderings. This is a choice vector type, the structure of every supported annotation type is defined by its own X_xxx_ANNOTATION property-
text compound
rectangle compound
ellipse compound
roundedrectangle compound
polyline compound
bracket compound
A_XY never
X_ARROW compound Reaction arrow style
none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow
style byte
overtext stringvector
undertext stringvector
p1 floatpair
p2 floatpair
never
X_ASCII_IMAGE string
(switchable between string unicode)
Ascii (or Unicode) rendering of a reaction.

Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the last line.
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
showreagent: { value: 1 datatype: boolean}
showproduct: { value: 1 datatype: boolean}
showintermediate: { value: 1 datatype: boolean}
Compiled C module E_ASCII_IMAGE E_REACTION_ROLE atomchange bondchange stereochange merge mol atom bond mod_x_ascii_image.so
X_ATOM_ECONOMY double Sum of the molecular weight of the products divided by the sum of the molecular weight of the reagents
Tcl script atomchange bondchange atom bond x_atom_economy.xpd
X_AUTHOR compound Information about the original author of a reaction or related document
name string
author string
email string
phone string
orcid string
authorurl url
date date
version string
affiliation string
affiliationurl url
affiliationduns string
doi string
infourl url
street string
city string
zip string
state string
country string
literature string
keywords string
comment string
license string
licenseurl url
category string
repopath string
baseuuid string
versionuuid string
never
X_BRACKET_ANNOTATION compound Bracket annotation for reaction renderings. This is a choice vector branch of property X_ANNOTATION.
{} {} {} ROUND:SQUARE:BRACES:CHEVRONS SINGLE:DOUBLE
coords floatvector
linecolor color
linewidth float
type int
orientation int
A_XY never
X_CGR structure Condensed graph representation of the reaction. This format includes a superset of all atoms and bonds (marked in B_REACTION_CENTER) which participate in the reaction. The result pseudo structure usually violates valence bond rules. Hoonakker, F.; Lachiche, N.; Varnek, A. Condensed Graph of Reaction: Considas one single pseudo molecule. Int. J. Artif. Intell. Tools 2011, 20, 253–270.
Tcl script atomchange bondchange atom bond pi reaction ringsystem x_cgr.xpd
X_CLASS string Free-form reaction classification
atomchange bondchange stereochange atom bond
X_CML_STRING string CML reaction encoding as a string
pedantic: { value: 1 datatype: boolean}
Tcl script never x_cml_string.xpd
X_COLOR color Background color to use in plots
never
X_COMMENT stringvector Free form comment for reaction
never
X_CONVENTION string Free-form textual description of reaction encoding convention
never
X_DELTA_ALIRING_COUNT int Change in number of aliphatic ESSSR rings in the reaction
Tcl script E_ALIRING_COUNT atomchange bondchange atom bond x_delta_aliring_count.xpd
X_DELTA_ARORING_COUNT int Change in number of aromatic ESSSR rings in the reaction
Tcl script E_ARORING_COUNT atomchange bondchange atom bond x_delta_aroring_count.xpd
X_DELTA_RING_COUNT int Change in number of ESSSR rings in the reaction
Tcl script E_NESSSR atomchange bondchange atom bond x_delta_ring_count.xpd
X_DIRECTION byte Reaction direction encoding
undefined:forward:equilibrium,both:backward,reverse
atomchange bondchange stereochange atom bond
X_ELLIPSE_ANNOTATION compound Ellipse or circle annotation for reaction renderings. This is a choice vector branch of property X_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
A_XY never
X_EMF_IMAGE diskfile
(switchable between blob diskfile url)
EMF/WMF reaction depiction
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
height: { value: 180 datatype: int}
width: { value: 400 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
crop: { value: -1 datatype: int}
header: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
footer: { value: {} datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
border: { value: 12 datatype: int}
bgcolor: { value: transparent datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: X_NAME datatype: string}
