def replace(self, probe_smiles: str, probe_resn: str,
probe_name: str) -> str:
"""
The target probe needs a un-taken PDB 3 letter residue name if the flag ``load_PDB_components`` is left.
Else the PDB component library version will win!
:param probe_smiles: Valid Smiles, protons optional.
:param probe_resn: untaken 3 letter residue name
:param probe_name: file friend!
:return:
"""
probe = self.make_probe(probe_smiles)
cid = self.align_probe_to_target(probe)
aligned_file = f'{probe_name}.aligned.mol'
#Chem.MolToMolFile(probe, aligned_file, confId=cid)
writer = rdmolfiles.SDWriter(aligned_file)
writer.write(probe, confId=cid)
for i in range(probe.GetNumConformers()):
if i == cid:
continue
writer.write(probe, confId=i)
writer.close()
molfile_to_params.run(aligned_file,
conformers_in_one_file=True,
name=probe_resn,
amino_acid=None,
chain='X',
pdb=probe_name,
clobber=True)
pdbblocks = self.combine(probe_name, probe_resn)
return pdbblocks.all
def save_confs(self, out, file) -> True:
# Chem.MolToMolFile(out,'test.mol')
writer = rdmolfiles.SDWriter(file)
writer.SetKekulize(False)
for i in range(out.GetNumConformers()):
writer.write(out, confId=i)
writer.close()
return True
def sdf_file(test_mols):
# Create directory for test file(s)
tmp_dir = maybe_create_dir('data/tmp/')
fname = os.path.join(tmp_dir, 'test.sdf')
# Store molecules
writer = rdmolfiles.SDWriter(fname)
for mol in test_mols:
writer.write(mol)
writer.close()
return fname
def write_probe(self, cid):
aligned_file = f'{self.work_path}/{self.name}/{self.name}.aligned.mol'
# Chem.MolToMolFile(probe, aligned_file, confId=cid)
writer = rdmolfiles.SDWriter(aligned_file)
writer.SetKekulize(False)
writer.write(self.dethio_mol, confId=cid)
for i in range(self.dethio_mol.GetNumConformers()):
if i == cid:
continue
writer.write(self.dethio_mol, confId=i)
writer.close()
return aligned_file
def save_output(output_list, file_name):
"""
Write the output to an SD file
:param output_list: list of pairs
:param file_name: output file name
:return: None
"""
writer = rdmolfiles.SDWriter(file_name)
for mol, name, val in output_list:
mol.SetProp("_Name", name)
mol.SetProp("Value", str(val))
writer.write(mol)
mols = {cid: Chem.MolFromSmiles(smi) for cid, smi in smiles.items()}
print("Computing 3D coordinates...")
s = SaltRemover.SaltRemover()
for i, (cid, mol) in enumerate(mols.items()):
if i > 0 and i % 100 == 0:
print("Finished %d" % i)
try:
mol.SetProp("_Name","%d: %s" % (cid, smiles[cid]))
mol = s.StripMol(mol,dontRemoveEverything=True)
mol = Chem.AddHs(mol)
AllChem.Compute2DCoords(mol)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol) # Is this deterministic?
except Exception as e:
print('Exception for %d' % cid)
mols[cid] = None
else:
mols[cid] = mol
mols = {cid: mol for cid, mol in mols.items() if mol}
writer = rdmolfiles.SDWriter('data/cids-smiles.sdf')
for smile, mol in mols.items():
writer.write(mol)
writer.close()
suppl = rdmolfiles.SDMolSupplier('data/cids-smiles.sdf')
for mol in suppl:
print(mol.GetNumAtoms())