Abstract
A new effective algorithm for handling of geometry at chiral centers for the processing of stereochemical structures during their unambiguous registration in databases was designed, programmed and implemented. The chemical and mathematical reasoning behind the algorithm are discussed in detail. Its advantages- in comparison to the methods used so far - are illustrated for the manual as well as for the computer-assisted assignment of stereodescriptors based on the CIP ranking procedure.
Highlights
Chemical structures represent separate entities, which exist in nature or can be synthesized, and are widely studied and described in publications
The most acceptable visual representation of a chemical compound is a two-dimensional plan of the three-dimensional structure, and this usually gives an adequate view of the structure, and is understood, drawn and copied
The structure diagram conventions are established as an international standard and so far are the only unique method of communicating information on a chemical compound
Summary
Chemical structures represent separate entities, which exist in nature or can be synthesized, and are widely studied and described in publications. The connection table - as referred to in this paper – is understood as a labelled graph for which nodes are stored either as atom adjacency matrices of bond order labels (single, double, triple, single up, single down, etc.) or as an atom adjacency lists which, for each atom separately, contain bond order labels only to directly connected atoms (neighbours) For both representations each atom is specified by the atom property vector containing such information as atomic number, atomic mass (if non-standard), charge, valency (in non standard), etc. The only purpose of the canonicalization is to generate - independent of the used structure coding method – a numeric or alphanumeric identifier (strictly numeric for the Beilstein File, for example) which uniquely and unambiguously labels the structural diagram of the input compound Such an identifier – specific within a particular database - is called a registry number (CRN for CAS or BRN for Beilstein). Correct and unique interpretation of the steric information contained in graphs of such structures – by the computer programs - provides for reliable registration of different stereoisomers of the same compound in databases of chemical compounds
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