Connection table canonicalization

The task is now to take one of the numberings as the standard one and to derive a unique code from it, which is called canonicalization. This can be accomplished by numbering the atoms of a molecule so that it is represented later by only one connection table or bond matrix. Such a unique and reproducible numbering or labeling of the atoms is obtained by a set of rules. 

Algorithm I - Registration - Canonicalization of Connection Tables. A connection table for a chemical substance with n atoms can be numbered in as many as n different ways. The problem of generating a canonical form involves selecting a... 

W.T. Wipke H) first achieved the canonicalization of a molecular structure representation in a computer program that includes all aspects of stereochemistry. In some other schemes, stereochemistry is not invoked to aid in the mambering of the atoms. Such schemes are incomplete. If we relegate stereochemistry to a footnote and the numbering of the atoms and the connection tables of two isomers can be the same, then we lose most of the above-stated advantages of canonicalizing. 

For the number of atoms involved, usually 25-40, the straight selection sort was noticeably faster than the tree selection sorts discussed by Knuth. (] ) The optimum sorting procedure in this case is very much an open question. The numbers of the ligands in each row were sorted by the bubble sort (17) because these numbers are usually in order before canonicaliza-tion, since they are usually in the same order in the reactant molecule at hand as they are in the already canonicalized product molecule connection table. The most efficient sort for an almost sorted list is the bubble sort. 

The first solution uses some algorithm that transforms any connection table of a molecule into a unique, canonical, form. The best known of these, the Morgan algorithm, chooses the numbering based on the numbers and properties of the neighbors of each atom of the structure. It is the basis of the Chemical Abstracts System Chemical Registry Service. There is also a canonicalization scheme for the SMILES notation of a chemical structure. ... 

An alternative, and highly efficient, structure search uses a hashing function, a computational procedure that takes some data record, such as a connection table or unique SMILES, and converts it to the computer address at which that record is stored." Although hashing functions may lead to more than one record with the same address, the detailed molecular comparisons need to be carried out for just those few molecules." " Because of canonicalization and hashing functions, identity searching is generally very fast. 

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