class DeformationEvaluationFunction:
def __init__(self,
universe,
fc_length=0.7,
cutoff=1.2,
factor=46402.,
form='exponential'):
self.universe = universe
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
nothing = Numeric.zeros((0, 2), Numeric.Int)
self.pairs = NonbondedList(nothing, nothing, nothing, universe._spec,
cutoff)
self.pairs.update(universe.configuration().array)
self.normalize = 0
try:
self.version = self.forms.index(form)
except ValueError:
raise ValueError("unknown functional form")
forms = ['exponential', 'calpha']
def newConfiguration(self):
self.pairs.update(self.universe.configuration().array)
def nonbondedList(self, universe, subset1, subset2, global_data):
try:
from MMTK_forcefield import NonbondedList, NonbondedListTerm
except ImportError:
return None, None
nbl = None
update = None
if 'nonbondedlist' in global_data.get('initialized'):
nbl, update, cutoff = global_data.get('nonbondedlist')
if nbl is None:
excluded_pairs, one_four_pairs, atom_subset = \
self.excludedPairs(subset1, subset2, global_data)
excluded_pairs = N.array(excluded_pairs)
one_four_pairs = N.array(one_four_pairs)
if atom_subset is not None:
atom_subset = N.array(atom_subset)
else:
atom_subset = N.array([], N.Int)
nbl = NonbondedList(excluded_pairs, one_four_pairs, atom_subset,
universe._spec, self.cutoff)
update = NonbondedListTerm(nbl)
update.info = 0
global_data.set('nonbondedlist', (nbl, update, self.cutoff))
global_data.add('initialized', 'nonbondedlist')
else:
if cutoff is not None and \
(self.cutoff is None or self.cutoff > cutoff):
nbl.setCutoff(self.cutoff)
return nbl, update
def test_nonbondedList(self):
self.universe.configuration()
atoms = self.universe.atomList()
atom_indices = N.array([a.index for a in self.universe.atomList()])
empty = N.zeros((0, 2), N.Int)
for cutoff in [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.]:
nblist = NonbondedList(empty, empty, atom_indices,
self.universe._spec, cutoff)
nblist.update(self.universe.configuration().array)
distances = nblist.pairDistances()
pairs1 = nblist.pairIndices()
pairs1 = [sorted_tuple(pairs1[i]) for i in range(len(pairs1))
if distances[i] < cutoff]
pairs1.sort(lambda a, b: cmp(a[0], b[0]) or cmp(a[1], b[1]))
pairs2 = []
for i in range(len(atoms)):
for j in range(i+1, len(atoms)):
d = self.universe.distance(atoms[i], atoms[j])
if d < cutoff:
pairs2.append(sorted_tuple((atoms[i].index,
atoms[j].index)))
pairs2.sort(lambda a, b: cmp(a[0], b[0]) or cmp(a[1], b[1]))
self.assertEqual(pairs1, pairs2)
def evaluatorTerms(self, universe, subset1, subset2, global_data):
if subset1 is not None:
for s1, s2 in [(subset1, subset2), (subset2, subset1)]:
set = {}
for a in s1.atomList():
set[a.index] = None
for a in s2.atomList():
try:
del set[a.index]
except KeyError: pass
set = {}
for a in subset1.atomList():
set[a.index] = None
for a in subset2.atomList():
set[a.index] = None
atom_subset = set.keys()
atom_subset.sort()
atom_subset = Numeric.array(atom_subset)
else:
atom_subset = Numeric.array([], Numeric.Int)
nothing = Numeric.zeros((0,2), Numeric.Int)
nbl = NonbondedList(nothing, nothing, atom_subset, universe._spec,
self.cutoff)
update = NonbondedListTerm(nbl)
cutoff = self.cutoff
if cutoff is None:
cutoff = 0.
ev = CalphaTerm(universe._spec, nbl, cutoff,
self.scale_factor, self.version)
return [update, ev]
class DeformationEvaluationFunction:
def __init__(self, universe, fc_length = 0.7, cutoff = 1.2,
factor = 46402.):
self.universe = universe
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
nothing = Numeric.zeros((0,2), Numeric.Int)
self.pairs = NonbondedList(nothing, nothing, nothing,
universe._spec, cutoff)
self.pairs.update(universe.configuration().array)
self.normalize = 0
def newConfiguration(self):
self.pairs.update(self.universe.configuration().array)
def test_nonbondedList(self):
self.universe.configuration()
atoms = self.universe.atomList()
atom_indices = N.array([a.index for a in self.universe.atomList()])
empty = N.zeros((0, 2), N.Int)
for cutoff in [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.]:
nblist = NonbondedList(empty, empty, atom_indices,
self.universe._spec, cutoff)
nblist.update(self.universe.configuration().array)
distances = nblist.pairDistances()
pairs1 = nblist.pairIndices()
pairs1 = [
sorted_tuple(pairs1[i]) for i in range(len(pairs1))
if distances[i] < cutoff
]
pairs1.sort(lambda a, b: cmp(a[0], b[0]) or cmp(a[1], b[1]))
pairs2 = []
for i in range(len(atoms)):
for j in range(i + 1, len(atoms)):
d = self.universe.distance(atoms[i], atoms[j])
if d < cutoff:
pairs2.append(
sorted_tuple((atoms[i].index, atoms[j].index)))
pairs2.sort(lambda a, b: cmp(a[0], b[0]) or cmp(a[1], b[1]))
self.assertEqual(pairs1, pairs2)
class DeformationEvaluationFunction(object):
def __init__(self, universe, fc_length = 0.7, cutoff = 1.2,
factor = 46402., form = 'exponential'):
self.universe = universe
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
nothing = N.zeros((0,2), N.Int)
self.pairs = NonbondedList(nothing, nothing, nothing,
universe._spec, cutoff)
self.pairs.update(universe.configuration().array)
self.normalize = 0
try:
self.version = self.forms.index(form)
except ValueError:
raise ValueError("unknown functional form")
forms = ['exponential', 'calpha']
def newConfiguration(self):
self.pairs.update(self.universe.configuration().array)
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]