reaction: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
format: { value: emf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int}
arrowsize: { value: 35 datatype: int}
bonds: { value: 8 datatype: int}
arrowcolor: { value: black datatype: color}
showsolvent: { value: 1 datatype: boolean}
annotationfontsize: { value: -1 datatype: double}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
solventcolor: { value: blue datatype: color}
reagentcolor: { value: blue datatype: color}
framecolor: { value: black datatype: color}
suppressedfragmentsfile: { value: reagents.tbin datatype: diskfile constraints: readable}
showplus: { value: 1 datatype: boolean}
arrowtext_over: { value: {} datatype: string}
arrowtext_under: { value: {} datatype: string}
showempty: { value: 1 datatype: boolean}
font: { value: arialn datatype: string}
showmapping: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int}
usesubscripts: { value: 1 datatype: boolean}
arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int}
compact: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
usereagenttable: { value: 0 datatype: boolean}
showintermediate: { value: 0 datatype: boolean}
Compiled C module M_EMF_IMAGE atomchange bondchange stereochange merge mol atom bond mod_x_emf_image.so
X_ENZYMES stringvector IDs of enzymes participating in the reaction
atomchange bondchange stereochange atom bond
X_FILE compound Info about the file the reaction was read from
filename string
startrecord int
endrecord int
line int
format string
offset int64
length int
atomchange bondchange stereochange merge
X_GIF diskfile
(switchable between string blob diskfile url)
GIF/PNG reaction depiction
height: { value: 180 datatype: int}
width: { value: 400 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 datatype: int}
crop: { value: -1 datatype: int}
header: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
footer: { value: {} datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: color constraints: property}
border: { value: 12 datatype: int}
bgcolor: { value: white datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: X_NAME datatype: string}
reaction: { value: none enumeration: none:cactvs,blob:rxnfile:rdfile datatype: int}
metadata: { value: 1 datatype: boolean}
format: { value: gif enumeration: png,png24:png8:gif datatype: string}
arrowsize: { value: 35 datatype: int}
bonds: { value: 8 datatype: double}
arrowcolor: { value: black datatype: color}
showsolvent: { value: 1 datatype: boolean}
showcatalyst: { value: 1 datatype: boolean}
annotationfontsize: { value: -1 datatype: double}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
solventcolor: { value: blue datatype: color}
framecolor: { value: black datatype: color}
antialiasing: { value: 3 datatype: int}
suppressedfragmentsfile: { value: reagents.tbin datatype: diskfile constraints: readable}
showplus: { value: 1 datatype: boolean}
arrowtext_over: { value: {} datatype: string}
arrowtext_under: { value: {} datatype: string}
showempty: { value: 1 datatype: boolean}
font: { value: dejavusans datatype: string}
showmapping: { value: 0 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
frame: { value: 0 datatype: boolean}
arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int}
compact: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
showintermediate: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
invert: { value: 0 description: If set, reverse drawing of reaction direction datatype: boolean}
interlace: { value: 1 datatype: boolean}
usereagenttable: { value: 0 datatype: boolean}
Compiled C module M_GIF E_REACTION_ROLE X_XYEXTENT atomchange bondchange stereochange atom bond mod_x_gif.so
X_HASH uint64 Reaction hashcode, without stereochemistry and isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_HASHY E_REACTION_ROLE atomchange bondchange atom bond mod_x_hash.so
X_HASH128 uint128 128 bit reaction hashcode, without stereochemistry and isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_HASH128 E_REACTION_ROLE atomchange bondchange atom bond mod_x_hash128.so
X_HISTORY compoundvector Reaction data record processing history
