def test_fully_saturated(self):
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('C', '', '4')), '(ch4)')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('N', '', '3')), '(nh3)')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('O', '', '2')), '(oh2)')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('F', '', '1')), '(fh)')
def test_one_heavy(self):
got = smu_utils_lib.create_bond_topology('C', '', '4')
expected_str = '''
atoms: ATOM_C
atoms: ATOM_H
atoms: ATOM_H
atoms: ATOM_H
atoms: ATOM_H
bonds {
atom_b: 1
bond_type: BOND_SINGLE
}
bonds {
atom_b: 2
bond_type: BOND_SINGLE
}
bonds {
atom_b: 3
bond_type: BOND_SINGLE
}
bonds {
atom_b: 4
bond_type: BOND_SINGLE
}
'''
expected = str_to_bond_topology(expected_str)
self.assertEqual(str(expected), str(got))
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
with gfile.GFile(FLAGS.output_csv, 'w') as outfile:
writer = csv.writer(outfile, dialect='unix', quoting=csv.QUOTE_MINIMAL)
writer.writerow([
'id', 'num_atoms', 'atoms_str', 'connectivity_matrix', 'hydrogens',
'smiles'
])
infiles = sorted(gfile.Glob(FLAGS.input_glob))
bt_id = 1
for infn in infiles:
logging.info('Opening %s at id %d', infn, bt_id)
with gfile.GFile(infn) as infile:
for line in infile:
num_atoms, atoms, connectivity, hydrogens = (
smu_utils_lib.parse_bond_topology_line(line))
# The atoms strings looks like 'C N N+O O-' where every atom has a
# space, +, or - after it. create_bond_topology doesn't want the
# charge markings (just a string like 'CNNOO') so the [::2] skips
# those.
bond_topology = smu_utils_lib.create_bond_topology(
atoms[::2], connectivity, hydrogens)
smiles = smu_utils_lib.compute_smiles_for_bond_topology(
bond_topology, include_hs=False)
writer.writerow(
[bt_id, num_atoms, atoms, connectivity, hydrogens, smiles])
bt_id += 1
# Add the special cases for SMU 1
for _, bt_id, atom, valence in smu_utils_lib.SPECIAL_ID_CASES:
# Note that the SMILES is just the atom. Convenient
writer.writerow([bt_id, 1, atom, '', valence, atom])
def add_bond_topology_to_conformer(self, conformer, btid):
# We'll use a simple rule for making smiles. The SMILES is just btid
# number of Cs
def make_connectivity_matrix(num_c):
if num_c == 2:
return '1'
return '1' + ('0' *
(num_c - 2)) + make_connectivity_matrix(num_c - 1)
if btid == 1:
bt = smu_utils_lib.create_bond_topology('C', '', '4')
else:
bt = smu_utils_lib.create_bond_topology(
'C' * btid, make_connectivity_matrix(btid),
'3' + ('2' * (btid - 2)) + '3')
bt.bond_topology_id = btid
bt.smiles = 'C' * btid
conformer.bond_topologies.append(bt)
def test_charged(self):
# This is actually C N N+O-
got = smu_utils_lib.create_bond_topology('CNNO', '200101', '2020')
expected_str = '''
atoms: ATOM_C
atoms: ATOM_N
atoms: ATOM_NPOS
atoms: ATOM_ONEG
atoms: ATOM_H
atoms: ATOM_H
atoms: ATOM_H
atoms: ATOM_H
bonds {
atom_b: 1
bond_type: BOND_DOUBLE
}
bonds {
atom_a: 1
atom_b: 2
bond_type: BOND_SINGLE
}
bonds {
atom_a: 2
atom_b: 3
bond_type: BOND_SINGLE
}
bonds {
atom_b: 4
bond_type: BOND_SINGLE
}
bonds {
atom_b: 5
bond_type: BOND_SINGLE
}
bonds {
atom_a: 2
atom_b: 6
bond_type: BOND_SINGLE
}
bonds {
atom_a: 2
atom_b: 7
bond_type: BOND_SINGLE
}
'''
expected = str_to_bond_topology(expected_str)
self.assertEqual(str(expected), str(got))
def parse_bond_topology(self):
"""Parse region with adjancy matrix, hydrogen count, smiles, and atom types."""
adjacency_code = str(self.parse(ParseModes.RAW, num_lines=1)[0]).strip()
hydrogen_counts = [
int(count)
for count in str(self.parse(ParseModes.RAW, num_lines=1)[0]).strip()
]
smiles = self.parse(ParseModes.RAW, num_lines=1)[0]
entry_id = str(self.parse(ParseModes.RAW, num_lines=1)[0]).strip()
assert entry_id.startswith('x'), 'Expected line like x02_c2h2'
atom_types = entry_id[4:].lower()
expanded_atom_types = self.expand_atom_types(atom_types)
self._conformer.bond_topologies.add()
self._conformer.bond_topologies[-1].CopyFrom(
smu_utils_lib.create_bond_topology(expanded_atom_types, adjacency_code,
hydrogen_counts))
self._conformer.bond_topologies[-1].smiles = str(smiles).replace(
'\'', '').strip()
def test_no_charged(self):
got = smu_utils_lib.create_bond_topology('CNFF', '111000', '1200')
expected_str = '''
atoms: ATOM_C
atoms: ATOM_N
atoms: ATOM_F
atoms: ATOM_F
atoms: ATOM_H
atoms: ATOM_H
atoms: ATOM_H
bonds {
atom_b: 1
bond_type: BOND_SINGLE
}
bonds {
atom_b: 2
bond_type: BOND_SINGLE
}
bonds {
atom_b: 3
bond_type: BOND_SINGLE
}
bonds {
atom_b: 4
bond_type: BOND_SINGLE
}
bonds {
atom_a: 1
atom_b: 5
bond_type: BOND_SINGLE
}
bonds {
atom_a: 1
atom_b: 6
bond_type: BOND_SINGLE
}
'''
expected = str_to_bond_topology(expected_str)
self.assertEqual(str(expected), str(got))
def test_ethylene(self):
bt = smu_utils_lib.create_bond_topology('CC', '2', '22')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt), '(ch2)2')
def test_cyclobutane(self):
bt = smu_utils_lib.create_bond_topology('CCCC', '110011', '2222')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt), '(ch2)4')
def test_nplus_oneg(self):
bt = smu_utils_lib.create_bond_topology('NO', '1', '30')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt),
'(nh3)(o)')
def test_fluorine(self):
bt = smu_utils_lib.create_bond_topology('OFF', '110', '000')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt), '(o)(f)2')
def test_acrylic_acid(self):
bt = smu_utils_lib.create_bond_topology('CCCOO', '2000100210', '21001')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt),
'(c)(ch)(ch2)(o)(oh)')
