def _initializeMolObj(self, mol, force_reading, ignore_errors):
"""
Read the input and tries to convert it into a rdkit.Chem.rdchem.Mol obj
Parameters
----------
mol: str or rdkit.Chem.rdchem.Mol or moleculekit.smallmol.smallmol.SmallMol
i) rdkit.Chem.rdchem.Mol ii) The path to the pdb/mol2 to load iii) The smile string iv) SmallMol object
v) moleculekit.molecule.nolecule.Molecule
force_reading: bool
If the mol provided is not accepted, the molecule will be initially converted into sdf
Returns
-------
_mol: rdkit.Chem.Molecule object
The rdkit molecule
smallMol: moleculekit.smallmol.smallmol.SmallMol
The smallMol object if SmallMol was passed
"""
from moleculekit.molecule import Molecule
_mol = None
if isinstance(mol, Chem.Mol):
_mol = mol
elif isinstance(mol, Molecule):
_mol = self._fromMolecule(mol)
elif isinstance(mol, str):
if os.path.isfile(mol):
name_suffix = os.path.splitext(mol)[-1]
# load mol2 file
if name_suffix == ".mol2":
_mol = Chem.MolFromMol2File(mol, removeHs=False)
# load pdb file
elif name_suffix == ".pdb":
_mol = Chem.MolFromPDBFile(mol, removeHs=False)
# if the file failed to be loaded and 'force_reading' = True, file convert to sdf and than loaded
if _mol is None and force_reading:
logger.warning(
'Reading {} with force_reading procedure'.format(mol))
sdf = openbabelConvert(mol, name_suffix, 'sdf')
_mol = Chem.SDMolSupplier(sdf, removeHs=False)[0]
os.remove(sdf)
# assuming is a smile
# TODO validate it. Implement smarts recognition
else:
# try with smiles
psmile = Chem.SmilesParserParams()
psmile.removeHs = False
_mol = Chem.MolFromSmiles(mol, psmile)
if _mol is None and not ignore_errors:
if isinstance(mol, str):
frerr = ' Try by setting the force_reading option as True.' if not force_reading else ''
raise ValueError('Failed to read file {}.{}'.format(
mol, frerr))
if isinstance(mol, Molecule):
raise ValueError('Failed convering Molecule to SmallMol')
return _mol
def _initializeMolObj(self, mol, force_reading, ignore_errors, verbose=True):
"""
Read the input and tries to convert it into a rdkit.Chem.rdchem.Mol obj
Parameters
----------
mol: str or rdkit.Chem.rdchem.Mol or moleculekit.smallmol.smallmol.SmallMol
i) rdkit.Chem.rdchem.Mol ii) The path to the pdb/mol2 to load iii) The smile string iv) SmallMol object
v) moleculekit.molecule.nolecule.Molecule
force_reading: bool
If the mol provided is not accepted, the molecule will be initially converted into sdf
Returns
-------
_mol: rdkit.Chem.Molecule object
The rdkit molecule
smallMol: moleculekit.smallmol.smallmol.SmallMol
The smallMol object if SmallMol was passed
"""
from moleculekit.molecule import Molecule
message = None
# If we are converting a Molecule object to a SmallMol object
remove = False
natoms = None
if isinstance(mol, Molecule):
natoms = mol.numAtoms
mol = self._fromMolecule(mol) # Returns a temp filename
remove = True
_mol = None
if isinstance(mol, Chem.Mol):
_mol = mol
elif isinstance(mol, str):
if os.path.isfile(mol):
name_suffix = os.path.splitext(mol)[-1]
# load mol2 file
if name_suffix == ".mol2":
_mol = Chem.MolFromMol2File(mol, removeHs=False)
# load pdb file
elif name_suffix == ".pdb":
_mol = Chem.MolFromPDBFile(mol, removeHs=False)
# load single-molecule sdf file
elif name_suffix == ".sdf":
sms = Chem.SDMolSupplier(mol, removeHs=False)
if len(sms) != 1:
logger.warning(f"More than one molecules found in {mol}. SmallMol will only read the first. If you want to read them all use the SmallMolLib class.")
