Cactvs Toolkit Structure and Reaction I/O Module Summary
| ShortName | ShortNameAliases | FullName | Description | DefaultSuffixes | CapabilityFlags | ModuleFunctions | MimeType | Module |
|---|---|---|---|---|---|---|---|---|
| 441 | 441 | 441 | Toyohashi university 441 modelling software file | 441, 2D | canstore3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-441 | filex_441.so |
| aa1 | aa1 aa pln | AA1 | Text file with 1-letter amino acid sequences | aa1, aa, pln | stringoutput, canstoreensemble, canstorebiologics | skip, read, write, detect | chemical/x-aa1 | filex_aa1.so |
| aa3 | aa3 condensed | AA3 | Text file with 3-letter amino acid sequences | aa3, condensed | stringoutput, canstoreensemble, canstorebiologics | skip, read, write, detect | chemical/x-aa3 | filex_aa3.so |
| alchemy | alchemy alc | Alchemy | ALCHEMY mol file | alc | need3d, canstore3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemistry/x-alchemy | filex_alchemy.so |
| asn | asn asn1 ber asnb asnbinary | PubChem ASN/Binary | PubChem binary ASN.1 PCSubstance/PCCompound file | asn, asn1, ber, asnb | binary, stringoutput, canstoreensemble, blobinput | skip, read, write, detect, close, init | chemical/x-ncbi-asn1-binary | filex_asn.so |
| asnt | asnt asntext | PubChem ASN/Text | PubChem ASCII-encoded ASN.1 PCSubstance/PCCompound file | asnt | stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-ncbi-asn1 | filex_asnt.so |
| bdb | bdb | BDB | CACTVS BDB-based, query-optimized structure and reaction database file | bdb, cdb | nommap, canstore3d, canstorereaction, binary, fullindex, kekule, nosequence, dynamicindex, keepindex, keepopenondelete, canstoreensemble, noemptyinput, complexfields | skip, read, write, detect, close, init, module, delete, update, setfields, position, find, prepare | chemical/x-bdb | filex_bdb.so |
| bxml | bxml beilsteinxml | Beilstein XML | Beilstein XML File (incomplete implementation) | bxml | canstoreensemble | skip, read, write, detect, close, init | chemical/x-beilstein | filex_bxml.so |
| car | car biosyma bsa biosym | CAR | CAR Biosym format | car, bsa, bio | need3d, canstore3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-car | filex_car.so |
| cas | cas | CAS | Text file with ACS CAS numbers, dynamically resolved on input | cas | stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-acs-cas | filex_cas.so |
| cbin | cbin cactvs/bin binary cactvs/binary | Cactvs/Binary | CACTVS native binary format, the recommended format for lossless storage of structure, reaction or dataset data | cbin, bin | nommap, canstore3d, canstorereaction, binary, kekule, canstoredataset, stringoutput, canstoretables, canstoreensemble | skip, read, write, detect | chemical/x-cactvs-binary | (builtin) |
| cbs | cbs cbase cscan cquery cactvs/base cactvs/scan cactvs/query | Cactvs/Queryfile | CACTVS query-optimized file for structures and reactions | cbase, cbs, cscan | nommap, canstore3d, canstorereaction, binary, writelock, fullindex, kekule, nosequence, dynamicindex, togglebyreopen, canstoreensemble, complexfields | skip, read, write, detect, close, init, reorganize, delete, update, setfields, position, find, setstatus | chemical/x-cactvs-scan | (builtin) |
| cda | cda sqlite db | CDA | CDA dataset archive | db, sqlite, cda | nommap, canstorereaction, binary, fullindex, nostream, canstoredataset, nosequence, dynamicindex, keepindex, keepopenondelete, noeofcheck, canstoreensemble, defaultscope_ens, noemptyinput | skip, read, write, detect, close, init, position | chemical/x-cactvs-dataset-archive | filex_cda.so |
| cdx | cdx chemdraw | CDX | CambridgeSoft ChemDraw binary CDX file | cdx | nommap, canstorereaction, binary, singlerecord, fullindex, togglebyreopen, stringoutput, noeofcheck, canstoreensemble, hydrogenfilter | skip, read, write, detect, close, init | chemical/x-cdx | filex_cdx.so |
| cdxml | cdxml | CDXML | CambridgeSoft ChemDraw CDXML text file | cdxml | nommap, canstorereaction, singlerecord, fullindex, togglebyreopen, stringoutput, noeofcheck, canstoreensemble, hydrogenfilter | skip, read, write, detect, close, init | chemical/x-cdxml | filex_cdxml.so |
