def runAntechamber(force_field, file, output_ext="mol2", charge=None):
"""
A wrapper around antechamber.
Parameters
----------
force_field : str
Which force field to use. Only "gaff" and "gaff2" are accepted.
file : str
Name of input file.
output_ext : str
Output extension.
charge : int
The net charge of the molecule. Default: automatic detection by antechamber.
Returns
-------
output_name : str
Absolute path of the output parametrised file.
"""
input_base, input_ext = _os.path.splitext(file)[0], file.split(".")[-1]
if input_ext.lower() in ["mol", "sdf"]:
_babel.babelTransform(file, output_extension="mol2", pH=None)
input_ext = "mol2"
output_name = "%s_antechamber.%s" % (input_base, output_ext)
commandstr = "antechamber -i '%s' -fi %s -o '%s' -fo %s -c bcc -at %s -s 2" % (
file, input_ext, output_name, output_ext, force_field)
if charge is not None:
commandstr += " -nc {}".format(charge)
_runexternal.runExternal(commandstr, procname="antechamber")
return _os.path.abspath(output_name)
def protonate(self,
reprotonate=False,
babel_parameters=None,
rdkit_parameters=None):
"""
Protonates the ligand using OpenBabel.
Parameters
----------
reprotonate : bool
Whether to reprotonate an already protonated ligand.
babel_parameters : dict
Keyword arguments to be passed to ProtoCaller.Wrappers.babelwrapper
rdkit_parameters : dict
Keyword arguments to be passed to ProtoCaller.Wrappers.rdkitwrapper
"""
with self.workdir:
if babel_parameters is None: babel_parameters = {}
babel_parameters = {"pH": 7.0, **babel_parameters}
if rdkit_parameters is None: rdkit_parameters = {}
if self.protonated and not reprotonate:
_logging.info("Ligand %s is already protonated." % self.name)
else:
filename_temp = _rdkit.saveFromRdkit(self.molecule,
filename="%s.mol" %
self.name)
# here we use PDB because of parser differences between OpenBabel and RDKit concerning mol and mol2 files
self.protonated_filename = _babel.babelTransform(
filename_temp, "pdb", **babel_parameters)
_os.remove(filename_temp)
self.molecule = _rdkit.openFileAsRdkit(
self.protonated_filename,
removeHs=False,
**rdkit_parameters)
def parametrise(self,
params=None,
molecule_type="ligand",
id=None,
reparametrise=False):
"""
Parametrises the ligand using ProtoCaller.Parametrise.
Parameters
----------
params : ProtoCaller.Parametrise.Params
Force field parameters.
molecule_type : str
The type of the molecule. One of: "ligand" and "cofactor".
id : str
The name of the molecule. Default: equal to the ligand name.
reparametrise : bool
Whether to reparametrise an already parametrised ligand.
"""
with self.workdir:
if self._parametrised and not reparametrise:
_logging.debug("Ligand %s is already parametrised." %
self.name)
return
_logging.info("Parametrising ligand %s..." % self.name)
if not self.protonated:
_logging.warning(
"Cannot parametrise unprotonated ligand. Protonating first with default parameters..."
)
self.protonate()
if params is None:
params = _parametrise.Params()
# we convert the protonated file into a pdb so that antechamber can read it
filename = _babel.babelTransform(self.protonated_filename, "pdb")
if id is None: id = self.name
charge = _rdmolops.GetFormalCharge(self.molecule)
self.parametrised_files = _parametrise.parametriseFile(
params=params,
filename=filename,
molecule_type=molecule_type,
id=id,
charge=charge)