def createGroups(self, mapping): groups = [] for name in self.molecules.keys(): full_name = mapping.get(name, None) if full_name is not None: for molecule in self.molecules[name]: g = ChemicalObjects.Group(full_name) setConfiguration(g, [molecule], toplevel=0) groups.append(g) return groups
def makeChemicalObjects(self, template, top_level): self.groups[template.name].locked = True if top_level: if template.attributes.has_key('sequence'): object = ChemicalObjects.ChainMolecule(None) else: object = ChemicalObjects.Molecule(None) else: object = ChemicalObjects.Group(None) object.atoms = [] object.bonds = Bonds.BondList([]) object.groups = [] object.type = self.groups[template.name] object.parent = None child_objects = [] for child in template.children: if isinstance(child, GroupTemplate): group = self.makeChemicalObjects(child, False) object.groups.append(group) object.atoms.extend(group.atoms) object.bonds.extend(group.bonds) group.parent = object child_objects.append(group) else: atom = ChemicalObjects.Atom(child.element) object.atoms.append(atom) atom.parent = object child_objects.append(atom) for name, index in template.names.items(): setattr(object, name, child_objects[index]) child_objects[index].name = name for name, value in template.attributes.items(): path = name.split('.') setattr(self.namePath(object, path[:-1]), path[-1], value) for atom1, atom2 in template.bonds: atom1 = self.namePath(object, atom1) atom2 = self.namePath(object, atom2) object.bonds.append(Bonds.Bond((atom1, atom2))) for name, vector in template.positions.items(): path = name.split('.') self.namePath(object, path).setPosition(vector) return object