| cerius | cerius | Cerius | Cerius II file format | msi, cer | need3d, canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-cerius | filex_cerius.so |
| chai | chai | Chai | Data exchange format of the Discovery Innovation CHAI software | chai, xml | canstoredataset, stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-chai | filex_chai.so |
| charmm | charmm charm chm card crd | CHARMM | CHARMM modelling software CARD file | crd, card, chm | nocharge, need3d, canstore3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-charmm | filex_charmm.so |
| chembl | chembl | ChEMBL | ChEMBL XML Output | chembl | singlerecord, canstoreensemble | skip, read, write, detect | application/xml | filex_chembl.so |
| chemwin | chemwin chemwindow cw2 cw | CHEMWIN | ChemWindow CW2 file format | cw2 | nommap, canstorereaction, binary, singlerecord, canstoreensemble | skip, detect | chemical/x-chemwindow-cw2 | filex_chemwin.so |
| chiron | chiron cif | Chiron Cif | Structure file of the CHIRON synthesis planning software | cif | canstoreensemble | skip, read, write, detect | chemical/x-chiron-cif | filex_chiron.so |
| cid | cid | CID | Text file with PubChem CID identifiers, dynamically resolved on input | cid | stringoutput, canstoreensemble, supportsinputcache, blobinput | skip, read, write, detect, close, init | chemical/x-pubchem-cid | filex_cid.so |
| cif | cif | Crystallographic CIF | Crystallographic Information File | cif | stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-crystallographic-cif | filex_cif.so |
| cmf | cmf chime cmol | CMF | MDL Chime compressed molfile (unencrypted variant) | cmf, cmol, chime | firstblank, canstore3d, canfixdoublespace, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-chime-compressed-molfile | filex_cmf.so |
| cml | cml | CML | CML (Chemical Markup Language) format | xml, cml | canstore3d, canstorereaction, markprops, cansplitens, stringoutput, canstoreensemble, defaultscope_auto | skip, read, write, detect, close, init | chemical/x-cml | filex_cml.so |
| cml | cml | CML | CML (Chemical Markup Language) format | xml, cml | canstore3d, canstorereaction, markprops, cansplitens, stringoutput, canstoreensemble, defaultscope_auto | skip, read, write, detect, close, init | chemical/x-cml | filex_cml.so |
| compass | compass | Compass | Toyohashi university COMPASS modelling software file | cpa, com | firstblank, need3d, canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-compass | filex_compass.so |
| cosmo | cosmo cos | COSMO | File format of the COSMO software | cosmo, cos | nocharge, singlerecord, canstoreensemble | skip, read, detect | chemical/x-cosmo | filex_cosmo.so |
| cpacked | cpacked cpc serialized | Cactvs/Serialized | Packed CACTVS serialized objects | cpc | canstore3d, kekule, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-cactvs-packed | filex_cpc.so |
| ctx | ctx | CTX | CTX file format (EROS, CORINA and other Gasteiger group applications) | ctx | canstore3d, canstorereaction, kekule, canstoreensemble | skip, read, write, detect | chemical/x-ctx | filex_ctx.so |
| dropbox | dropbox | Dropbox file | Meta file wrapper for direct access to structure and reaction files stored in a DropBox account | nommap, canstorereaction, binary, canstoredataset, togglebyreopen, canstoreensemble, defaultscope_auto, canstorenetwork, storewithoutfp, iswrapper, canstorehierarchy, canstorebiologics | skip, write, close, init, module, magicname | application/dropbox | filex_dropbox.so | |
| emf | emf emfimage | EMF Image | Microsoft Windows EMF rendering, potentially with embedded structure data | emf, wmf | nommap, canstorereaction, binary, singlerecord, stringoutput, canstoreensemble, defaultscope_auto, hydrogenfilter | skip, read, write, detect | image/x-emf | filex_emf.so |
| emolecules | emolecules emol | EMolecules | Text file with EMOLECULES IDs, dynamically resolved on input | emolecules, emol | stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-emolecules | filex_emolecules.so |