program string
version string
patchlevel string
pgmdate date
user string
date date
machine string
never
X_IDENT string Free-form Reaction ID
Tcl script never
X_INCHI string RInChI string of reaction
prefix: { value: 1 description: Wether to include the RInChI= prefix datatype: boolean}
Compiled C module X_DIRECTION X_RDF_STRING E_REACTION_ROLE atomchange bondchange stereochange atom bond mod_x_inchi.so
X_INCHI_AUXINFO string Auxinfo part of reaction InChI (RINCHI)
atomchange bondchange stereochange atom bond
X_ISOTOPE_HASH uint64 Reaction hashcode, without stereochemistry and with isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_HASHIY E_REACTION_ROLE atomchange bondchange atom bond mod_x_isotope_hash.so
X_ISOTOPE_HASH128 uint128 128 bit reaction hashcode, without stereochemistry but with isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_ISOTOPE_HASH128 E_REACTION_ROLE atomchange bondchange atom bond mod_x_isotope_hash128.so
X_ISOTOPE_STEREO_HASH uint64 Reaction hashcode, with stereochemistry and isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_HASHISY E_REACTION_ROLE atomchange bondchange atom bond mod_x_isotope_stereo_hash.so
X_ISOTOPE_STEREO_HASH128 uint128 128 bit reaction hashcode, with stereochemistry and isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_ISOTOPE_STEREO_HASH128 E_REACTION_ROLE atomchange bondchange atom bond mod_x_isotope_stereo_hash128.so
X_KEGG_ID string Reaction KEGG ID (www.genome.jp)
atomchange bondchange stereochange merge
X_LEVEL int Reaction level
never
X_LHASA_GIF diskfile
(switchable between blob diskfile url)
GIF/PNG rendering of a Lhasa transform result (from X_LHASA_SCORE data)
format: { value: png enumeration: png,png24:png8:gif datatype: int}
height: { value: 220 datatype: int}
width: { value: 500 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 datatype: int}
reaction: { value: none enumeration: none:cactvs,blob:rxnfile:rdfile datatype: int}
antialiasing: { value: 3 datatype: int}
downloadfilename: { value: {} datatype: string}
bgcolor: { value: transparent datatype: color}
font: { value: dejavusans datatype: string}
border: { value: 12 datatype: int}
interlace: { value: 1 datatype: boolean}
arrowsize: { value: 35 datatype: int}
arrowcolor: { value: black datatype: color}
bonds: { value: 8 datatype: double}
showintermediate: { value: 1 datatype: boolean}
showattackpoints: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset}
showlocants: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset}
locants: { value: 0 datatype: string constraints: list}
annotationfontsize: { value: -1 datatype: double}
showplus: { value: 1 datatype: boolean}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
showpath: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset}
showbondchanges: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset}
arrowtext_over: { value: {} datatype: string}
arrowtext_under: { value: {} datatype: string}
arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int}
asymbol: { value: symbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: color constraints: property}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
Compiled C module X_LHASA_SCORE X_XYEXTENT M_GIF E_REACTION_ROLE atomchange bondchange atom bond mod_x_lhasa_gif.so
X_LHASA_LOCANTS compoundvector Atom and bond locant set used by the Lhasa engine, describing a set of atoms and/or bonds which participated in a score, Contains atoms and/or bond labels.
atomset intvector
bondset intvector
atomchange bondchange stereochange mol atom bond ring
X_LHASA_REPORT diskfile
(switchable between blob diskfile url)
HTML-formatted report on a scored Lhasa reaction
templatefile: { value: report.htpl datatype: diskfile constraints: readable}
filename: { value: {} datatype: diskfile constraints: writeable}
pagewrapper: { value: 1 datatype: boolean}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: string}
Tcl script X_LHASA_SCORE X_LHASA_GIF atomchange bondchange atom bond x_lhasa_report.xpd
X_LHASA_SCORE compound Retroreaction scores, ratings and reaction conditions computed via a Lhasa CHMTRN rule.
