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
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
