Manual Reference Pages - CHEMISTRY::CANONICALIZE (3)
Chemistry::Canonicalize - Number the atoms in a molecule in a unique way
use Chemistry::Canonicalize :all;
# $mol is a Chemistry::Mol object
print "The canonical number for atom 1 is: ",
print "The symmetry class for for atom 1 is: ",
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
The unique canonical number; it is an integer going from 1 to the number of
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.
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:
If true, sort the atoms in the molecule in ascending canonical number order.
This should be a subroutine reference that takes an atom and returns a number.
These number should be based on the topological invariant properties of the
atom, such as symbol, charge, number of bonds, etc.
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 dont know of any
real-looking structure (meaning something that someone would actually
synthesize or find in nature) that fails, but dont say I didnt warn you!
Chemistry::Mol, Chemistry::Atom, Chemistry::Obj,
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 v5.20.3 ||CANONICALIZE (3) ||2009-05-10 |
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