def test_map_order_geometry(permute, toolkit, toolkit_name):
"""Test map ordered geometry"""
hooh = {
'symbols': ['H', 'O', 'O', 'H'],
'geometry': [
1.84719633, 1.47046223, 0.80987166, 1.3126021, -0.13023157,
-0.0513322, -1.31320906, 0.13130216, -0.05020593, -1.83756335,
-1.48745318, 0.80161212
],
'name':
'HOOH',
'connectivity': [[0, 1, 1], [1, 2, 1], [2, 3, 1]],
}
mol = utils.load_molecule(hooh, toolkit=toolkit_name, permute_xyz=permute)
mapped_smiles = utils.mol_to_smiles(mol,
isomeric=True,
explicit_hydrogen=True,
mapped=True)
atom_map = utils.get_atom_map(mol, mapped_smiles)
symbols, geometry = toolkit.get_map_ordered_geometry(mol, atom_map)
json_geom = np.asarray(hooh['geometry']).reshape(int(len(geometry) / 3), 3)
geometry_array = np.asarray(geometry).reshape(int(len(geometry) / 3), 3)
for m in atom_map:
for i in range(3):
assert json_geom[atom_map[m]][i] == pytest.approx(
geometry_array[m - 1][i], 0.0000001)
if not permute:
assert hooh['geometry'] == pytest.approx(geometry, 0.0000001)
def test_atom_map(smiles):
"""Test that atom map orders geometry the same way every time no matter the SMILES used to create the molecule"""
import cmiles
mapped_smiles = '[H:5][C:1]([H:6])([C:2]([H:7])([H:8])[O:4][H:10])[O:3][H:9]'
mol_id_oe = cmiles.get_molecule_ids(mapped_smiles, toolkit='openeye')
oemol = utils.load_molecule(mapped_smiles, toolkit='openeye')
mapped_symbols = ['C', 'C', 'O', 'O', 'H', 'H', 'H', 'H', 'H', 'H']
mapped_geometry = [
-1.6887193912042044, 0.8515190939276903, 0.8344587822904272,
-4.05544806361675, -0.3658269566455062, -0.22848169646448416,
-1.6111611950422127, 0.4463128276938808, 3.490617694146934,
-3.97756355964586, -3.0080934853087373, 0.25948499322223956,
-1.6821252026076652, 2.891135395246369, 0.4936556190978574, 0.0, 0.0,
0.0, -4.180315034973438, -0.09210893239246959, -2.2748227320305525,
-5.740516456782416, 0.4115539217904015, 0.6823267491485907,
-0.07872657410528058, 1.2476492272884379, 4.101615944163073,
-5.514569080545831, -3.7195945404657222, -0.4441653010509862
]
mol = cmiles.utils.load_molecule(smiles, toolkit='openeye')
if not utils.has_explicit_hydrogen(mol):
mol = utils.add_explicit_hydrogen(mol)
atom_map = utils.get_atom_map(mol, mapped_smiles=mapped_smiles)
# use the atom map to add coordinates to molecule. First reorder mapped geometry to order in molecule
mapped_coords = np.array(mapped_geometry, dtype=float).reshape(
int(len(mapped_geometry) / 3), 3)
coords = np.zeros((mapped_coords.shape))
for m in atom_map:
coords[atom_map[m]] = mapped_coords[m - 1]
# flatten
coords = coords.flatten()
# convert to Angstroms
coords = coords * utils.BOHR_2_ANGSTROM
# set coordinates in oemol
mol.SetCoords(coords)
mol.SetDimension(3)
# Get new atom map
atom_map = utils.get_atom_map(mol, mapped_smiles)
symbols, geometry = _cmiles_oe.get_map_ordered_geometry(mol, atom_map)
assert geometry == mapped_geometry
assert symbols == mapped_symbols
def test_atom_map_order(self):
"""Test 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_from_tagged_smiles = chemi.smiles_to_oemol(tagged_smiles)
atom_map = get_atom_map(mol_from_tagged_smiles, tagged_smiles)
# Compare atom map to tag
for i in range(1, len(atom_map) + 1):
atom_1 = mol_from_tagged_smiles.GetAtom(
oechem.OEHasAtomIdx(atom_map[i]))
self.assertEqual(i, atom_1.GetMapIdx())
def test_connectivity(mapped_smiles, expected_table, toolkit):
"""Test connectivity table"""
molecule = utils.load_molecule(mapped_smiles, toolkit)
atom_map = utils.get_atom_map(molecule, mapped_smiles)
connectivity_table = utils.get_connectivity_table(molecule, atom_map)
for bond in connectivity_table:
xi = np.isin(expected_table, bond[:2])
match = np.where(np.array([i[:2].sum() for i in xi]) == 2)[0]
# assert that a match was found and only one was found
assert len(match) == 1
# assert that bond order is the same
assert expected_table[match][0][-1] == bond[-1]
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_permute_json(toolkit):
"""Test permute json xyz, symbols and connectivity to match mapped smiles"""
molecule_ids = {
'canonical_smiles': 'OO',
'canonical_isomeric_smiles': 'OO',
'canonical_isomeric_explicit_hydrogen_smiles': '[H]OO[H]',
'canonical_explicit_hydrogen_smiles': '[H]OO[H]',
