def test_dihedral_angles_tpa(self):
molecule = self.load_molecule("tpa.xyz")
pattern = DihedralAnglePattern([
CriteriaSet(atom_criteria(1, 6, 6, 1), tag="HCCH"),
CriteriaSet(atom_criteria(1, 6, 6, 7), tag="HCCN"),
CriteriaSet(atom_criteria(1, 6, 7, 6), tag="HCNC"),
])
expected_results = {
'HCCH':
set([
(16, 2, 1, 14), (15, 2, 1, 14), (16, 2, 1, 13), (15, 2, 1, 13),
(17, 3, 2, 16), (19, 3, 2, 16), (18, 3, 2, 16), (17, 3, 2, 15),
(19, 3, 2, 15), (18, 3, 2, 15), (23, 5, 4, 20), (22, 5, 4, 20),
(23, 5, 4, 21), (22, 5, 4, 21), (25, 6, 5, 23), (26, 6, 5, 23),
(24, 6, 5, 23), (25, 6, 5, 22), (26, 6, 5, 22), (24, 6, 5, 22),
(29, 8, 7, 27), (30, 8, 7, 27), (29, 8, 7, 28), (30, 8, 7, 28),
(31, 9, 8, 29), (33, 9, 8, 29), (32, 9, 8, 29), (31, 9, 8, 30),
(33, 9, 8, 30), (32, 9, 8, 30), (37, 11, 10, 35),
(36, 11, 10, 35), (37, 11, 10, 34), (36, 11, 10, 34),
(39, 12, 11, 37), (40, 12, 11, 37), (38, 12, 11, 37),
(39, 12, 11, 36), (40, 12, 11, 36), (38, 12, 11, 36)
]),
'HCCN':
set([(16, 2, 1, 0), (15, 2, 1, 0), (23, 5, 4, 0), (22, 5, 4, 0),
(29, 8, 7, 0), (30, 8, 7, 0), (37, 11, 10, 0),
(36, 11, 10, 0)]),
'HCNC':
set([(14, 1, 0, 10), (13, 1, 0, 10), (20, 4, 0, 10),
(21, 4, 0, 10), (27, 7, 0, 10), (28, 7, 0, 10),
(35, 10, 0, 1), (34, 10, 0, 1), (20, 4, 0, 1), (21, 4, 0, 1),
(27, 7, 0, 1), (28, 7, 0, 1), (35, 10, 0, 4), (34, 10, 0, 4),
(14, 1, 0, 4), (13, 1, 0, 4), (27, 7, 0, 4), (28, 7, 0, 4),
(35, 10, 0, 7), (34, 10, 0, 7), (14, 1, 0, 7), (13, 1, 0, 7),
(20, 4, 0, 7), (21, 4, 0, 7)])
}
test_results = dict((key, []) for key in expected_results)
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
yield test_item
a, b, c, d = test_item
if (molecule.numbers[a]
== molecule.numbers[d]) and (molecule.numbers[b]
== molecule.numbers[c]):
yield d, c, b, a
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def test_rings_precursor(self):
molecule = self.load_molecule("precursor.xyz")
pattern = RingPattern(21)
all_rings = {}
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
l = all_rings.setdefault(len(match.ring_nodes), set([]))
l.add(match.ring_nodes)
for size, solutions in all_rings.iteritems():
tag = '%i-ring' % size
pattern = NRingPattern(size, [CriteriaSet(tag=tag)], strong=True)
expected_results = {tag: solutions}
test_results = {tag: []}
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
for i in xrange(size):
test_item = (test_item[-1], ) + test_item[:-1]
yield test_item
yield tuple(reversed(test_item))
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def test_dihedral_angles_precursor(self):
molecule = self.load_molecule("precursor.xyz")
pattern = DihedralAnglePattern([CriteriaSet(tag="all")])
# construct all dihedral angles:
all_dihedrals = set([])
for b, c in molecule.graph.pairs:
for a in molecule.graph.neighbors[b]:
if a != c:
for d in molecule.graph.neighbors[c]:
if d != b:
all_dihedrals.add((a, b, c, d))
expected_results = {
'all': all_dihedrals,
}
test_results = dict((key, []) for key in expected_results)
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
yield test_item
a, b, c, d = test_item
yield d, c, b, a
