nbody_Bonds.py
def6733a9a4clammm-master-deprecated

nbody_Bonds.py
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			from nbody_graph_search import Ugraph

			# To find 2-body "bond" interactions, we would use this subgraph:
			#
			#
			# --- => one bond connects atoms 0 and 1
			# 0 1
			#

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


			# The next function eliminates the redundancy between 0-1 and 1-0:
			def canonical_order(match):
			"""
			It does not make sense to define a separate bond between atoms 1 and 2,
			and between atoms 2 and 1. This function will swap the atoms in the bond
			if the first atom > second atom.

			"""
			# match[0][0:2] contains the ID numbers for the 2 atoms in the match
			atom0 = match[0][0]
			atom1 = match[0][1]
			# match[1][0:1] contains the ID numbers for the 1 bond
			bond0 = match[1][0]
			if atom0 < atom1:
			#return ((atom0, atom1), (bond0)) same thing as:
			return match
			else:
			return ((atom1, atom0), (bond0))