{} {} {} {} {} {} {} {} {} {} {} {} {} {^none:protected:interfering:participating} {} {} {} {} {} {} {} {} {} {} {}
ident int
name string
url url
authorlitref string
score int
basescore int
ratings dictionary
conditions stringvector
conditioncodes intvector
descriptiveconditions stringvector
actualconditions stringvector
warnings stringvector
warningcodes intvector
atommarks int
variables dictionary
pathatoms intvector
pathbondatoms intpairvector
brokenbondatoms intpairvector
changedbondatoms intpairvector
newbondatoms intpairvector
scorefactors compoundvector
genericlitrefs stringvector
optlitrefs stringvector
title string
atomchange bondchange stereochange atom bond
X_LHASA_SCORE_FACTORS compoundvector Registered atom and bond configurations which influenced the Lhasa score for this retroreaction.
undefined,undef,none:reagent,educt,reactant:product:solvent:catalyst:intermediate:impurity:byproduct:agent:waste:precursor:altreagent
reactionstep int
locants compoundvector
condition dictionary
atomchange bondchange stereochange mol atom bond ring
X_LONG_INCHIKEY string Long reaction InChI (RINCHI) key variant
Compiled C module X_INCHI atomchange bondchange stereochange atom bond mod_x_long_inchikey.so
X_METADATA dictionary Dublin Core metadata on this reaction
never
X_MINIMOL blob Minimol representation of a reaction
Compiled C module atomchange bondchange stereochange merge 3dabsolute atom bond mod_x_minimol.so
X_MRV_STRING string MRV reaction reacord encoding as a string (with newlines)
Tcl script never x_mrv_string.xpd
X_NAME string Long reaction identification string
Tcl script never
X_NUMBER int Reaction number intended to be used as identifier
never
X_POLYLINE_ANNOTATION compound Polyline as reaction drawing annotation. This is one of the choice variants of property X_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
style bitset
headskip double
tailskip double
headwidth double
tailwidth double
headlength double
taillength double
headflags bitset
tailflags bitset
arcangle double
curved boolean
A_XY never
X_PRODUCT_NUMBERS shortvector ID number of reaction products
never
X_RDF_STRING string RDF reaction record encoded as a string
reverse: { value: 0 description: if set, reverse direction of reaction datatype: boolean}
Tcl script E_REACTION_ROLE atomchange bondchange stereochange merge hadd atom bond x_rdf_string.xpd
X_REACTION_TEMPLATE reaction Reaction template extracted from full reaction Coley, Connor, JCIM 2019
Tcl script A_MAPPING atomchange bondchange stereochange atom bond x_reaction_template.xpd
X_REAGENT_NUMBERS shortvector ID number of reaction reagents
never
X_RECTANGLE_ANNOTATION compound Rectangular annotation object for reaction renderings. This is a choice vector branch of property X_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
A_XY never
X_REREG string MDL external registry number
never
X_REVERSE_REACTION reaction Reverse reaction, i.e. with swapped reagent and product, other reaction roles unchanged
Tcl script E_REACTION_ROLE never x_reverse_reaction.xpd
X_RHEA_ID string Reaction registration ID in the RHEA database (https://www.rhea-db.org/)
atomchange bondchange atom bond
X_RHEA_URL url Display URL for a reaction the RHEA database (https://www.rhea-db.org)
Tcl script atomchange bondchange atom bond x_rhea_url.xpd
X_RIREG string MDL internal registry number
never
X_ROUNDED_RECTANGLE_ANNOTATION compound Rounded rectangle annotation for reaction renderings. This is a choice vector branch of property X_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
arcwidth float
archeight float
A_XY never
X_RULE_NUMBER short Reaction rule number
never
X_RXN_STRING string RXN reaction record encoded as a string
reverse: { value: 0 description: if set, reverse direction of reaction datatype: boolean}
Tcl script E_REACTION_ROLE atomchange bondchange stereochange merge hadd atom bond x_rxn_string.xpd
X_SCREEN bitvector Screen bits for reacting bonds, used to filter reaction queries
Tcl script B_TYPE A_ELEMENT B_ORDER A_TYPE atomchange bondchange atom bond
X_SHORT_INCHIKEY string Short reaction InChI (RINCHI) key variant
prefix: { value: 1 description: Flag whether to include RInChIKey= prefix datatype: boolean}
Compiled C module X_INCHI atomchange bondchange stereochange atom bond mod_x_short_inchikey.so
X_SMILES string Reaction SMIRKS (SMILES) string
usearo: { value: 0 datatype: boolean}
unique: { value: 0 datatype: boolean}
usestereo: { value: 1 datatype: boolean}
usesuperatom: { value: 0 datatype: boolean}
useisotope: { value: 1 datatype: boolean}
usemapping: { value: 1 datatype: boolean}
smarts: { value: 0 datatype: boolean}
usehcount: { value: 1 datatype: boolean}
useexplicith: { value: 0 datatype: boolean}
Tcl script E_REACTION_ROLE E_SMILES atomchange bondchange stereochange merge hadd
X_SMIRKS string Transform for a reaction in Daylight SMIRKS notation. Computation function for this property is limited, it performs a simple topological change and reaction MCSS analysis.
