System Tables

Cactvs Tcl interpreters with table support start up with three predefined tables, which are accessible via their standard handles table0 , table1 and table2 . They are write-protected by default, but by setting the editable attribute this can be changed.

If an interpreter is started in a KNIME context, additional tables may be automatically present.

The PSE table

This table has handle table0 . It contains basic physical and display data for all elements. The rows are addressable via the periodic system number or the standard element symbol. Row zero contains pseudo data for an undefined element.

The columns are:

symbol
The element symbol as a string.
name
The English name of the element.
number
The element number in the PSE as an integer.
group
The PSE group using new-style IUPAC group indices 1..18, plus 19 for lanthanides and 20 for actinides.
pserow
PSE row, starting with 1.
shellelectrons
The standard number of shell electrons.
ismetal
Flag for metals
weight
The standard atomic weight in gr/mol.
vdwradius
Standard Van-der-Waals radius in Ångstrom.
covradius
Standard covalent bonding radius in Ångstrom.
color1
Default rendering color for bright backgrounds
color2
Default rendering color for dark backgrounds.
valences
Standard accessible atomic valences in compounds with this element. This column is an integer vector. For example, for sulfur the cell contains the values 2, 4 and 6.
isotopes
Standard isotopes of the element occurring naturally, or with precedence for chemical use as isotope label etc. This column is a compound vector. Every vector element is a list of the nucleon count (integer), the isotope mass (double, gr/mol), the natural abundance (double, range 0..1) and the half life in seconds. Stable isotopes have an infinite half life.
allisotopes
As above, but with a full set of known isotopes, obtained from http://www.sisweb.com/referenc/source/exactmas.htm
sequence
The precedence of the element in constructing an elemental formula, following the C/H/alphabetic convention (Hill formula). The value for C is one.

The Superatom table

This table has handle table1 . It contains information about common superatom fragments. This information is for example used superatom expansion or contraction of chemical groups for display.

The columns are:

name
An expanded, human-readable name of the fragment
codes
A string list of recognized names for the fragment. There is often more than one code, and the list contains reversed entries such as MeO plus OMe , since superatom name matching does not automatically match reversed names - that could lead to mis-classifications in some cases.
smiles
A SMILES representation of the fragment. The first atom is always a * placeholder indicating the primary connection point. Secondary connection points may be present in any position. On expansion, the connection points are not used.
expandable
Flag indicating that this fragment is handled by normal expansion commands, such as ens expand .
contractable
Flag indicating that this fragment can be contracted as superatom in structure renderings.
level
The minimum contraction level to actually perform group contraction for rendering. This is currently a value between 1 (routinely abbreviated) to 3 (exotic case only recognized by specialists).
flags
Substructure match flags to be added to the standard set when trying to detect the fragment in a structure, such as forcing a match which does not link via a simple alkyl chain, preventing for example the use of an n-propyl group as a partial abbreviation for an n-octyl group.
textlabel
The standard display symbol of the contracted group, as it is stored in property A_TEXTLABEL .
structure
The handle of the decoded SMILES from the third column. Decoding is performed in a lazy fashion, so initially this cell is empty.
substructure
The handle of the SMARTS -decoded SMILES from the third column. Decoding is performed in a lazy fashion, to initially this cell is empty.

The SMARTS Macro table

This table has handle table2 and is initially empty. If content is added, it is automatically used in all SMILES and SMARTS expansions which use macro syntax.

The columns are

name
A name for the macro. This is what is recognized in the input SMILES .
pattern
The SMILES / SMARTS pattern this macro expands to
set
A set name for this fragment. Set names are an argument to SMILES / SMARTS decoder functions. Only those macros in the table that match the set name are used, if it is not an empty string.