def excludedPairs(self, subset1, subset2, global_data):
if 'excluded_pairs' not in global_data.get('initialized'):
excluded_pairs = set(global_data.get('excluded_pairs'))
if subset1 is not None:
set1 = set(a.index for a in subset1.atomList())
set2 = set(a.index for a in subset2.atomList())
excluded_pairs |= set(Utility.orderedPairs(list(set1-set2)))
excluded_pairs |= set(Utility.orderedPairs(list(set2-set1)))
atom_subset = list(set1 | set2)
atom_subset.sort()
else:
atom_subset = None
global_data.set('atom_subset', atom_subset)
global_data.set('excluded_pairs', list(excluded_pairs))
one_four_pairs = set(global_data.get('1_4_pairs')) \
- excluded_pairs
global_data.set('1_4_pairs', list(one_four_pairs))
global_data.add('initialized', 'excluded_pairs')
return global_data.get('excluded_pairs'), \
global_data.get('1_4_pairs'), \
global_data.get('atom_subset')
def excludedPairs(self, subset1, subset2, global_data):
if 'excluded_pairs' not in global_data.get('initialized'):
excluded_pairs = set(global_data.get('excluded_pairs'))
if subset1 is not None:
set1 = set(a.index for a in subset1.atomList())
set2 = set(a.index for a in subset2.atomList())
excluded_pairs |= set(Utility.orderedPairs(list(set1 - set2)))
excluded_pairs |= set(Utility.orderedPairs(list(set2 - set1)))
atom_subset = list(set1 | set2)
atom_subset.sort()
else:
atom_subset = None
global_data.set('atom_subset', atom_subset)
global_data.set('excluded_pairs', list(excluded_pairs))
one_four_pairs = set(global_data.get('1_4_pairs')) \
- excluded_pairs
global_data.set('1_4_pairs', list(one_four_pairs))
global_data.add('initialized', 'excluded_pairs')
return global_data.get('excluded_pairs'), \
global_data.get('1_4_pairs'), \
global_data.get('atom_subset')
def evaluatorTerms(self, universe, subset1, subset2, global_data):
nothing = N.zeros((0, 2), N.Int)
if subset1 is not None:
set1 = set(a.index for a in subset1.atomList())
set2 = set(a.index for a in subset2.atomList())
excluded_pairs = set(Utility.orderedPairs(list(set1-set2))) \
| set(Utility.orderedPairs(list(set2-set1)))
excluded_pairs = N.array(list(excluded_pairs))
atom_subset = list(set1 | set2)
atom_subset.sort()
atom_subset = N.array(atom_subset)
else:
atom_subset = N.array([], N.Int)
excluded_pairs = nothing
nbl = NonbondedList(excluded_pairs, nothing, atom_subset, universe._spec,
self.cutoff)
update = NonbondedListTerm(nbl)
cutoff = self.cutoff
if cutoff is None:
cutoff = 0.
ev = ANTerm(universe._spec, nbl, cutoff, self.scale_factor)
return [update, ev]
def evaluatorTerms(self, universe, subset1, subset2, global_data):
nothing = N.zeros((0, 2), N.Int)
if subset1 is not None:
set1 = set(a.index for a in subset1.atomList())
set2 = set(a.index for a in subset2.atomList())
excluded_pairs = set(Utility.orderedPairs(list(set1-set2))) \
| set(Utility.orderedPairs(list(set2-set1)))
excluded_pairs = N.array(list(excluded_pairs))
atom_subset = list(set1 | set2)
atom_subset.sort()
atom_subset = N.array(atom_subset)
else:
atom_subset = N.array([], N.Int)
excluded_pairs = nothing
nbl = NonbondedList(excluded_pairs, nothing, atom_subset,
universe._spec, self.cutoff)
update = NonbondedListTerm(nbl)
cutoff = self.cutoff
if cutoff is None:
cutoff = 0.
ev = ANTerm(universe._spec, nbl, cutoff, self.scale_factor)
return [update, ev]