# Filter out receptor atoms with atom names of UNK
for atom in receptor.GetAtoms():
if atom.GetName() == 'UNK':
receptor.DeleteAtom(atom)
# Write joined PDB with ligand and receptor
output_filename = os.path.join(docking_basedir, f'{molecule.GetTitle()} - complex.pdb')
if not os.path.exists(output_filename):
with oechem.oemolostream(output_filename) as ofs:
oechem.OEClearResidues(docked_molecule)
#oechem.OEWriteMolecule(ofs, docked_molecule)
oechem.OETriposAtomNames(docked_molecule)
oechem.OEWritePDBFile(ofs, docked_molecule, oechem.OEOFlavor_PDB_Default | oechem.OEOFlavor_PDB_BONDS)
set_serial(receptor, 'X', docked_molecule.NumAtoms()+1)
#oechem.OEWritePDBFile(ofs, receptor, oechem.OEOFlavor_PDB_Default | oechem.OEOFlavor_PDB_BONDS)
oechem.OEWriteMolecule(ofs, receptor)
# Write PDB of just ligand
output_filename = os.path.join(docking_basedir, f'{molecule.GetTitle()} - ligand.pdb')
if not os.path.exists(output_filename):
with oechem.oemolostream(output_filename) as ofs:
oechem.OEClearResidues(docked_molecule)
#oechem.OEWriteMolecule(ofs, docked_molecule)
oechem.OETriposAtomNames(docked_molecule)
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
def generate_torsions(inp_mol,
output_path,
interval,
base_name=None,
tar=True):
"""
This function takes a 3D molecule (pdf, mol2 or sd file) and generates structures for a torsion drive on all torsions
in the molecule. This function uses OpenEye
Parameters
----------
mol : OEMol
molecule to generate 1D torsion scans
output_path: str
path to output file directory
interval: int
angle (in degrees) of interval for torsion drive
base_name: str
base name for file. Default is None. If default, use title in OEMol for base name
tar: bool
If true, will compress output
"""
if not base_name:
base_name = inp_mol.GetTitle()
mid_tors = [[tor.a, tor.b, tor.c, tor.d]
for tor in oechem.OEGetTorsions(inp_mol)]
# This smarts should match terminal torsions such as -CH3, -NH2, -NH3+, -OH, and -SH
smarts = '[*]~[*]-[X2H1,X3H2,X4H3]-[#1]'
qmol = oechem.OEQMol()
if not oechem.OEParseSmarts(qmol, smarts):
warnings.warn('OEParseSmarts failed')
ss = oechem.OESubSearch(qmol)
mol = oechem.OEMol(inp_mol)
h_tors = []
oechem.OEPrepareSearch(mol, ss)
unique = True
for match in ss.Match(mol, unique):
tor = []
for ma in match.GetAtoms():
tor.append(ma.target)
h_tors.append(tor)
# Combine middle and terminal torsions
all_tors = mid_tors + h_tors
# Sort all_tors so that it's grouped by central bond
central_bonds = np.zeros((len(all_tors), 3), dtype=int)
for i, tor in enumerate(all_tors):
central_bonds[i][0] = i
central_bonds[i][1] = tor[1].GetIdx()
central_bonds[i][2] = tor[2].GetIdx()
grouped = central_bonds[central_bonds[:, 2].argsort()]
sorted_tors = [all_tors[i] for i in grouped[:, 0]]
# Keep only one torsion per rotatable bond
tors = []
best_tor = [
sorted_tors[0][0], sorted_tors[0][0], sorted_tors[0][0],
sorted_tors[0][0]
]
first_pass = True
for tor in sorted_tors:
logger().info("Idxs: {} {} {} {}".format(tor[0].GetIdx(),
tor[1].GetIdx(),
tor[2].GetIdx(),
tor[3].GetIdx()))
logger().info("Atom Numbers: {} {} {} {}".format(
tor[0].GetAtomicNum(), tor[1].GetAtomicNum(),
tor[2].GetAtomicNum(), tor[3].GetAtomicNum()))
if tor[1].GetIdx() != best_tor[1].GetIdx() or tor[2].GetIdx(
) != best_tor[2].GetIdx():
new_tor = True
if not first_pass:
logger().info("Adding to list: {} {} {} {}".format(
best_tor[0].GetIdx(), best_tor[1].GetIdx(),
best_tor[2].GetIdx(), best_tor[3].GetIdx()))
tors.append(best_tor)
first_pass = False
best_tor = tor
best_tor_order = tor[0].GetAtomicNum() + tor[3].GetAtomicNum()
logger().info(
"new_tor with central bond across atoms: {} {}".format(
tor[1].GetIdx(), tor[2].GetIdx()))
else:
logger().info("Not a new_tor but now with end atoms: {} {}".format(
tor[0].GetIdx(), tor[3].GetIdx()))
tor_order = tor[0].GetAtomicNum() + tor[3].GetAtomicNum()
if tor_order > best_tor_order:
best_tor = tor
best_tor_order = tor_order
logger().info("Adding to list: {} {} {} {}".format(best_tor[0].GetIdx(),
best_tor[1].GetIdx(),
best_tor[2].GetIdx(),
best_tor[3].GetIdx()))
tors.append(best_tor)
logger().info("List of torsion to drive:")
for tor in tors:
logger().info("Idx: {} {} {} {}".format(tor[0].GetIdx(),
tor[1].GetIdx(),
tor[2].GetIdx(),
tor[3].GetIdx()))
logger().info("Atom numbers: {} {} {} {}".format(
tor[0].GetAtomicNum(), tor[1].GetAtomicNum(),
tor[2].GetAtomicNum(), tor[3].GetAtomicNum()))
conf = mol.GetConfs().next()
coords = oechem.OEFloatArray(conf.GetMaxAtomIdx() * 3)
conf.GetCoords(coords)
# Check if coordinates are not zero
values = np.asarray(
[coords.__getitem__(i) == 0 for i in range(coords.__len__())])
if values.all():
# Generate new coordinates.
mol2 = generate_conformers(mol, max_confs=1)
conf = mol2.GetConfs().next()
coords = oechem.OEFloatArray(conf.GetMaxAtomIdx() * 3)
conf.GetCoords(coords)
mol2.DeleteConfs()
mol.DeleteConfs()
for tor in tors:
tor_name = str((tor[0].GetIdx()) + 1) + '_' + str(
(tor[1].GetIdx()) + 1) + '_' + str(
(tor[2].GetIdx()) + 1) + '_' + str((tor[3].GetIdx()) + 1)
folder = os.path.join(output_path, tor_name)
try:
os.makedirs(folder)
except FileExistsError:
logger().info("Overwriting existing directory {}".format(tor_name))
for angle in range(0, 360, interval):
angle_folder = os.path.join(folder, str(angle))
try:
os.mkdir(angle_folder)
except FileExistsError:
logger().info(
"Overwriting existing directory {}".format(tor_name))
newconf = mol.NewConf(coords)
oechem.OESetTorsion(newconf, tor[0], tor[1], tor[2], tor[3],
radians(angle))
pdb = oechem.oemolostream('{}/{}_{}_{}.pdb'.format(
angle_folder, base_name, tor_name, angle))
oechem.OEWritePDBFile(pdb, newconf)
if tar:
# tar archive output
out = tarfile.open('{}.tar.gz'.format(output_path), mode='w:gz')
os.chdir(output_path)
os.chdir('../')
out.add('{}'.format(base_name))
out.close()