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def test_bonds_tpa(self):
molecule = self.load_molecule("tpa.xyz")
pattern = BondPattern([
CriteriaSet(atom_criteria(1, 6), tag="HC"),
CriteriaSet(atom_criteria(6, 6), tag="CC"),
CriteriaSet(atom_criteria(6, 7), tag="CN"),
CriteriaSet(atom_criteria(6, HasNumNeighbors(4)), tag="C-sp3"),
CriteriaSet(atom_criteria(
6, CritOr(HasAtomNumber(6), HasAtomNumber(7))),
tag="C-[CN]"),
CriteriaSet(relation_criteria={0: BondLongerThan(1.3 * angstrom)},
tag="long"),
CriteriaSet(atom_criteria(
6, HasNeighbors(*atom_criteria(1, 1, 6, 7).values())),
tag="C-C(-NHH)"),
])
expected_results = {
"HC":
set([(14, 1), (13, 1), (16, 2), (15, 2), (17, 3), (19, 3), (18, 3),
(20, 4), (21, 4), (23, 5), (22, 5), (25, 6), (26, 6), (24, 6),
(27, 7), (28, 7), (29, 8), (30, 8), (31, 9), (33, 9), (32, 9),
(35, 10), (34, 10), (37, 11), (36, 11), (39, 12), (40, 12),
(38, 12)]),
"CC":
set([(2, 1), (3, 2), (5, 4), (6, 5), (8, 7), (9, 8), (11, 10),
(12, 11)]),
"CN":
set([(10, 0), (1, 0), (4, 0), (7, 0)]),
"C-sp3":
set([(10, 0), (1, 0), (4, 0), (7, 0), (2, 1), (3, 2), (5, 4),
(6, 5), (8, 7), (9, 8), (11, 10), (12, 11)]),
"C-[CN]":
set([(10, 0), (1, 0), (4, 0), (7, 0), (2, 1), (3, 2), (5, 4),
(6, 5), (8, 7), (9, 8), (11, 10), (12, 11)]),
"long":
set([(10, 0), (1, 0), (4, 0), (7, 0), (2, 1), (3, 2), (5, 4),
(6, 5), (8, 7), (9, 8), (11, 10), (12, 11)]),
"C-C(-NHH)":
set([(5, 4), (7, 8), (1, 2), (10, 11)])
}
test_results = dict((key, []) for key in expected_results)
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
yield test_item
a, b = test_item
if molecule.numbers[a] == molecule.numbers[b] or key == "long":
yield b, a
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def _add_graph_bonds(self, molecular_graph, offset, atom_types, molecule):
# add bonds
match_generator = GraphSearch(BondPattern([CriteriaSet()]))
tmp = sorted([(
match.get_destination(0),
match.get_destination(1),
) for match in match_generator(molecular_graph)])
new = len(tmp)
if new > 0:
prev = len(self.bonds)
self.bonds.resize((prev + len(tmp), 2))
self.bonds[-len(tmp):] = tmp
self.bonds[-len(tmp):] += offset
def _add_graph_dihedrals(self, molecular_graph, offset, atom_types,
molecule):
# add dihedrals
match_generator = GraphSearch(DihedralAnglePattern([CriteriaSet()]))
tmp = sorted([(
match.get_destination(0),
match.get_destination(1),
match.get_destination(2),
match.get_destination(3),
) for match in match_generator(molecular_graph)])
new = len(tmp)
if new > 0:
prev = len(self.dihedrals)
self.dihedrals.resize((prev + len(tmp), 4))
self.dihedrals[-len(tmp):] = tmp
self.dihedrals[-len(tmp):] += offset
def test_tetra_tpa(self):
molecule = self.load_molecule("tpa.xyz")
pattern = TetraPattern(
[CriteriaSet(atom_criteria(6, 1, 6, 6, 1), tag="C-(HCCH)")],
node_tags={
0: 1,
1: 1
}) # node tags are just a silly example
expected_results = {
'C-(HCCH)':
set([
(8, 29, 9, 7, 30),
(8, 30, 9, 7, 29),
(2, 1, 15, 16, 3),
(2, 3, 15, 16, 1),
(11, 10, 36, 37, 12),
(11, 12, 36, 37, 10),
(5, 4, 22, 23, 6),
(5, 6, 22, 23, 4),
]),
}
test_results = dict((key, []) for key in expected_results)
