uses a combination of graphs and hashing to determine if two molecules are topologically equivalent, and if so, finds the one by one mapping More...

Functions/Subroutines
subroutine, public	hash_molecule (reference, kind_ref, hash)
	hashes a molecule to a number. Molecules that are the (topologically) the same have the same hash. However, there is a small chance that molecules with the same hash are different More...

subroutine, public	reorder_graph (reference, unordered, order, matches)
	If two molecules are topologically the same, finds the ordering that maps the unordered one on the ordered one. More...

Detailed Description

uses a combination of graphs and hashing to determine if two molecules are topologically equivalent, and if so, finds the one by one mapping

Note: the graph isomorphism being solved is a computationally hard one and can not be solved in polynomial time in the general case http://mathworld.wolfram.com/IsomorphicGraphs.html the problem arises if many atoms are topologically equivalent the current algorithm is able to solve the problem for benzene (C6H6) but not for a fullerene (C60). Large systems are not really a problem (JAC). as almost all atoms are topologically unique.

History: 09.2006 [Joost VandeVondele]

Author: Joost VandeVondele

Function/Subroutine Documentation

◆ hash_molecule()

subroutine, public graphcon::hash_molecule	(	type(vertex), dimension(:), intent(in)	reference,
		integer, dimension(:), intent(out)	kind_ref,
		integer, intent(out)	hash
	)

hashes a molecule to a number. Molecules that are the (topologically) the same have the same hash. However, there is a small chance that molecules with the same hash are different

Parameters

reference	IN : molecule with atomic kinds and bonds
kind_ref	OUT : an atomic hash which is the same for topologically equivalent atoms
hash	OUT : a hash which is the same for topologically equivalent molecules

History: 09.2006 created [Joost VandeVondele]

Note: Although relatively fast in general, might be quadratic with molecule size for some systems (e.g. linear alkanes)

Definition at line 79 of file graphcon.F.

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◆ reorder_graph()

subroutine, public graphcon::reorder_graph	(	type(vertex), dimension(:), intent(in)	reference,
		type(vertex), dimension(:), intent(in)	unordered,
		integer, dimension(:), intent(out)	order,
		logical, intent(out)	matches
	)

If two molecules are topologically the same, finds the ordering that maps the unordered one on the ordered one.