| fps | fps | fps | Dalke fingerprint exchange format | fps | stringoutput | skip, read, write, detect | chemical/x-dalke-fps | filex_fps.so |
| gausscube | gausscube gaussiancube cube cub | Gaussian/Cube | GAUSSIAN software Cube file | cub | nocharge, singlerecord, canstoreensemble | skip, read, write, detect | chemical/x-gaussian-cube | filex_gausscube.so |
| gaussian/archive | gaussian/archive gaussarc garc arc | Gaussian/Archive | GAUSSIAN software archive file | garc, arc | need3d, canstore3d, canstoreensemble | skip, read, detect | chemical/x-gaussian-archive | filex_gaussarc.so |
| gaussian/output | gaussian/output gaussout gaussianout gout out | Gaussian/Output | GAUSSSIAN software output file | out, gout | nocharge, need3d, canstoreensemble | skip, read, detect | chemical/x-gaussian-output | filex_out.so |
| gif | gif bmp | GIF Image | GIF image file, potentially with embededded structure data | gif, bmp | nommap, canstorereaction, binary, singlerecord, stringoutput, noeofcheck, canstoreensemble, hydrogenfilter | skip, read, write, detect, close, init | image/gif | filex_gif.so |
| gjf | gjf gaussin gaussianinput gaussian/input gau gaussian gauss gin | Gaussian/Input | Input file for the GAUSSIAN software | gin, gau, gjf | need3d, canstore3d, stringoutput, canstoreensemble, canstorenullrecord | skip, read, write, detect | chemical/x-gaussian-input | filex_gaussin.so |
| gpr | gpr ghemical | Ghemical | File format of the Ghemical program | gpr | nocharge, need3d, singlerecord, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | application/x-ghemical | filex_gpr.so |
| gromacs | gromacs gro | GROMACS | File format of the GROMACS program | gro | nocharge, need3d, singlerecord, canstoreensemble | skip, read, write, detect | chemical/x-gromacs | filex_gro.so |
| hitlist | hitlist cactvs/hitlist | Hitlist | Hitlist file storing a matched structure or reaction subset of another file | hit | canstorereaction, canstoredataset, stringoutput, canstoreensemble, isreference, canstorehierarchy | skip, read, write, detect, close | chemical/x-cactvs-hitlist | (builtin) |
| hyperchem | hyperchem hin | Hyperchem | File format of the Hyperchem software | hin | need3d, canstore3d, singlerecord, cansplitens, canstoreensemble | skip, read, write, detect | chemical/x-hyperchem | filex_hyperchem.so |
| iff | iff vega riff | IFF | File format of the VEGA modelling system | iff | nommap, canstore3d, binary, singlerecord, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-iff | filex_iff.so |
| inchi | inchi ichi inc ich | InChI | IUPAC InChI file format | ich, inchi, inc | stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-inchi | filex_inchi.so |
| index | index idx cactvs/index | Index | Index file storing record identifiers referencing another file | idx | nommap, canstorereaction, canstoredataset, togglebyreopen, stringoutput, canstoreensemble, canstorenetwork, isreference, canstorehierarchy, canstorebiologics | write, detect | application/x-index | (builtin) |
| jcamp | jcamp jcp jca jcm jdx jcamp-dx jcamp-cs | JCAMP | JCAMP spectroscopy data exchange format | jcp, jca, dx, jdx, cs | canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-jcamp-dx | filex_dx.so |
| jme | jme | JME | JME strings text file, as used by the JME/JSME structure editor | jme | nocharge, canstorereaction, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-jme | filex_jme.so |
| jpg | jpg jpeg jpgimage | JPG Image | JPG structure rendering, potentiallly with embedded structure data | jpg, jpeg | nommap, binary, singlerecord, canstoreensemble | skip, read, detect, close, init | image/jpg | filex_jpg.so |
| kcf | kcf kegg | KCF | Native KEGG database structure file | kcf | singlerecord, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-kcf | filex_kcf.so |
| keggrp | keggrp kegg-rp rp | KEGGRP | KEGG reaction pair format | rp | canstorereaction, singlerecord, defaultscope_reaction | skip, read, detect | chemical/x-kegg-rp | filex_rp.so |
