def test_get_mol2_gaff_atom_types(self):
"""Test that a warning is raised OpenEyeToolkitWrapper when it detects GAFF atom types in a mol2 file."""
toolkit_wrapper = OpenEyeToolkitWrapper()
mol2_file_path = get_data_file_path(
'molecules/AlkEthOH_test_filt1_ff.mol2')
with pytest.warns(GAFFAtomTypeWarning, match='SYBYL'):
Molecule.from_file(mol2_file_path,
toolkit_registry=toolkit_wrapper)
def qcmiles(jsmol, toolkit='rdkit'):
import cmiles
from openbabel import openbabel
from openforcefield.topology.molecule import Molecule
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("xyz", "sdf")
obmol = openbabel.OBMol()
xyz_str = dict_to_xyz_string(jsmol)
obConversion.ReadString(obmol, xyz_str)
sdf = obConversion.WriteString(obmol)
with io.StringIO(sdf) as sdf_stream:
qcmol = Molecule.from_file(sdf_stream,
file_format='SDF').to_qcschema().dict()
# would be nice if oFF could handle data as strings to avoid IO
#with open('mol.sdf','w') as f:
# f.write(sdf)
#qcmol = Molecule.from_file('mol.sdf').to_qcschema().dict()
#os.remove("mol.sdf")
# cmiles wants the schema with a flat xyz
if len(qcmol['geometry'].shape) > 1:
qcmol['geometry'] = np.reshape(qcmol['geometry'], (-1, ))
attribs = cmiles.generator.get_molecule_ids(qcmol, toolkit=toolkit)
return attribs
def test_load_aromatic_pdb(self):
"""Test OpenEyeToolkitWrapper for importing molecule conformers"""
toolkit_wrapper = RDKitToolkitWrapper()
filename = get_data_file_path('molecules/toluene.pdb')
molecule = Molecule.from_file(filename,
toolkit_registry=toolkit_wrapper)
assert len(molecule._conformers) == 1
assert molecule._conformers[0].shape == (15, 3)
def test_get_pdb_coordinates(self):
"""Test RDKitToolkitWrapper for importing a single set of coordinates from a pdb file"""
toolkit_wrapper = RDKitToolkitWrapper()
filename = get_data_file_path('molecules/toluene.pdb')
molecule = Molecule.from_file(filename,
toolkit_registry=toolkit_wrapper)
assert len(molecule._conformers) == 1
assert molecule._conformers[0].shape == (15, 3)
def test_get_multiconformer_sdf_coordinates(self):
"""Test RDKitToolkitWrapper for importing a single set of coordinates from a sdf file"""
raise NotImplementedError
toolkit_wrapper = RDKitToolkitWrapper()
filename = get_data_file_path('molecules/toluene.sdf')
molecule = Molecule.from_file(filename,
toolkit_registry=toolkit_wrapper)
assert len(molecule._conformers) == 1
assert molecule._conformers[0].shape == (15, 3)
def test_get_sdf_coordinates(self):
"""Test RDKitToolkitWrapper for importing a single set of coordinates from a sdf file"""
toolkit_wrapper = RDKitToolkitWrapper()
filename = get_data_file_path('molecules/toluene.sdf')
molecule = Molecule.from_file(filename,
toolkit_registry=toolkit_wrapper)
assert len(molecule._conformers) == 1
assert molecule._conformers[0].shape == (15, 3)
assert_almost_equal(molecule.conformers[0][5][1] / unit.angstrom,
2.0104,
decimal=4)
def test_get_mol2_charges(self):
"""Test OpenEyeToolkitWrapper for importing a mol2 file specifying partial charges"""
toolkit_wrapper = OpenEyeToolkitWrapper()
filename = get_data_file_path('molecules/toluene_charged.mol2')
molecule = Molecule.from_file(filename,
toolkit_registry=toolkit_wrapper)
assert len(molecule._conformers) == 1
assert molecule._conformers[0].shape == (15, 3)
target_charges = unit.Quantity(
np.array([
-0.1342, -0.1271, -0.1271, -0.1310, -0.1310, -0.0765, -0.0541,
0.1314, 0.1286, 0.1286, 0.1303, 0.1303, 0.0440, 0.0440, 0.0440
]), unit.elementary_charge)
for pc1, pc2 in zip(molecule._partial_charges, target_charges):
pc1_ul = pc1 / unit.elementary_charge
pc2_ul = pc2 / unit.elementary_charge
assert_almost_equal(pc1_ul, pc2_ul, decimal=4)
def test_get_mol2_coordinates(self):
"""Test OpenEyeToolkitWrapper for importing a single set of molecule coordinates"""
toolkit_wrapper = OpenEyeToolkitWrapper()
filename = get_data_file_path('molecules/toluene.mol2')
molecule1 = Molecule.from_file(filename,
toolkit_registry=toolkit_wrapper)
assert len(molecule1._conformers) == 1
assert molecule1._conformers[0].shape == (15, 3)
assert_almost_equal(molecule1.conformers[0][5][1] / unit.angstrom,
22.98,
decimal=2)
# Test loading from file-like object
with open(filename, 'r') as infile:
molecule2 = Molecule(infile,
file_format='MOL2',
toolkit_registry=toolkit_wrapper)
assert molecule1.is_isomorphic(molecule2)
assert len(molecule2._conformers) == 1
assert molecule2._conformers[0].shape == (15, 3)
assert_almost_equal(molecule2.conformers[0][5][1] / unit.angstrom,
22.98,
decimal=2)
# Test loading from gzipped mol2
import gzip
with gzip.GzipFile(filename + '.gz', 'r') as infile:
molecule3 = Molecule(infile,
file_format='MOL2',
toolkit_registry=toolkit_wrapper)
assert molecule1.is_isomorphic(molecule3)
assert len(molecule3._conformers) == 1
assert molecule3._conformers[0].shape == (15, 3)
assert_almost_equal(molecule3.conformers[0][5][1] / unit.angstrom,
22.98,
decimal=2)
