Chemistry::Canonicalize - Number the atoms in a molecule in a unique way
use Chemistry::Canonicalize ':all'; # $mol is a Chemistry::Mol object canonicalize($mol); print "The canonical number for atom 1 is: ", $mol->atoms(1)->attr("canon/class"); print "The symmetry class for for atom 1 is: ", $mol->atoms(1)->attr("canon/symmetry_class");
This module provides functions for "canonicalizing" a molecular structure; that is, to number the atoms in a unique way regardless of the input order.
The canonicalization algorithm is based on: Weininger, et. al., J. Chem. Inf. Comp. Sci. 29, 97-101 (1989)
This module is part of the PerlMol project, http://www.perlmol.org/.
During the canonicalization process, the following attributes are set on each atom:
The unique canonical number; it is an integer going from 1 to the number of atoms.
The symmetry class number. Atoms that have the same symmetry class are considered to be topologicaly equivalent. For example, the two methyl carbons on 2-propanol would have the same symmetry class.
These functions may be exported, although nothing is exported by default.
- canonicalize($mol, %opts)
Canonicalizes the molecule. It adds the canon/class and canon/symmetry class to every atom, as discussed above. This function may take the following options:
Add some tests.
Currently there is an atom limit of about 430 atoms.
These algorithm is known to fail to discriminate between non-equivalent atoms for some complicated cases. These are usually highly bridged structures explicitly designed to break canonicalization algorithms; I don't know of any "real-looking structure" (meaning something that someone would actually synthesize or find in nature) that fails, but don't say I didn't warn you!
Ivan Tubert <email@example.com>
Copyright (c) 2009 Ivan Tubert. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.