def _setupActiveFragmentsInformation(self):
active_atoms = self._getActiveAtomsFromFragments()
if self._active_atoms_distance > 0.0:
active_atoms = self._getActiveAtomsFromDistance()
#print "found %i atoms which should be active" % (len(active_atoms))
self._active_atoms = active_atoms[:]
atoms = self._active_atoms[:]
frags = self._fragmentation.getFragments()
fragment_layers = self._fragment_layers[:]
if self._central_fragment == 0:
self._active_frags = []
return
if len(self._active_atoms) > 0:
#print "extending region A to include all atoms of close fragments"
active_frags = [] #self._active_fragments[:]
active_frags.append(self._central_fragment -
1) # central must also be active
for atom in atoms:
ifrg = self._getFragmentFromAtom(atom)
active_frags.extend([ifrg])
active_frags = Uniqify(active_frags)
active_frags = sorted(active_frags)
self._active_fragments = active_frags[:]
# promote active fragments to layer 2
for active_fragment_id in active_frags:
self._fragment_layers[active_fragment_id] = 2
# add active fragment atoms to list of active atoms
fragments = self._fragmentation.getFragments()
for frag in active_frags:
atoms.extend(fragments[frag])
atoms = Uniqify(atoms)
atoms = sorted(atoms)
#print "active region is now %i atoms large (%i fragments)" % (len(atoms),len(active_frags))
#print atoms
if self._freeze_backbone:
#print "attempting to find and freeze backbone atoms in the active region"
for item in self._fragmentation.getBackboneAtoms():
if item in atoms:
atoms.remove(item)
continue
#print "active region is now %i atoms large (%i fragments)" % (len(atoms),len(active_frags))
#print atoms
atoms = Uniqify(atoms)
atoms = sorted(atoms)
self._active_atoms = atoms[:]
def _getBasisAtoms(self, ilayer):
atom_numbers = Uniqify(
[atom.GetAtomicNum() for atom in self._fragmentation.getAtoms()])
atom_numbers.sort()
atoms = [
self._elements.GetSymbol(atom_number)
for atom_number in atom_numbers
]
return "".join(
[self._formatSingleAtomBasis(ilayer, atom) for atom in atoms])
def _getActiveAtomsFromDistance(self):
atoms = []
central_atoms = self._fragmentation.getFragments()[
self._central_fragment - 1]
atoms.extend(central_atoms)
all_atoms = range(1, len(self._fragmentation.getAtoms()) + 1)
for atom_idx in central_atoms:
for atom_jdx in all_atoms:
if atom_jdx in central_atoms: continue
if atom_jdx in atoms: continue
R = self._getDistanceBetweenAtoms(atom_idx, atom_jdx)
if R < self._active_atoms_distance:
atoms.append(atom_jdx)
continue
atoms = Uniqify(atoms)
return sorted(atoms)