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
a, b, c, d, e = test_item
yield test_item
yield a, c, b, e, d
if (molecule.numbers[b] == molecule.numbers[e]):
yield a, e, c, d, b
yield a, c, e, b, d
if (molecule.numbers[c] == molecule.numbers[d]):
yield a, b, d, c, e
yield a, d, b, e, c
if (molecule.numbers[b]
== molecule.numbers[e]) and (molecule.numbers[c]
== molecule.numbers[d]):
yield a, e, d, c, b
yield a, d, e, b, c
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def test_bending_angles_tpa(self):
molecule = self.load_molecule("tpa.xyz")
pattern = BendingAnglePattern([
CriteriaSet(atom_criteria(1, 6, 1), tag="HCH"),
CriteriaSet(atom_criteria(1, 6, 6), tag="HCC"),
CriteriaSet(atom_criteria(6, 6, 6), tag="CCC"),
CriteriaSet(atom_criteria(6, 6, 7), tag="CCN"),
CriteriaSet(atom_criteria(6, 7, 6), tag="CNC"),
CriteriaSet(atom_criteria(1, 6, 7), tag="HCN"),
])
expected_results = {
'HCC':
set([(14, 1, 2), (13, 1, 2), (16, 2, 1), (15, 2, 1), (16, 2, 3),
(15, 2, 3), (17, 3, 2), (19, 3, 2), (18, 3, 2), (20, 4, 5),
(21, 4, 5), (23, 5, 6), (23, 5, 4), (22, 5, 6), (22, 5, 4),
(25, 6, 5), (26, 6, 5), (24, 6, 5), (27, 7, 8), (28, 7, 8),
(29, 8, 9), (30, 8, 9), (29, 8, 7), (30, 8, 7), (31, 9, 8),
(33, 9, 8), (32, 9, 8), (35, 10, 11), (34, 10, 11),
(37, 11, 12), (36, 11, 12), (37, 11, 10), (36, 11, 10),
(39, 12, 11), (40, 12, 11), (38, 12, 11)]),
'CCN':
set([(2, 1, 0), (5, 4, 0), (8, 7, 0), (11, 10, 0)]),
'CNC':
set([(1, 0, 10), (4, 0, 10), (7, 0, 10), (4, 0, 1), (7, 0, 1),
(7, 0, 4)]),
'HCH':
set([(13, 1, 14), (15, 2, 16), (19, 3, 17), (18, 3, 17),
(18, 3, 19), (21, 4, 20), (22, 5, 23), (26, 6, 25),
(24, 6, 25), (24, 6, 26), (28, 7, 27), (30, 8, 29),
(33, 9, 31), (32, 9, 31), (32, 9, 33), (34, 10, 35),
(36, 11, 37), (40, 12, 39), (38, 12, 39), (38, 12, 40)]),
'HCN':
set([(14, 1, 0), (13, 1, 0), (20, 4, 0), (21, 4, 0), (27, 7, 0),
(28, 7, 0), (35, 10, 0), (34, 10, 0)]),
'CCC':
set([(3, 2, 1), (4, 5, 6), (7, 8, 9), (10, 11, 12)])
}
test_results = dict((key, []) for key in expected_results)
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
yield test_item
a, b, c = test_item
if molecule.numbers[a] == molecule.numbers[c]:
yield c, b, a
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def _add_graph_impropers(self, molecular_graph, offset, atom_types,
molecule):
# add improper dihedrals, only when center has three bonds
match_generator = GraphSearch(
OutOfPlanePattern(
[CriteriaSet(vertex_criteria={0: HasNumNeighbors(3)}, )],
vertex_tags={1: 1}))
tmp = sorted([(
match.get_destination(0),
match.get_destination(1),
match.get_destination(2),
match.get_destination(3),
) for match in match_generator(molecular_graph)])
new = len(tmp)
if new > 0:
prev = len(self.impropers)
self.impropers.resize((prev + len(tmp), 4))
self.impropers[-len(tmp):] = tmp
self.impropers[-len(tmp):] += offset
def test_rings_5ringOH(self):
molecule = self.load_molecule("5ringOH.xyz")
pattern = NRingPattern(10, [CriteriaSet(tag="all")])
expected_results = {
'all': set([(14, 25, 11, 26, 21, 29, 18, 28, 17, 27)])
}