'canonical_isomeric_explicit_hydrogen_mapped_smiles':
'[H:3][O:1][O:2][H:4]',
'unique_protomer_representation': 'OO',
'unique_tautomer_representation': 'OO',
'provenance': 'cmiles_v0.1.1+59.g0b7a12d.dirty_openeye_2018.Oct.b7',
'standard_inchi': 'InChI=1S/H2O2/c1-2/h1-2H',
'inchi_key': 'MHAJPDPJQMAIIY-UHFFFAOYSA-N',
'molecular_formula': 'H2O2'
}
hooh = {
'symbols': ['H', 'O', 'O', 'H'],
'geometry': [
1.84719633, 1.47046223, 0.80987166, 1.3126021, -0.13023157,
-0.0513322, -1.31320906, 0.13130216, -0.05020593, -1.83756335,
-1.48745318, 0.80161212
],
'name':
'HOOH',
'connectivity': [[0, 1, 1], [1, 2, 1], [2, 3, 1]],
'molecular_multiplicity':
1
}
mapped_smiles = molecule_ids[
'canonical_isomeric_explicit_hydrogen_mapped_smiles']
mol = utils.mol_from_json(hooh, toolkit=toolkit)
atom_map = utils.get_atom_map(mol, '[H:3][O:1][O:2][H:4]')
permuted_hooh = utils.permute_qcschema(hooh,
mapped_smiles,
toolkit=toolkit)
json_geom = np.asarray(hooh['geometry']).reshape(
int(len(hooh['geometry']) / 3), 3)
permuted_geom = np.asarray(permuted_hooh['geometry']).reshape(
int(len(hooh['geometry']) / 3), 3)
assert hooh['geometry'] != permuted_hooh['geometry']
for m in atom_map:
for i in range(3):
assert json_geom[atom_map[m]][i] == pytest.approx(
permuted_geom[m - 1][i], 0.0000001)
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_get_atom_map(toolkit, toolkit_name):
smiles = 'C[C@@H](c1c(ccc(c1Cl)F)Cl)OC'
mol = utils.load_molecule(smiles, toolkit_name)
if toolkit_name == 'openeye':
from openeye import oechem
oechem.OEAddExplicitHydrogens(mol)
for a in mol.GetAtoms():
a.SetMapIdx(a.GetIdx() + 1)
mapped_smiles = oechem.OEMolToSmiles(mol)
if toolkit_name == 'rdkit':
from rdkit import Chem
mol = Chem.AddHs(mol)
for a in mol.GetAtoms():
a.SetAtomMapNum(a.GetIdx() + 1)
mapped_smiles = Chem.MolToSmiles(mol)
atom_map = utils.get_atom_map(mol, mapped_smiles)
for m in atom_map:
assert m == (atom_map[m] + 1)
def generate_constraint_opt_input(qc_molecule, dihedrals, maximum_rotation=30, interval=5, filename=None):
"""
Parameters
----------
qc_molecule
dihedrals
Returns
-------
QCFractal optimization jobs input
"""
from openeye import oechem
optimization_jobs = {}
tagged_smiles = qc_molecule['identifiers']['canonical_isomeric_explicit_hydrogen_mapped_smiles']
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, tagged_smiles)
atom_map = get_atom_map(mol, tagged_smiles)
coords = chemi.from_mapped_xyz_to_mol_idx_order(qc_molecule['geometry'], atom_map)
# convert coord to Angstrom
coords = coords * utils.BOHR_2_ANGSTROM
conf = mol.GetConfs().next()
conf.SetCoords(oechem.OEFloatArray(coords))
# new molecule for setting dihedral angles
mol_2 = oechem.OEMol(mol)
conf_2 = mol_2.GetConfs().next()
coords_2 = oechem.OEFloatArray(conf_2.GetMaxAtomIdx()*3)
conf.GetCoords(coords_2)
mol_2.DeleteConfs()
interval = radians(interval)
max_rot = radians(maximum_rotation)
for dihedral in dihedrals:
#j = 0
dih_idx = dihedrals[dihedral]
tor = []
for i in dih_idx:
a = mol.GetAtom(oechem.OEHasMapIdx(i+1))
tor.append(a)
dih_angle = oechem.OEGetTorsion(conf, tor[0], tor[1], tor[2], tor[3])
for i, angle in enumerate(np.arange(dih_angle-max_rot, dih_angle+max_rot, interval)):
newconf = mol.NewConf(coords_2)
oechem.OESetTorsion(newconf, tor[0], tor[1], tor[2], tor[3], angle)
#new_angle = oechem.OEGetTorsion(newconf, tor[0], tor[1], tor[2], tor[3])
# if new_angle == dih_angle:
# j += 1
# if j > 1:
# # One equivalent angle should be generated.
# logger().warning("Openeye did not generate a new conformer for torsion and angle {} {}. Will not generate"
# "qcfractal optimizaiton input".format(dih_idx, angle))
# break
if filename:
pdb = oechem.oemolostream("{}_{}.pdb".format(filename, i))
oechem.OEWritePDBFile(pdb, newconf)
symbols, geometry = chemi.to_mapped_geometry(newconf, atom_map)
qc_molecule = copy.deepcopy(qc_molecule)
qc_molecule['geometry'] = geometry
qc_molecule['symbols'] = symbols
degree = degrees(angle)
optimization_jobs['{}_{}'.format(dih_idx, int(round(degree)))] = {
'type': 'optimization_input',
'initial_molecule': qc_molecule,
'dihedral': dih_idx,
'constraints': {
"set": [{
"type": "dihedral",
"indices": dih_idx,
"value": degree
}]
}
}
return optimization_jobs
