def cdfMol_pdb(pdb, output, name):
initial_time = time.time()
cdf_mol = Chem.BasicMolecule()
pdb_mol = Chem.BasicMolecule()
pdb_str = open(pdb, 'r').read().replace('WAT', 'HOH').replace('HIE', 'HIS')
pdb_reader = Biomol.PDBMoleculeReader(Base.StringIOStream(pdb_str))
Biomol.setPDBApplyDictAtomBondingToNonStdResiduesParameter(
pdb_reader, True)
if not pdb_reader.read(pdb_mol):
return None
Chem.calcImplicitHydrogenCounts(pdb_mol, False)
Chem.perceiveHybridizationStates(pdb_mol, False)
Chem.setAtomSymbolsFromTypes(pdb_mol, False)
Chem.perceiveSSSR(pdb_mol, False)
Chem.setRingFlags(pdb_mol, False)
Chem.setAromaticityFlags(pdb_mol, False)
cdf_mol.assign(pdb_mol)
for atom in cdf_mol.atoms:
Chem.set3DCoordinatesArray(atom, Math.Vector3DArray())
i = 0
while i < cdf_mol.numAtoms:
Chem.get3DCoordinatesArray(cdf_mol.getAtom(i)).addElement(
Chem.get3DCoordinates(pdb_mol.getAtom(i)))
i += 1
tmp_output = output + name + ".cdf"
try:
Chem.FileCDFMolecularGraphWriter(tmp_output).write(cdf_mol)
except:
print('> Cdf_mol writing failure.')
raise
residues = Biomol.ResidueList(cdf_mol)
tmp_output = output + name + "_residue_info.txt"
with open(tmp_output, 'w') as txt_writer:
txt_writer.write('residue name_resid_chain\n')
for res in residues:
res_id = getResidueID(res)
txt_writer.write('{}: \n'.format(res_id))
calc_time = time.time() - initial_time
print('> Cdf and amino acid residue number list files generated in {}s'.
format(int(calc_time)))
def mol_to_smiles(mol,
kekulized=False,
canonical=True,
atom_stereo=True,
hydrogen_deplete=True,
bond_stereo=False):
stream = Base.StringIOStream()
w = Chem.SMILESMolecularGraphWriter(stream)
Chem.setSMILESWriteKekuleFormParameter(w, kekulized)
Chem.setSMILESWriteCanonicalFormParameter(w, canonical)
Chem.setSMILESRecordFormatParameter(w, 'S')
Chem.setSMILESWriteAtomStereoParameter(w, atom_stereo)
Chem.setSMILESWriteBondStereoParameter(w, bond_stereo)
Chem.setSMILESNoOrganicSubsetParameter(w, False)
Chem.setOrdinaryHydrogenDepleteParameter(w, hydrogen_deplete)
Chem.calcImplicitHydrogenCounts(mol, True)
w.write(mol)
w.close()
return stream.value
def mol_from_smiles(smiles: str) -> Chem.BasicMolecule:
ifs = Base.StringIOStream(smiles)
mol = Chem.BasicMolecule()
r = Chem.SMILESMoleculeReader(ifs)
r.read(mol)
return sanitize_mol(mol)
def readPDBFromString(string: str) -> Chem.BasicMolecule:
s = Base.StringIOStream(string)
protein = readPDBFromStream(s)
return protein