def confab_conformers(self, forcefield="mmff94", freeze_atoms=None,
rmsd_cutoff=0.5, energy_cutoff=50.0,
conf_cutoff=100000, verbose=False):
"""
Conformer generation based on Confab to generate all diverse low-energy
conformers for molecules. This is different from rotor_conformer or
gen3d_conformer as it aims to not simply to find a low energy
conformation but to generate several different conformations.
Args:
forcefield (str): Default is mmff94. Options are 'gaff', 'ghemical',
'mmff94', 'mmff94s', and 'uff'.
freeze_atoms ([int]): index of atoms to be freezed when performing
conformer search, default is None.
rmsd_cutoff (float): rmsd_cufoff, default is 0.5 Angstrom.
energy_cutoff (float): energy_cutoff, default is 50.0 kcal/mol.
conf_cutoff (float): max number of conformers to test,
default is 1 million.
verbose (bool): whether to display information on torsions found,
default is False.
Returns:
(list): list of pymatgen Molecule objects for generated conformers.
"""
if self._obmol.GetDimension() != 3:
self.make3d()
else:
self.add_hydrogen()
ff = ob.OBForceField_FindType(forcefield)
if ff == 0:
print("Could not find forcefield {} in openbabel, the forcefield "
"will be reset as default 'mmff94'".format(forcefield))
ff = ob.OBForceField_FindType("mmff94")
if freeze_atoms:
print('{} atoms will be freezed'.format(len(freeze_atoms)))
constraints = ob.OBFFConstraints()
for atom in ob.OBMolAtomIter(self._obmol):
atom_id = atom.GetIndex() + 1
if id in freeze_atoms:
constraints.AddAtomConstraint(atom_id)
ff.SetConstraints(constraints)
# Confab conformer generation
ff.DiverseConfGen(rmsd_cutoff, conf_cutoff, energy_cutoff,
verbose)
ff.GetConformers(self._obmol)
# Number of conformers generated by Confab conformer generation
conformer_num = self._obmol.NumConformers()
conformers = []
for i in range(conformer_num):
self._obmol.SetConformer(i)
conformer = copy.deepcopy(BabelMolAdaptor(self._obmol).pymatgen_mol)
conformers.append(conformer)
self._obmol.SetConformer(0)
return conformers
def rotor_conformer(self,
*rotor_args,
algo="WeightedRotorSearch",
forcefield="mmff94"):
"""
Conformer search based on several Rotor Search algorithms of openbabel.
If the input molecule is not 3D, make3d will be called (generate 3D
structure, add hydrogen, a quick localopt). All hydrogen atoms need
to be made explicit.
Args:
rotor_args: pass args to Rotor Search in openbabel.
for "WeightedRotorSearch": (conformers, geomSteps,
sampleRingBonds-default False)
for "SystematicRotorSearch": (geomSteps-default 2500,
sampleRingBonds-default False)
for "RandomRotorSearch": (conformers, geomSteps-default 2500,
sampleRingBonds-default False)
algo (str): Default is "WeightedRotorSearch". Options are
"SystematicRotorSearch", "RandomRotorSearch", and
"WeightedRotorSearch".
forcefield (str): Default is mmff94. Options are 'gaff', 'ghemical',
'mmff94', 'mmff94s', and 'uff'.
"""
if self._obmol.GetDimension() != 3:
self.make3d()
else:
self.add_hydrogen()
ff = ob.OBForceField_FindType(forcefield)
if ff == 0:
warnings.warn("This input forcefield {} is not supported "
"in openbabel. The forcefield will be reset as "
"default 'mmff94' for now.".format(forcefield))
ff = ob.OBForceField_FindType("mmff94")
try:
rotor_search = getattr(ff, algo)
except AttributeError:
warnings.warn("This input conformer search algorithm {} is not "
"supported in openbabel. Options are "
"'SystematicRotorSearch', 'RandomRotorSearch' "
"and 'WeightedRotorSearch'. "
"The algorithm will be reset as default "
"'WeightedRotorSearch' for now.".format(algo))
rotor_search = ff.WeightedRotorSearch
rotor_search(*rotor_args)
ff.GetConformers(self._obmol)
def run_confab(mol,
rmsd_cutoff=0.5,
conf_cutoff=100000,
energy_cutoff=50.0,
confab_verbose=False):
"""
Generate ensemble of conformers to perform calculations on
:param mol: initial molecule to generate conformers from
:param rmsd_cutoff: similarity threshold for conformers, default: 0.5
:param conf_cutoff: max number of conformers to generate, default: 100,000
:param energy_cutoff: max relative energy between conformers, default: 50
:param confab_verbose: whether confab should report on rotors
:type mol: openbabel.OBMol
:type rmsd_cutoff: float
:type conf_cutoff: int
:type energy_cutoff: float
:type confab_verbose: bool
:return: list of conformers for a given molecule
:rtype: openbabel.OBMol
"""
pff = ob.OBForceField_FindType("mmff94")
pff.Setup(mol)
pff.DiverseConfGen(rmsd_cutoff, conf_cutoff, energy_cutoff, confab_verbose)
pff.GetConformers(mol)
return mol
