def test_has_conformer(self):
"""Test has conformer"""
infile = get_fn('butane.pdb')
ifs = oechem.oemolistream(infile)
molecule_with_conf = oechem.OEMol()
oechem.OEReadMolecule(ifs, molecule_with_conf)
self.assertTrue(chemi.has_conformer(molecule_with_conf))
molecule_without_conf = chemi.smiles_to_oemol('CCCC')
self.assertFalse(chemi.has_conformer(molecule_without_conf))
def test_atom_map(self):
"""Test get atom map"""
from openeye import oechem
tagged_smiles = '[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]'
mol_1 = chemi.smiles_to_oemol('CC[N+]#C')
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = get_atom_map(mol_1, tagged_smiles)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1),
oechem.OECreateCanSmiString(mol_2))
# Test aromatic molecule
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = chemi.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = get_atom_map(mol_1, tagged_smiles)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1),
oechem.OECreateCanSmiString(mol_2))
def test_generate_torsions(self):
""" Tests finding torsion to drive """
from openeye import oechem
infile = get_fn('butane.pdb')
ifs = oechem.oemolistream(infile)
inp_mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, inp_mol)
needed_torsion_scans = torsions.find_torsions(molecule=inp_mol)
self.assertEqual(len(needed_torsion_scans['internal']), 1)
self.assertEqual(len(needed_torsion_scans['terminal']), 2)
self.assertEqual(needed_torsion_scans['internal']['torsion_0'],
(0, 2, 3, 1))
self.assertEqual(needed_torsion_scans['terminal']['torsion_0'],
(3, 2, 0, 4))
self.assertEqual(needed_torsion_scans['terminal']['torsion_1'],
(2, 3, 1, 7))
def test_tagged_smiles(self):
"""Test index-tagges smiles"""
from openeye import oechem
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
inp_mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, inp_mol)
tagged_smiles = mol_to_smiles(inp_mol,
isomeric=True,
mapped=True,
explicit_hydrogen=True)
# Tags should always be the same as mol2 molecule ordering
self.assertEqual(
tagged_smiles,
'[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]')
def test_mapped_xyz(self):
"""Test writing out mapped xyz"""
from openeye import oechem, oeomega
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = chemi.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
mol_1 = chemi.generate_conformers(mol_1, max_confs=1)
atom_map = get_atom_map(mol_1, tagged_smiles)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
xyz_1 = chemi.to_mapped_xyz(mol_1, atom_map, xyz_format=False)
# molecule generated from mol2 should be in the right order.
atom_map_mol2 = {
1: 0,
2: 1,
3: 2,
4: 3,
5: 4,
6: 5,
7: 6,
8: 7,
9: 8,
10: 9,
11: 10,
12: 11,
13: 12,
14: 13,
15: 14
}
xyz_2 = chemi.to_mapped_xyz(mol_2, atom_map_mol2, xyz_format=False)
for ele1, ele2 in zip(xyz_1.split('\n')[:-1], xyz_2.split('\n')[:-1]):
self.assertEqual(ele1.split(' ')[2], ele2.split(' ')[2])
def test_workflow(fractal_compute_server):
"""Fragmenter regression test"""
pytest.importorskip("torsiondrive")
pytest.importorskip("geometric")
pytest.importorskip("rdkit")
client = portal.FractalClient(fractal_compute_server)
smiles = 'CCCCC'
workflow_id = 'example'
workflow_json = get_fn('workflows.json')
workflow = workflow_api.WorkFlow(client=client,
workflow_json=workflow_json,
workflow_id=workflow_id)
workflow.workflow(molecules_smiles=smiles, molecule_titles=['pentane'])
assert len(workflow.qcfractal_jobs) == 1
key = list(workflow.qcfractal_jobs.keys())[0]
assert len(workflow.qcfractal_jobs[key]) == 3
assert len(workflow.qcfractal_jobs[key]['optimization_input']) == 0
assert len(workflow.qcfractal_jobs[key]['torsiondrive_input']) == 3
assert len(workflow.qcfractal_jobs[key]['torsiondrive_input']
['(0, 2, 3, 1)']['initial_molecule']) == 8