| knime | knime table | KNIME | KNIME native binary table interpreted as structure or reaction file | table, knime | nommap, canstore3d, canstorereaction, binary, fullindex, kekule, nostream, nosequence, dynamicindex, togglebyreopen, canstoreensemble, defaultscope_auto | skip, read, write, detect, close, init | application/x-knime | filex_knime.so |
| lincs | lincs lsm | LINCS | Text file with LINCS IDs, dynamically resolved on input | lincs, lsm | stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-lincs | filex_lsm.so |
| m3d | m3d molecules marts | M3D | Molecules 3D Molecular Arts/molecules.com file | m3d, frg | nocharge, need3d, canstore3d, singlerecord, cansplitens, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-molecules-3d | filex_m3d.so |
| maestro | maestro mae | Maestro | Schroedinger MAESTRO file | mae | canstoreensemble | skip, read, write, detect | chemical/x-schrodinger-maestro | filex_maestro.so |
| mailbox | mailbox | Mailbox | Wrapper for mailbox files containing structure or reaction attachments | mbx, mail | canstorereaction, canstoredataset, nosequence, canstoreensemble, canstorenetwork, iswrapper, canstorehierarchy, canstorebiologics | skip, read, write, detect | application/mailbox | (builtin) |
| mmd | mmd mmod macromodel | MMD | File format of the Macromodel program | mmd, mmod | need3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-macromodel-input | filex_mmd.so |
| molconnz | molconnz mcz b | Molconn-Z | Molconn-Z file | b, mcz | nocharge, canstoreensemble | skip, read, write, detect, close | chemical/x-molconn-z | filex_molconnz.so |
| molfile | molfile mdl mol sdf sdf2000 v2000 sdf2k v2k sdf2 | MDL SD-File | Plain MDL Molfile and derivatives (SD-File) | mdl, mol, sdf, sd | firstblank, canstore3d, canfixdoublespace, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-mdl-sdf | (builtin) |
| molgen | molgen bayreuth | Molgen | Native format of the MOLGEN structure generator | gen, mg | stringoutput, nocoordinates, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-molgen | filex_molgen.so |
| mopacin | mopacin mopacinput in dat data mop | Mopac/Input | Input file for the MOPAC software | mop, in, data, dat | need3d, canstore3d, singlerecord, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-mopac-input | filex_mopacin.so |
| mopacout | mopacout mopacoutput oo | Mopac/Output | Output format of the MOPAC software | out, 012 | need3d, canstore3d, singlerecord, canstoreensemble | skip, read, detect | chemical/x-mopac-output | filex_mopacout.so |
| mrv | mrv marvin | MRV | ChemAxon MRV (Marvin Documents) format | mrv | canstore3d, canstorereaction, markprops, cansplitens, stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-marvin-document | filex_mrv.so |
| mxyz | mxyz | MXYZ | MXYZ format | mxyz | need3d, canstore3d, canstoreensemble | skip, detect | chemical/x-mxyz | filex_mxyz.so |
| mysql | mysql | Mysql | MYSQL databases table as virtual structure file, accessed via url like mysql://user:pw@host/db/table | MYD, MYI | nommap, canstore3d, fullindex, nosequence, dynamicindex, keepindex, noeofcheck, canstoreensemble, storewithoutfp | skip, read, write, close, init, setfields, magicname | chemical/x-db-mysql | filex_mysql.so |
| ole | ole ole2 msole msole2 xls excel msexcel doc word msword bin | OLE | MS Windows OLE2 file with embedded structure or reaction data | ole, ole2, doc, xls, bin | nommap, canstorereaction, binary, singlerecord, fullindex, togglebyreopen, stringoutput, noeofcheck, canstoreensemble, defaultscope_auto, iswrapper | skip, read, write, detect, close, init | application/oleobject | filex_doc.so |
| pcd | pcd pcdump | PCDump | PubChem Minimol dump file | pcd | multifile, binary, nostream, noeofcheck, canstoreensemble | skip, read, write, detect, close, init | chemical/x-pubchem-dump | filex_pcd.so |
| pdb | pdb ipdb ent | PDB | Protein Data Bank file | pdb, ipdb, ent | nocharge, need3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-pdb | filex_pdb.so |
| pdbcode | pdbcode pdbc pdbentry pdbe | PDBCODE | Text file with PDB codes, read with dynamic structure expansion from PDB database | pdbcode, pdbc, pdbentry, pdbe | nocharge, need3d, canstoreensemble | skip, read, detect, close | chemical/x-pdbentry | filex_pdbcode.so |
