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nbody_Angles.py
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Mon, Aug 5, 20:50

nbody_Angles.py

from nbody_graph_search import Ugraph
# To find 3-body "angle" interactions, we would use this subgraph:
#
#
# *---*---* => 1st bond connects atoms 0 and 1
# 0 1 2 2nd bond connects atoms 1 and 2
#
bond_pattern = Ugraph([(0,1), (1,2)])
# (Ugraph atom indices begin at 0, not 1)
# The next function eliminates the redundancy between 0-1-2 and 2-1-0:
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 3-body angle
interaction between atoms 1, 2, 3 AND 3, 2, 1. This is the same triplet
of atoms, and the angle between them is the same.)
"""
# match[0][0:2] contains the ID numbers for the 3 atoms in the match
atom0 = match[0][0]
atom1 = match[0][1]
atom2 = match[0][2]
# match[1][0:1] contains the ID numbers for the 2 bonds
bond0 = match[1][0]
bond1 = match[1][1]
if atom0 < atom2:
#return ((atom0, atom1, atom2), (bond0, bond1)) same thing as:
return match
else:
return ((atom2, atom1, atom0), (bond1, bond0))

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