def convert_obatoms_to_molecule(self,
atoms,
residue_name=None,
site_property="ff_map"):
"""
Convert list of openbabel atoms to MOlecule.
Args:
atoms ([OBAtom]): list of OBAtom objects
residue_name (str): the key in self.map_residue_to_mol. Usec to
restore the site properties in the final packed molecule.
site_property (str): the site property to be restored.
Returns:
Molecule object
"""
restore_site_props = True if residue_name is not None else False
if restore_site_props and not hasattr(self, "map_residue_to_mol"):
self._set_residue_map()
coords = []
zs = []
for atm in atoms:
coords.append(list(atm.coords))
zs.append(atm.atomicnum)
mol = Molecule(zs, coords)
if restore_site_props:
props = []
ref = self.map_residue_to_mol[residue_name].copy()
# sanity check
assert len(mol) == len(ref)
assert ref.formula == mol.formula
# the packed molecules have the atoms in the same order..sigh!
for i, site in enumerate(mol):
assert site.specie.symbol == ref[i].specie.symbol
props.append(getattr(ref[i], site_property))
mol.add_site_property(site_property, props)
return mol
def convert_obatoms_to_molecule(self, atoms, residue_name=None, site_property="ff_map"):
"""
Convert list of openbabel atoms to MOlecule.
Args:
atoms ([OBAtom]): list of OBAtom objects
residue_name (str): the key in self.map_residue_to_mol. Usec to
restore the site properties in the final packed molecule.
site_property (str): the site property to be restored.
Returns:
Molecule object
"""
restore_site_props = True if residue_name is not None else False
if restore_site_props and not hasattr(self, "map_residue_to_mol"):
self._set_residue_map()
coords = []
zs = []
for atm in atoms:
coords.append(list(atm.coords))
zs.append(atm.atomicnum)
mol = Molecule(zs, coords)
if restore_site_props:
props = []
ref = self.map_residue_to_mol[residue_name].copy()
# sanity check
assert len(mol) == len(ref)
assert ref.formula == mol.formula
# the packed molecules have the atoms in the same order..sigh!
for i, site in enumerate(mol):
assert site.specie.symbol == ref[i].specie.symbol
props.append(getattr(ref[i], site_property))
mol.add_site_property(site_property, props)
return mol