test_results = dict((key, []) for key in expected_results)
match_generator = GraphSearch(pattern, debug=False)
for match in match_generator(molecule.graph):
test_results[match.tag].append(
tuple(
match.get_destination(index)
for index in xrange(len(match))))
def iter_alternatives(test_item, key):
for i in xrange(10):
test_item = (test_item[-1], ) + test_item[:-1]
yield test_item
yield tuple(reversed(test_item))
self.verify_graph_search(molecule.graph, expected_results,
test_results, iter_alternatives)
def __init__(self, label, calculate_eg, atom_criteria):
ValenceTerm.__init__(self, label, calculate_eg, BondPattern(
[CriteriaSet(dict((index, criterion) for index, criterion in enumerate(atom_criteria)))]
))
def add_molecular_graph(self,
molecular_graph,
atom_types=None,
charges=None,
split=True):
# add atom numbers and molecule indices
new = len(molecular_graph.numbers)
if new == 0: return
prev = len(self.numbers)
offset = prev
self.numbers.resize(prev + new)
self.numbers[-new:] = molecular_graph.numbers
if atom_types is None:
atom_types = [
periodic[number].symbol for number in molecular_graph.numbers
]
self.atom_types.extend(atom_types)
if charges is None:
charges = [0.0] * len(molecular_graph.numbers)
self.charges.extend(charges)
self.molecules.resize(prev + new)
# add names (autogenerated)
if split:
groups = molecular_graph.independent_nodes
names = [
self._get_name(molecular_graph, group) for group in groups
]
group_indices = numpy.zeros(new, int)
for group_index, group in enumerate(groups):
for index in group:
group_indices[index] = group_index
self.names.extend(
[names[group_index] for group_index in group_indices])
if prev == 0:
self.molecules[:] = group_indices
else:
self.molecules[
-new:] = self.molecules[-new] + group_indices + 1
else:
if prev == 0:
self.molecules[-new:] = 0
else:
self.molecules[-new:] = self.molecules[-new] + 1
name = self._get_name(molecular_graph)
self.names.extend([name] * new)
# add bonds
match_generator = GraphSearch(BondPattern([CriteriaSet()]))
tmp = [(
match.get_destination(0),
match.get_destination(1),
) for match in match_generator(molecular_graph)]
tmp.sort()
new = len(tmp)
if new > 0:
prev = len(self.bonds)
self.bonds.resize((prev + len(tmp), 2))
self.bonds[-len(tmp):] = tmp
self.bonds[-len(tmp):] += offset
# add bends
match_generator = GraphSearch(BendingAnglePattern([CriteriaSet()]))
tmp = [(
match.get_destination(0),
match.get_destination(1),
match.get_destination(2),
) for match in match_generator(molecular_graph)]
tmp.sort()
new = len(tmp)
if new > 0:
prev = len(self.bends)
self.bends.resize((prev + len(tmp), 3))
self.bends[-len(tmp):] = tmp
self.bends[-len(tmp):] += offset
# add dihedrals
match_generator = GraphSearch(DihedralAnglePattern([CriteriaSet()]))
tmp = [(
match.get_destination(0),
match.get_destination(1),
match.get_destination(2),
match.get_destination(3),
) for match in match_generator(molecular_graph)]
tmp.sort()
new = len(tmp)
if new > 0:
prev = len(self.dihedrals)
self.dihedrals.resize((prev + len(tmp), 4))
self.dihedrals[-len(tmp):] = tmp
self.dihedrals[-len(tmp):] += offset