_mol = sms[0]
# if the file failed to be loaded and 'force_reading' = True, file convert to sdf and than loaded
if _mol is None and force_reading:
logger.warning('Reading {} with force_reading procedure'.format(mol))
sdf = openbabelConvert(mol, name_suffix, 'sdf')
_mol = Chem.SDMolSupplier(sdf, removeHs=False)[0]
os.remove(sdf)
else:
# assuming it is a smile
psmile = Chem.SmilesParserParams()
psmile.removeHs = False
_mol = Chem.MolFromSmiles(mol, psmile)
if remove: # Remove temp file
os.remove(mol)
if _mol is None and not ignore_errors:
if isinstance(mol, str):
frerr = ' Try by setting the force_reading option as True.' if not force_reading else ''
raise ValueError(f'Failed to read file {mol}.{frerr}')
elif isinstance(mol, Molecule):
raise ValueError('Failed converting Molecule to SmallMol')
else:
raise RuntimeError(f"Failed reading molecule {mol}.")
if natoms is not None and natoms != _mol.GetNumAtoms():
raise RuntimeError("Number of atoms changed while converting to rdkit molecule")
return _mol
def _initializeMolObj(self,
mol,
force_reading,
ignore_errors,
verbose=True):
"""
Read the input and tries to convert it into a rdkit.Chem.rdchem.Mol obj
Parameters
----------
mol: str or rdkit.Chem.rdchem.Mol or moleculekit.smallmol.smallmol.SmallMol
i) rdkit.Chem.rdchem.Mol ii) The path to the pdb/mol2 to load iii) The smile string iv) SmallMol object
v) moleculekit.molecule.nolecule.Molecule
force_reading: bool
If the mol provided is not accepted, the molecule will be initially converted into sdf
Returns
-------
_mol: rdkit.Chem.Molecule object
The rdkit molecule
smallMol: moleculekit.smallmol.smallmol.SmallMol
The smallMol object if SmallMol was passed
"""
from moleculekit.molecule import Molecule
message = None
# If we are converting a Molecule object to a SmallMol object
remove = False
natoms = None
if isinstance(mol, Molecule):
natoms = mol.numAtoms
mol = self._fromMolecule(mol) # Returns a temp filename
remove = True
_mol = None
if isinstance(mol, Chem.Mol):
_mol = mol
elif isinstance(mol, str):
if os.path.isfile(mol):
name_suffix = os.path.splitext(mol)[-1]
with tempfile.TemporaryFile(mode='w+') as stderr:
# Redirect stderr to a file
temp_fileno = os.dup(sys.stderr.fileno())
os.dup2(stderr.fileno(),
sys.stderr.fileno()) # Change process stderr
sys.stderr = stderr # Change Python stderr
# load mol2 file
if name_suffix == ".mol2":
_mol = Chem.MolFromMol2File(mol, removeHs=False)
# load pdb file
elif name_suffix == ".pdb":
_mol = Chem.MolFromPDBFile(mol, removeHs=False)
# if the file failed to be loaded and 'force_reading' = True, file convert to sdf and than loaded
if _mol is None and force_reading:
logger.warning(
'Reading {} with force_reading procedure'.format(
mol))
sdf = openbabelConvert(mol, name_suffix, 'sdf')
_mol = Chem.SDMolSupplier(sdf, removeHs=False)[0]
os.remove(sdf)
# Reset stderr
os.dup2(temp_fileno, sys.__stderr__.fileno())
os.close(temp_fileno)
sys.stderr = sys.__stderr__
# Read RDKit warnings
stderr.flush()
stderr.seek(0)
message = stderr.read()
if verbose:
logger.warning(message)
else:
# assuming it is a smile
psmile = Chem.SmilesParserParams()
psmile.removeHs = False
_mol = Chem.MolFromSmiles(mol, psmile)
if remove: # Remove temp file
os.remove(mol)
if _mol is None and not ignore_errors:
if message is not None and not verbose:
# Print it anyway if there was an error
logger.warning(message)
if isinstance(mol, str):
frerr = ' Try by setting the force_reading option as True.' if not force_reading else ''
raise ValueError(f'Failed to read file {mol}.{frerr}')
elif isinstance(mol, Molecule):
raise ValueError('Failed converting Molecule to SmallMol')
else:
raise RuntimeError(f"Failed reading molecule {mol}.")
if natoms is not None and natoms != _mol.GetNumAtoms():
raise RuntimeError(
"Number of atoms changed while converting to rdkit molecule")
return _mol