debug: { value: 0 datatype: boolean}
useoldmapping: { value: 0 datatype: boolean}
Tcl script atomchange bondchange stereochange merge
X_STEREO_HASH uint64 Reaction hashcode, with stereochemistry and without isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_HASHSY E_REACTION_ROLE atomchange bondchange atom bond mod_x_stereo_hash.so
X_STEREO_HASH128 uint128 128 bit reaction hashcode, with stereochemistry but without isotope labelling
usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean}
useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean}
Compiled C module E_STEREO_HASH128 E_REACTION_ROLE atomchange bondchange atom bond mod_x_stereo_hash128.so
X_SVG_IMAGE diskfile
(switchable between blob diskfile url)
SVG reaction depiction
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
height: { value: 180 datatype: int}
width: { value: 400 datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
header: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
footer: { value: {} datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
border: { value: 12 datatype: int}
bgcolor: { value: transparent datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: X_NAME datatype: string}
metadata: { value: 1 datatype: boolean}
arrowsize: { value: 35 datatype: int}
bonds: { value: 8 datatype: int}
arrowcolor: { value: black datatype: color}
showsolvent: { value: 1 datatype: boolean}
annotationfontsize: { value: -1 datatype: double}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
solventcolor: { value: blue datatype: color}
framecolor: { value: black datatype: color}
reagentcolor: { value: blue datatype: color}
suppressedfragmentsfile: { value: reagents.tbin datatype: diskfile constraints: readable}
showplus: { value: 1 datatype: boolean}
arrowtext_over: { value: {} datatype: string}
arrowtext_under: { value: {} datatype: string}
showempty: { value: 1 datatype: boolean}
font: { value: arialn datatype: string}
showmapping: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
uselinecaps: { value: 1 datatype: boolean}
arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int}
compact: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
usereagenttable: { value: 0 datatype: boolean}
showintermediate: { value: 0 datatype: boolean}
usewebfont: { value: 0 datatype: boolean}
id: { value: {} datatype: string}
title: { value: {} datatype: string}
standalone: { value: 1 datatype: boolean}
xmlheader: { value: 1 datatype: boolean}
Compiled C module M_SVG_IMAGE atomchange bondchange stereochange merge mol atom bond mod_x_svg_image.so
X_TEXT_ANNOTATION compound Annotation string for reaction renderings. This is a choice vector branch of property X_ANNOTATION.
{} {} {} center:left:right center:top:bottom {} {} ^none:bold:italic:underline:outline:shadow:subscript:superscript:formula
coords floatpair
text stringvector
color color
align int
valign int
font string
fontsize float
style bitset
charset string
width double
height double
A_XY never
X_TITLE string Reaction title string
never
X_URL url URL of molecular data file
never
X_WEB_INCHIKEY string Web reaction InChI (RINCHI) key variant
prefix: { value: 1 description: Flag whether to include RInChIKey= prefix datatype: boolean}
Compiled C module X_INCHI atomchange bondchange stereochange atom bond mod_x_web_inchikey.so
X_XYEXTENT floatvector Reaction plot coordinate rectangles. This is computed from the complete reaction with the combined bounds of reagents and products, but without tsking the coordinates of other reaction components into account. Coordinates of those two ensembles are standardized to a common bond length, an moved so that the bounding boxes are a adjustable multiple of the standard bond length apart, and vertically centered.