| pdbml | pdbml pdbxml | PDBML | Protein Data Bank XML format | pdbml, pdbxml | nocharge, need3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-pdbml | filex_pdbml.so |
| pdbqt | pdbqt autodock | PDBQT | File format of the AutoDock program | pdbqt | singlerecord, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-autodock | filex_pdbqt.so |
| PDF Image | PDF file with embedded structure data | nommap, canstorereaction, binary, singlerecord, stringoutput, noeofcheck, canstoreensemble | skip, read, write, detect, close, init | application/pdf | filex_pdf.so | |||
| phar | phar pharao | Pharao | File format of the Silicos PHARAO software | phar | stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-silicos-pharao | filex_phar.so |
| pic | pic pct pict | PICT Image | Structure rendering in Apple QuickDraw PIC format, potentially with embedded structure data | pic, pct, pict | nommap, binary, singlerecord, canstoreensemble | skip, write, detect | image/pict | filex_pct.so |
| png | png pngimage | PNG Image | PNG image file, potentially with embededded structure data | png | nommap, canstorereaction, binary, singlerecord, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect, close, init | image/png | filex_png.so |
| postscript | postscript ps | Postscript Image | Structure rendering in Adobe PostScript format, potentially with embedded structure data | ps | canstoreensemble | skip, write, detect, close, init | application/postscript | filex_postscript.so |
| pubchem | pubchem pcvirtual | PubChem | PubChem virtual file I/O module | <pubchem> | fullindex, nosequence, canstoreensemble, suppressmtqueries, directfilequerysupport, 55 | skip, read, close, init, find, magicname, scan | chemical/x-pubchem | filex_pubchem.so |
| rdf | rdf | MDL RDF | MDL reaction data file | rdf | firstblank, canstore3d, canstorereaction, defaultscope_reaction, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-mdl-rdf | (builtin) |
| rinchi | rinchi xinchi reactioninchi rinc rich | RInChI | Text file with RInChI reaction line notation strings | rinchi, rinc, rich | canstorereaction, defaultscope_reaction, stringoutput | skip, read, write, detect | chemical/x-rinchi | filex_rinchi.so |
| rosdal | rosdal | ROSDAL | Beilstein ROSDAL format, incomplete implementation | ros | stringoutput, canstoreensemble | skip, write, detect | chemical/x-rosdal | filex_rosdal.so |
| rtf | rtf | RTF | MS Word file with embedded structures | rtf | nommap, canstorereaction, binary, fullindex, nosequence, stringoutput, noeofcheck, canstoreensemble, defaultscope_auto, hydrogenfilter | skip, read, write, detect, close, init | text/rtf | filex_rtf.so |
| rxn | rxn rxn2000 rxn2k rxn2 | MDL RXN | MDL reaction file | rxn | firstblank, canstore3d, canstorereaction, defaultscope_reaction, stringoutput, hydrogenfilter | skip, read, write, detect | chemical/x-mdl-rxnfile | (builtin) |
| rxn3000 | rxn3000 rxn3k rxn3 | RXN3000 | V3000 MDL/Symyx reaction file format | rxn3, rxn3000, rxn3k | canstore3d, canstorereaction, singlerecord, defaultscope_reaction, stringoutput, hydrogenfilter | skip, read, write, detect | chemical/x-mdl-rxn3000 | filex_rxn3000.so |
| scf | scf | SCF | SCF file | scf | nommap, singlerecord, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-scf | filex_scf.so |
| sddata | sddata sdd | SD-Data | SD pure data file (no CTAB block) | sdd | canstoreensemble | skip, read, write, detect | chemical/x-sd-pure-data | filex_sddata.so |
| sdf3000 | sdf3000 sdf3 v3000 sdf3k v3k mol3 mol3k mol3000 | SDF3000 | V3000 MDL/Symyx structure data file | sdf3, sdf3k, sdf3000, mol3, mol3k, mol3000 | firstblank, canstore3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-mdlv3000-sdf | filex_sdf3000.so |
| sharc | sharc shigo | Sharc | Sharc/Shigo NMR shift archive format | sharc, shigo, shc, shg | need3d, canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-sharc | filex_sharc.so |
| shelx | shelx res | SHELX | SHELX file | res | need3d, canstore3d, singlerecord, canstoreensemble | skip, read, detect | chemical/x-shelx | filex_shelx.so |
