C.AT

Table of atoms. This is the heart of C.MOL and represents an atom-centred description with optional bonds (C.BO). This is perhaps driven by my background as an inorganic crystallographer. Elemental identity, atomic positions and spacegroup are often necessary and sufficient to describe what the substance is. Many theoretical chemists would agree that, with the addition of the total electron count, everything else is opinion.

C.AT and C.BO can be used to give the molecular formula (connectivity) by the use of attributes such as formal ligand count, number of attached hydrogen atoms, formal charge, etc. Where possible, however, we recommend that C.FORM is used since standardisation is likely to be clearer in that format. The current conventions (SMILES and MOL) could be expanded to include others.

C.AT/C.BO may be difficult to relate to C.FORM. Where C.AT represents coordinate data, this might relate to multiple copies of a molecule (as in crystallography where an asymmetric unit can contain several identical molecules and all the coordinates must be included so that the crystal structure can be recreated.) A related problem is where some of the atomic coordinates are not determined, a frequent occurrence in some techniques.

C.AT and C.BO are linked by the SERID attribute. This need not be an integer, and could be a construct such as CA15. If the tables are edited or modified it will be important to make sure that consistency is obtained and that SERIDs are always unique.

The content model is simple: an optional description (X.DESC), followed by a number of (column) arrays all of length equivalent to the number of atoms. Each X.ARR corresponds to an atomic attribute. The semantics of the attribute is given by one of two mechanisms:

The actual enumeration of the attributes are given in a file 'builtin.ent' and this is definitive, rather than what is written below (although hopefully they are in sync!). It contains:
&mol_arr_builtin;
The semantics of the hardcoded atom attributes are:


Content


ATTRIBUTES
CONTENT DECLARATION

Tag Minimization
Open Tag: REQUIRED
Close Tag: REQUIRED

Parent Elements


Top Elements
All Elements
Tree


cml DTD