Source code for BioSimSpace.Parameters._utils
######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2024
#
# Authors: Lester Hedges <lester.hedges@gmail.com>
#
# BioSimSpace is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# BioSimSpace is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with BioSimSpace. If not, see <http://www.gnu.org/licenses/>.
#####################################################################
"""Utility functions."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["formalCharge"]
import tempfile as _tempfile
from .. import _is_notebook
from .. import IO as _IO
from .. import _Utils
from ..Units.Charge import electron_charge as _electron_charge
from .._SireWrappers import Molecule as _Molecule
[docs]
def formalCharge(molecule):
"""
Compute the formal charge on a molecule. This function requires that
the molecule has explicit hydrogen atoms.
Parameters
----------
molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
A molecule object.
Returns
-------
formal_charge : :class:`Charge <BioSimSpace.Types.Charge>`
The total formal charge on the molecule.
"""
if not isinstance(molecule, _Molecule):
raise TypeError(
"'molecule' must be of type 'BioSimSpace._SireWrappers.Molecule'"
)
from rdkit import Chem as _Chem
from rdkit import RDLogger as _RDLogger
# Disable RDKit warnings.
_RDLogger.DisableLog("rdApp.*")
# Create a temporary working directory.
tmp_dir = _tempfile.TemporaryDirectory()
work_dir = tmp_dir.name
# Zero the total formal charge.
formal_charge = 0
# Run in the working directory.
with _Utils.cd(work_dir):
# Save the molecule to a PDB file.
_IO.saveMolecules("tmp", molecule, "PDB")
# Read the ligand PDB into an RDKit molecule.
mol = _Chem.MolFromPDBFile("tmp.pdb")
# Compute the formal charge.
formal_charge = _Chem.rdmolops.GetFormalCharge(mol)
return formal_charge * _electron_charge