| sid | sid | SID | Text file with PubChem SID identifiers, dynamically resolved on input | sid | stringoutput, canstoreensemble, supportsinputcache, blobinput | skip, read, write, detect, close, init | chemical/x-pubchem-sid | filex_sid.so |
| sk2 | sk2 chemsketch acd | SK2 | ACD/Labs SK2 file | sk2 | nommap, canstorereaction, binary, fullindex, noeofcheck, canstoreensemble | skip, read, detect, close | chemical/x-sk2 | filex_sk2.so |
| skc | skc isis symyx isisdraw symyxdraw | SKC | MDL/Symyx Isis sketch file | skc | nommap, canstorereaction, binary, singlerecord, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect, close, init | chemical/x-mdl-isis | filex_skc.so |
| sln | sln hits | SLN | Standard Sybyl line notation file | sln, hits | checkstereo, checkwedges, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-sybyl-linenotation | filex_sln.so |
| sln+ | sln+ slnplus | SLN+ | Sybyl line notation file with custom extensions | sln+ | checkstereo, checkwedges, stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-custom-sybyl-linenotation | filex_slnplus.so |
| smarts | smarts sma smt | SMARTS | Daylight SMARTS file | sma, smt | stringoutput, nocoordinates, canstoreensemble | skip, read, write, detect | chemical/x-daylight-smarts | filex_smarts.so |
| smd4 | smd4 | SMD4 | SMD (Standard Molecular Data) V4.3 file | smd, smd4 | canstore3d, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-smd | filex_smd4.so |
| smd5 | smd5 | SMD5 | SMD (Standard Molecular Data) file format, version 5.0+, incomplete implementation | smd5 | canstoreensemble | skip, read, write, detect | chemical/x-smd5 | filex_smd5.so |
| smiles | smiles smi rxnsmiles reactionsmiles | SMILES | SMILES/SMARTS structure or reaction codes | smi | canstorereaction, stringoutput, nocoordinates, canstoreensemble | skip, read, write, detect, init | chemical/x-daylight-smiles | (builtin) |
| smirks | smirks sks | SMIRKS | Daylight SMIRKS file | smirks, sks | stringoutput, nocoordinates, canstoreensemble | skip, read, write, detect | chemical/x-daylight-smirks | filex_sks.so |
| spc | spc udf | SPC | Galactic UDF/SPC spectra file | spc, udf, cgm | nommap, binary, singlerecord, canstoreensemble | skip, read, detect, init | chemical/x-spc | filex_spc.so |
| spl | spl fda | SPL | EPA/FDA registration format | spl, fda, xml | singlerecord, canstoredataset, stringoutput, canstoreensemble, defaultscope_ens | skip, read, write, detect, close, init | chemical/x-fda-spl | filex_spl.so |
| sql | sql | SQL table load instructions | SQL table loader file | sql | canstorereaction, stringoutput, canstoreensemble, hydrogenfilter | write, close, init, setfields | application/x-sql | filex_sql.so |
| stdinchi | stdinchi stdichi stdinc stdich | StdInChI | Standard InChI file format | stdich, stdinchi, stdinc | stringoutput, canstoreensemble | skip, read, write, detect | chemical/x-inchi | filex_stdinchi.so |
| stf | stf | STF | STF grid volume file | stf | nocharge, canstoreensemble | skip, read, write, detect | chemical/x-stf | filex_stf.so |
| svg | svg | SVG Image | Structure rendering in SVG format, potentially with embedded structure information | svg | nommap, canstorereaction, singlerecord, stringoutput, canstoreensemble | skip, read, write, detect | image/svg+xml | filex_svg.so |
| sybyl | sybyl | SYBYL | SYBYL mol file (Sybyl mol1) | syb, mol | need3d, canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-sybyl-molfile | filex_sybyl.so |
| sybyl2 | sybyl2 mol2 | Sybyl2 Molfile | SYBYL mol file (Sybyl mol2) | syb2, mol2, sy2, ml2, sm2 | need3d, canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-sybyl2-molfile | filex_sybyl2.so |
| tab | tab tsv csv txt table | Table | Separator-controlled text table with a SMILES column as structure souce | tab, csv, tsv, txt | stringoutput, canstoreensemble, defaultscope_auto | skip, read, write, detect | chemical/x-table | filex_csv.so |
