nbody_Impropers.py
fadc25d704eflammm-devel

nbody_Impropers.py
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			from nbody_graph_search import Ugraph

			# To find 4-body "improper" interactions, we would use this subgraph:
			# 3
			# * 1st bond connects atoms 0 and 1
			# \| => 2nd bond connects atoms 0 and 2
			# _.*._ 3rd bond connects atoms 0 and 3
			# ' 0 `
			# 1 2
			#

			bond_pattern = Ugraph([(0,1), (0,2), (0,3)])
			# (Ugraph atom indices begin at 0, not 1)


			def canonical_order(match):
			"""
			When searching for atoms with matching bond patterns GraphMatcher
			often returns redundant results. We must define a "canonical_order"
			function which sorts the atoms and bonds in a way which is consistent
			with the type of N-body interaction being considered.
			The atoms (and bonds) in a candidate match are rearranged by the
			canonical_order(). Then the re-ordered list of atom and bond ids is
			tested against the list of atom/bond ids in the matches-found-so-far,
			before it is added to the list of interactions found so far.
			(For example, it does not make sense to define a separate 4-body improper-
			angle interaction between atoms 1, 2, 3, 4 AND 1, 3, 2, 4. The improper-
			angle is defined as the angle between planes formed by atoms 1,2,3 & 2,3,4.
			This is not effected by swapping the middle pair of atoms so we arbitrarily
			sort them so that the second atom has a lower atomID than the third atom.)

			"""
			atom0 = match[0][0]
			atom1 = match[0][1]
			atom2 = match[0][2]
			atom3 = match[0][3]
			if atom1 <= atom2:
			#return ((atom0,atom1,atom2,atom3), match[1]) same thing as:
			return match
			else:
			return ((atom0,atom2,atom1,atom3), match[1])