The result vector contains four bounding boxes in xmin,xmax,ymin,ymax order: The outer bounding box, the reagent bounding box and the product bounding box.
xmin float
xmax float
ymim float
ymax float
rxmin float
rxmax float
rymin float
rymax float
pxmin float
pxmax float
pymin float
pymax float
arrowgap: { value: 3 description: in standard bond lengths datatype: double}
Compiled C module A_XY merge mod_x_xyextent.so
X_YIELD float Reaction yield in percents
atomchange bondchange stereochange 3drelative atom bond
Y_ALIRING_COUNT short Number of aliphatic rings the ringsystem contains
Compiled C module R_AROMATIC R_TYPE Y_LABEL R_SYSTEM atomchange bondchange ring mod_y_aliring_count.so
Y_AROMATIC short Ringsystem aromaticity status, indicating whether none, some or all rings in the system are aromatic.
no,none:some,partially:full,all
Compiled C module B_ISAROMATIC B_TYPE atomchange bondchange atom bond ring mod_y_aromatic.so
Y_ARORING_COUNT int Number of aromatic ESSR rings in ringsystem
Compiled C module R_SYSTEM R_TYPE Y_LABEL R_AROMATIC atomchange bondchange ring mod_y_aroring_count.so
Y_DAYLIGHT_ARORING_COUNT int Number of aromatic ESSR rings in ringsystem, using alswys Daylight aromaticity definition
Compiled C module R_SYSTEM R_TYPE Y_LABEL R_DAYLIGHT_AROMATIC atomchange bondchange ring mod_y_daylight_aroring_count.so
Y_ELEMENT_COUNT shortvector Count of element types of atoms of ringsystem
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
Compiled C module A_ELEMENT A_TYPE atomchange merge hadd mod_y_element_count.so
Y_FORMULA string Elemental formula of the ringsystem
usecharges: { value: 0 datatype: boolean}
format: { value: ascii enumeration: ascii:html datatype: int}
useimplicith: { value: 0 datatype: boolean}
usequeryatoms: { value: 0 datatype: boolean}
Compiled C module Y_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_QUERY A_ISOTOPE A_FORMAL_CHARGE atomchange atom mod_y_formula.so
Y_FUSION byte Maximum fusion state of ring system. 0:isolated ring, 1:spiro (one common atom), 2:annealed/fused (two common atoms), 3: cage (more than two common atoms between any two ringsystem rings).
isolated,isolatedring:spiro:annealed,fusion,fused:cage
Compiled C module R_TYPE A_RINGSYSTEM_NUMBER atomchange bondchange atom bond ring mod_y_fusion.so
Y_HASHGROUP_COUNT intvector Ringsystem-oriented population of basic atom hash groups
Compiled C module A_EXTENDED_RINGHASH A_RINGSYSTEM_NUMBER atomchange bondchange merge hadd ring mod_y_hashgroup_count.so
Y_HASHY uint64 Perturbed ringsystem hashcode
usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
usesubstitution: { value: none description: none: pure ring system, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string}
Compiled C module A_RINGSYSTEM_NUMBER A_EXTENDED_RINGHASH A_EXTENDED_RINGHASH_GROUP B_TYPE A_LABEL Y_HASHGROUP_COUNT atomchange bondchange hadd atom bond ring mod_y_hashy.so
Y_HCOUNT short Number of hydrogen ligands on ringsystem
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange hadd atom bond ring mod_y_hcount.so
Y_HETEROATOM_COUNT int Number of hetero (not C or H) atoms in the ringsystems
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_y_heteroatom_count.so
Y_HETERO_SUBSTITUENT_COUNT short Number of non-hydrogen, non-carbon substituents outside ring system bonded via valence or complex bond
Compiled C module A_TYPE B_TYPE A_ELEMENT atomchange bondchange atom bond ring mod_y_hetero_substituent_count.so
Y_LABEL int Arbitrary ringsystem label