| tar | tar tgz | TAR | TAR meta file module, for accessing files within tar archives without unpacking | tar, tgz | nommap, canstorereaction, binary, canstoredataset, togglebyreopen, noeofcheck, canstoreensemble, defaultscope_auto, canstorenetwork, iswrapper, canstorehierarchy, canstorebiologics | write, detect, close, init | application/tar | filex_tar.so |
| tdt | tdt stg stigmata thor | STIGMATA | Daylight Stigmata/Thor data tree file | stg, tdt | canstoreensemble | skip, read, write, detect | chemical/x-daylight-thor | filex_stigmata.so |
| tex | tex latex chemfig | TEX Image | TEX/LaTEX structure rendering | tex, chemfig | canstorereaction, stringoutput, canstoreensemble, hydrogenfilter | write | application/x-tex | filex_tex.so |
| tgf | tgf | TGF | MDL/Symyx Isis sketch file, text variant | tgf | canstorereaction, singlerecord, stringoutput, canstoreensemble, hydrogenfilter | skip, read, write, detect, close, init | chemical/x-mdl-tgf | filex_tgf.so |
| tiff | tiff tif | TIFF | TIFF image file, potentially with embededded structure data | tiff, tif | nommap, binary, singlerecord, canstoreensemble | skip, read, detect, close, init | image/tiff | filex_tif.so |
| tinker | tinker | Tinker | Tinker modelling software data file | xyz, arc | nocharge, need3d, canstoreensemble | skip, read, write, detect | chemical/x-tinker | filex_tinker.so |
| unii | unii | UNII | Text file with FDA UNII identifiers, dynamically resolved on input | unii | stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-fda-unii | filex_unii.so |
| usmiles | usmiles uniquesmiles | USMILES | Unique Smiles | usmi, usm | canstorereaction, stringoutput, nocoordinates, canstoreensemble | skip, read, write, init | chemical/x-daylight-unique-smiles | filex_usmiles.so |
| vamp | vamp vmp | VAMP | VAMP QM software output file | vmp | nocharge, need3d, canstore3d, singlerecord, canstoreensemble | skip, read, detect | chemical/x-vamp | filex_vamp.so |
| vrml | vrml wrl | VRML Model | VRML 3D structure model file | wrl, vrml | nommap, need3d, canstore3d, singlerecord, stringoutput, canstoreensemble | skip, read, write, detect | model/vrml | filex_vrml.so |
| wln | wln | WLN | Wiswesser line data (framework, not a useful implementation) | wln | stringoutput, canstoreensemble | skip, write, detect | chemical/x-wln | filex_wln.so |
| wmf | wmf wmfimage | WMF Image | Microsoft Windows WMF rendering, potentially with embedded structure data | emf, wmf | nommap, canstorereaction, binary, singlerecord, stringoutput, canstoreensemble, defaultscope_auto, hydrogenfilter | skip, read, write, detect | image/x-wmf | filex_wmf.so |
| xbsa | xbsa bs | XBSA | XBSA file | bs, xbsa | need3d, canstore3d, multifile, singlerecord, canstoreensemble | skip, read, write, detect | chemical/x-xbsa | filex_xbsa.so |
| xdf | xdf xdfile xd xml | XDF | MDL/Symyx XDF format | xdf, xml, xd, xdfile | canstore3d, canstorereaction, canstoredataset, stringoutput, canstoreensemble | skip, read, write, detect, close, init | chemical/x-mdl-xdf | filex_xdf.so |
| xfig | xfig fig | XFIG | XFIG render file | fig, xfig | nocharge, singlerecord, canstoreensemble | skip, write, detect | application/xfig | filex_xfig.so |
| xtel | xtel xtelplot | XtelPlot | File format of the Xtelplot software | xtel, xte | need3d, canstore3d, canstoreensemble | skip, read, write, detect | chemical/x-xtel | filex_xtel.so |
| xyz | xyz | XYZ | File format of the Xmol program | xyz | nocharge, need3d, singlerecord, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-xyz | filex_xyz.so |
| xyzr | xyzr | XYZR | XYZR file, as used by the msms program (XYZ with extra atom radii column) | xyzr | nocharge, need3d, canstore3d, singlerecord, canstoreensemble, hydrogenfilter | skip, read, write, detect | chemical/x-xyzr | filex_xyzr.so |
| zip | zip docx | Zip | ZIP meta file handler module, for accessing files in ZIP archives without unpacking | zip, docx | nommap, canstorereaction, binary, canstoredataset, nosequence, stringoutput, canstoreensemble, defaultscope_auto, canstorenetwork, iswrapper, canstorehierarchy, canstorebiologics | skip, read, write, detect, close, init | application/zip | filex_zip.so |
Generated Thu Oct 06 19:46:04 CEST 2022 for toolkit version 3.4.8.22