def add_hydrogen(self):
from openbabel import pybel as pb
mol_0d = pb.readstring("smi", "CCCC").OBMol
self.assertEqual(len(pb.Molecule(mol_0d).atoms), 2)
adaptor = BabelMolAdaptor(mol_0d)
adaptor.add_hydrogen()
self.assertEqual(len(adaptor.pymatgen_mol.sites), 14)
def addh(self, mol):
#if len(mol) < len(self.ref_mol):
from pymatgen.io.babel import BabelMolAdaptor
ad = BabelMolAdaptor(mol)
ad.add_hydrogen()
ad.localopt()
mol = ad.pymatgen_mol
return mol
def addh(self, molecules):
"""
add hydrogen
"""
from pymatgen.io.babel import BabelMolAdaptor
for mol in molecules:
ad = BabelMolAdaptor(mol)
ad.add_hydrogen()
ad.localopt()
mol = ad.pymatgen_mol
return molecules
def __init__(self, molecule, optimize=False):
"""
Instantiation method for FunctionalGroupExtractor.
:param molecule: Either a filename, a pymatgen.core.structure.Molecule
object, or a pymatgen.analysis.graphs.MoleculeGraph object.
:param optimize: Default False. If True, then the input molecule will be
modified, adding Hydrogens, performing a simple conformer search,
etc.
"""
self.molgraph = None
if isinstance(molecule, str):
try:
if optimize:
obmol = BabelMolAdaptor.from_file(molecule,
file_format="mol")
# OBMolecule does not contain pymatgen Molecule information
# So, we need to wrap the obmol in a BabelMolAdapter
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = Molecule.from_file(molecule)
except OSError:
raise ValueError("Input must be a valid molecule file, a "
"Molecule object, or a MoleculeGraph object.")
elif isinstance(molecule, Molecule):
if optimize:
obmol = BabelMolAdaptor(molecule)
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = molecule
elif isinstance(molecule, MoleculeGraph):
if optimize:
obmol = BabelMolAdaptor(molecule.molecule)
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = molecule.molecule
self.molgraph = molecule
else:
raise ValueError("Input to FunctionalGroupExtractor must be"
"str, Molecule, or MoleculeGraph.")
if self.molgraph is None:
self.molgraph = MoleculeGraph.with_local_env_strategy(
self.molecule,
OpenBabelNN(),
reorder=False,
extend_structure=False)
# Assign a specie and coordinates to each node in the graph,
# corresponding to the Site in the Molecule object
self.molgraph.set_node_attributes()
self.species = nx.get_node_attributes(self.molgraph.graph, "specie")
def __init__(self, molecule, optimize=False):
"""
Instantiation method for FunctionalGroupExtractor.
:param molecule: Either a filename, a pymatgen.core.structure.Molecule
object, or a pymatgen.analysis.graphs.MoleculeGraph object.
:param optimize: Default False. If True, then the input molecule will be
modified, adding Hydrogens, performing a simple conformer search,
etc.
"""
self.molgraph = None
if isinstance(molecule, str):
try:
if optimize:
obmol = BabelMolAdaptor.from_file(molecule,
file_format="mol")
# OBMolecule does not contain pymatgen Molecule information
# So, we need to wrap the obmol in a BabelMolAdapter
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = Molecule.from_file(molecule)
except OSError:
raise ValueError("Input must be a valid molecule file, a "
"Molecule object, or a MoleculeGraph object.")
elif isinstance(molecule, Molecule):
if optimize:
obmol = BabelMolAdaptor(molecule)
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = molecule
elif isinstance(molecule, MoleculeGraph):
if optimize:
obmol = BabelMolAdaptor(molecule.molecule)
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = molecule.molecule
self.molgraph = molecule
else:
raise ValueError("Input to FunctionalGroupExtractor must be"
"str, Molecule, or MoleculeGraph.")
if self.molgraph is None:
self.molgraph = MoleculeGraph.with_local_env_strategy(self.molecule,
OpenBabelNN(),
reorder=False,
extend_structure=False)
# Assign a specie and coordinates to each node in the graph,
# corresponding to the Site in the Molecule object
self.molgraph.set_node_attributes()
self.species = nx.get_node_attributes(self.molgraph.graph, "specie")
def add_hydrogen(self):
mol_0d = pb.readstring("smi", "CCCC").OBMol
self.assertEqual(len(pb.Molecule(mol_0d).atoms), 2)
adaptor = BabelMolAdaptor(mol_0d)
adaptor.add_hydrogen()
self.assertEqual(len(adaptor.pymatgen_mol.sites), 14)
