def endElement(self, name):
#print "END", name
if name == 'molecule':
if len(self.current_numbers) > 0:
self.current_coordinates = numpy.array(self.current_coordinates)*angstrom
molecule = Molecule(self.current_numbers, self.current_coordinates, self.current_title)
molecule.extra = self.current_extra
molecule.atoms_extra = self.current_atoms_extra
name_to_index = {}
for counter, name in enumerate(self.current_atom_names):
name_to_index[name] = counter
pairs = set()
current_bonds_extra = {}
for name1, name2, extra in self.current_bonds:
i1 = name_to_index.get(name1)
i2 = name_to_index.get(name2)
if i1 is not None and i2 is not None:
pair = frozenset([i1,i2])
if len(extra) > 0:
current_bonds_extra[pair] = extra
pairs.add(pair)
molecule.bonds_extra = current_bonds_extra
if len(pairs) == 0:
molecule.graph = None
else:
molecule.graph = MolecularGraph(pairs, self.current_numbers)
del self.current_atom_names
del self.current_bonds
self.molecules.append(molecule)
self.current_title = None
def endElement(self, name):
#print "END", name
if name == 'molecule':
if len(self.current_numbers) > 0:
self.current_coordinates = np.array(self.current_coordinates)*angstrom
molecule = Molecule(self.current_numbers, self.current_coordinates, self.current_title)
molecule.extra = self.current_extra
molecule.atoms_extra = self.current_atoms_extra
name_to_index = {}
for counter, name in enumerate(self.current_atom_names):
name_to_index[name] = counter
edges = set()
current_bonds_extra = {}
for name1, name2, extra in self.current_bonds:
i1 = name_to_index.get(name1)
i2 = name_to_index.get(name2)
if i1 is not None and i2 is not None:
edge = frozenset([i1, i2])
if len(extra) > 0:
current_bonds_extra[edge] = extra
edges.add(edge)
molecule.bonds_extra = current_bonds_extra
if len(edges) == 0:
molecule.graph = None
else:
molecule.graph = MolecularGraph(edges, self.current_numbers)
del self.current_atom_names
del self.current_bonds
self.molecules.append(molecule)
self.current_title = None
def collect_molecules(self, parent, universe=None):
Atom = context.application.plugins.get_node("Atom")
Bond = context.application.plugins.get_node("Bond")
Frame = context.application.plugins.get_node("Frame")
if universe == None:
universe = parent
atom_to_index = {}
atoms_extra = {}
counter = 0
numbers = []
coordinates = []
for child in parent.children:
if isinstance(child, Atom):
atom_to_index[child] = counter
if len(child.extra) > 0:
atoms_extra[counter] = child.extra
counter += 1
numbers.append(child.number)
coordinates.append(child.get_frame_relative_to(universe).t)
if len(numbers) > 0:
molecule = Molecule(numbers, coordinates, parent.name)
molecule.extra = parent.extra
molecule.atoms_extra = atoms_extra
molecule.bonds_extra = {}
pairs = set([])
for child in parent.children:
if isinstance(child, Bond):
atoms = child.get_targets()
pair = frozenset([atom_to_index[atoms[0]], atom_to_index[atoms[1]]])
if len(child.extra) > 0:
molecule.bonds_extra[pair] = child.extra
pairs.add(pair)
if len(pairs) > 0:
molecule.graph = MolecularGraph(pairs, molecule.numbers)
else:
molecule.graph = None
result = [molecule]
else:
result = []
for child in parent.children:
if isinstance(child, Frame):
result.extend(self.collect_molecules(child, universe))
return result