(builtin) never
Y_MOL_NUMBER int
(builtin) A_MOL_NUMBER atomchange bondchange merge ring
Y_NAME string Ringsystem name
R_TYPE atomchange bondchange stereochange ring
Y_NATOMS int Number of atoms in ring system
Compiled C module ring mod_y_natoms.so
Y_PI_ELECTRON_COUNT short Number of pi electrons in ring system
Compiled C module A_FREE_ELECTRONS A_TYPE B_TYPE B_ORDER B_ISAROMATIC ring mod_y_pi_electron_count.so
Y_QUERY compound Query attributes for matched substructure ringsystems
^none:aromatic,fullyaromatic:aliphatic,fullyaromatic:saturated:unsaturated,insaturated:carbocyclic:heterocyclic:monocyclic:polycyclic:mixed,mixedaromaticaliphatic:partiallyaromatic:partiallyaliphatic
flags bitset
formula formulamatch
substituentcount bitset
valencecount bitset
neighborcount bitset
hydrogencount bitset
heterosubstituentcount bitset
ringbondcount bitset
pielectroncount bitset
query querytree
alphaformula formulamatch
atomchange bondchange atom bond
Y_RING_CONTRACTION_HASH uint64vector Hashcodes of the various pseudo structures generated by eliminating all different sequences of connected unsubstituted ring atoms.
Compiled C module A_TYPE A_ELEMENT atomchange bondchange merge shuffle hadd ring mod_y_ring_contraction_hash.so
Y_RING_COUNT int Number of ESSR rings in ringsystem
Compiled C module R_SYSTEM R_TYPE Y_LABEL atomchange bondchange ring mod_y_ring_count.so
Y_RING_SIZE_BITS bitset Bits set for rings of size n the ringsystem contains
Compiled C module R_SYSTEM Y_LABEL atomchange bondchange atom bond ring mod_y_ring_size_bits.so
Y_SMILES string SMILES of the ring systems
usearo: { value: 0 datatype: boolean}
unique: { value: 0 datatype: boolean}
usestereo: { value: 1 datatype: boolean}
usesuperatom: { value: 0 datatype: boolean}
useisotope: { value: 1 datatype: boolean}
usemapping: { value: 1 datatype: boolean}
smarts: { value: 0 datatype: boolean}
usehcount: { value: 1 datatype: boolean}
useexplicith: { value: 0 datatype: boolean}
Tcl script atomchange bondchange stereochange merge hadd ringsystem y_smiles.xpd
Y_STRONGLY_FUSED_RING_COUNT int Number of ESSSR rings in the ringsystem which are fused to another ring in the ring system by more than one bond
Compiled C module R_SYSTEM R_TYPE Y_LABEL atomchange bondchange atom bond ring mod_y_strongly_fused_ring_count.so
Y_SUBSTITUENT_COUNT short Number of non-hydrogen substituents outside ring system bonded via valence or complex bond
Compiled C module A_TYPE B_TYPE A_ELEMENT atomchange bondchange atom bond ring mod_y_substituent_count.so
Y_SUBSTITUENT_HASH uint64 Generalized molecule hash (of class M_HASHY) where all atoms in the ringsystem are set to a generic pseudo atom, and all ring hydrogens are ignored.
Compiled C module M_HASHY atomchange bondchange atom bond ring mod_y_substituent_hash.so
Y_UNSATURATION short Overall unsaturation of ring system (every non-aromatic multiple bond counts as n-1)
countarobonds: { value: 0 description: If set, aro bonds are counted with their Kekule bond order datatype: boolean}
Compiled C module B_TYPE B_ORDER B_ARORING_COUNT atomchange bondchange atom bond ring mod_y_unsaturation.so
Y_VB_NEIGHBOR_COUNT short Number of ligands on ringsystem
Compiled C module A_TYPE B_TYPE atomchange bondchange hadd atom bond ring mod_y_vb_neighbor_count.so
Z_ISOTOPE_DATA compoundvector Isotope information structure
isotope int
weight double
abundance double
halflife double
never

Generated Thu Oct 06 19:46:02 CEST 2022 for toolkit version 3.4.8.22