def penalty_birads_replacing_lone_pairs_test(self):
"""Test that birads on `S u2 p0` are penalized"""
adj = """
multiplicity 3
1 S u2 p0 c0 {2,D} {3,D}
2 O u0 p2 c0 {1,D}
3 O u0 p2 c0 {1,D}
"""
mol = Molecule().fromAdjacencyList(adj)
mol.update()
mol_list = generate_resonance_structures(mol, keep_isomorphic=False, filter_structures=True)
for mol in mol_list:
if mol.reactive:
for atom in mol.vertices:
if atom.isSulfur():
self.assertNotEquals(atom.radicalElectrons, 2)
self.assertEqual(len(mol_list), 3)
self.assertEqual(sum([1 for mol in mol_list if mol.reactive]), 2)
def penalty_birads_replacing_lone_pairs_test(self):
"""Test that birads on `S u2 p0` are penalized"""
adj = """
multiplicity 3
1 S u2 p0 c0 {2,D} {3,D}
2 O u0 p2 c0 {1,D}
3 O u0 p2 c0 {1,D}
"""
mol = Molecule().from_adjacency_list(adj)
mol.update()
mol_list = generate_resonance_structures(mol, keep_isomorphic=False, filter_structures=True)
for mol in mol_list:
if mol.reactive:
for atom in mol.vertices:
if atom.is_sulfur():
self.assertNotEquals(atom.radical_electrons, 2)
self.assertEqual(len(mol_list), 3)
self.assertEqual(sum([1 for mol in mol_list if mol.reactive]), 2)
def get_representative_molecule(self, mode='minimal', update=True):
if mode == 'minimal':
# create a molecule from fragment.vertices.copy
mapping = self.copyAndMap()
# replace CuttingLabel with H
atoms = []
for vertex in self.vertices:
mapped_vertex = mapping[vertex]
if isinstance(mapped_vertex, CuttingLabel):
# replace cutting label with atom H
atom_H = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
for bondedAtom, bond in mapped_vertex.edges.iteritems():
new_bond = Bond(bondedAtom, atom_H, order=bond.order)
bondedAtom.edges[atom_H] = new_bond
del bondedAtom.edges[mapped_vertex]
atom_H.edges[bondedAtom] = new_bond
mapping[vertex] = atom_H
atoms.append(atom_H)
else:
atoms.append(mapped_vertex)
# Note: mapping is a dict with
# key: self.vertex and value: mol_repr.atom
mol_repr = Molecule()
mol_repr.atoms = atoms
if update:
mol_repr.update()
return mol_repr, mapping
def assign_representative_molecule(self):
# create a molecule from fragment.vertices.copy
mapping = self.copyAndMap()
# replace CuttingLabel with CC
atoms = []
additional_atoms = []
additional_bonds = []
for vertex in self.vertices:
mapped_vertex = mapping[vertex]
if isinstance(mapped_vertex, CuttingLabel):
# replace cutting label with atom C
atom_C1 = Atom(element=getElement('C'),
radicalElectrons=0,
charge=0,
lonePairs=0)
for bondedAtom, bond in mapped_vertex.edges.iteritems():
new_bond = Bond(bondedAtom, atom_C1, order=bond.order)
bondedAtom.edges[atom_C1] = new_bond
del bondedAtom.edges[mapped_vertex]
atom_C1.edges[bondedAtom] = new_bond
# add hydrogens and carbon to make it CC
atom_H1 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H2 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_C2 = Atom(element=getElement('C'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H3 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H4 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H5 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atoms.append(atom_C1)
additional_atoms.extend(
[atom_H1, atom_H2, atom_H3, atom_H4, atom_H5, atom_C2])
additional_bonds.extend([
Bond(atom_C1, atom_H1, 1),
Bond(atom_C1, atom_H2, 1),
Bond(atom_C2, atom_H3, 1),
Bond(atom_C2, atom_H4, 1),
Bond(atom_C2, atom_H5, 1),
Bond(atom_C1, atom_C2, 1)
])
else:
atoms.append(mapped_vertex)
mol_repr = Molecule()
mol_repr.atoms = atoms
for atom in additional_atoms:
mol_repr.addAtom(atom)
for bond in additional_bonds:
mol_repr.addBond(bond)
# update connectivity
mol_repr.update()
# create a species object from molecule
self.mol_repr = mol_repr
return mapping