def iter_atom_pairs(self, bound=True, unique=True, sort=True):
"""
Iterator iterating over all pairs of atoms in the molecule
'exp'
:param bound: Boolean specifying whether all atom pairs are
returned or only those with chemical bonds between them.
"""
blacklist = []
for atom1 in self.iter_atoms(sort=sort):
# for atom2 in self.iter_atoms(sort=sort):
if bound:
for atom2 in atom1.partner:
# if not atom1 == atom2:
if not bound or is_bound(atom1.cart, atom1.element, atom2.cart, atom2.element):
blackstring = '{}{}'.format(*sorted([atom1.name, atom2.name]))
if unique and not blackstring in blacklist:
yield atom1, atom2
blacklist.append(blackstring)
elif not unique:
yield atom1, atom2
else:
break
else:
for atom2 in self.iter_atoms(sort=sort):
if not atom1 == atom2:
yield atom1, atom2
def find_rings(atoms):
graph = Graph()
for i, atom1 in enumerate(atoms):
for atom2 in atoms[i+1:]:
if is_bound(atom1.cart, atom1.element, atom2.cart, atom2.element):
graph.add_edge(atom1.name, atom2.name)
ring_list = cycle_basis(graph)
return ring_list
def _get_bonds(self, unique=True, hydrogen=True):
for atom1 in self.atom_dict.values():
for atom2 in self.atom_dict.values():
if not atom1 == atom2:
if hydrogen == False and (atom1.get_element() == 'H' or atom2.get_element() == 'H'):
continue
if is_bound(atom1.get_cart(),
atom1.get_element(),
atom2.get_cart(),
atom2.get_element()):
bondatoms = [atom1.get_id(), atom2.get_id()]
if unique:
bondatoms = sorted(bondatoms)
bondatoms = ':'.join(bondatoms)
self.bonds[bondatoms] = [atom1, atom2]
def find_rings(atoms, bonds=None):
graph = Graph()
# bonds = None
class DummyMolecule(object):
pass
mol = DummyMolecule()
mol.atoms = atoms
if bonds is None:
for atom1, atom2 in iter_atom_pairs():
graph.add_edge(atom1.name, atom2.name)
else:
blacklist = []
for b in bonds:
for atom2i in b[1:10]:
string = ' : '.join(sorted([atoms[b[0]].name, atoms[atom2i].name]))
if not string in blacklist:
if is_bound(atoms[b[0]].cart, atoms[b[0]].element, atoms[atom2i].cart, atoms[atom2i].element):
graph.add_edge(atoms[b[0]].name, atoms[atom2i].name)
blacklist.append(string)
ring_list = cycle_basis(graph)
return ring_list
