Source code for bonafide.features.multiwfn_connectivity
"""Atom connectivity features from ``Multiwfn``."""
import os
from typing import List, Union
from bonafide.utils.base_featurizer import BaseFeaturizer
from bonafide.utils.constants import PROGRAM_ENVIRONMENT_VARIABLES
from bonafide.utils.driver import multiwfn_driver
from bonafide.utils.io_ import write_xyz_file_from_coordinates_array
[docs]
class _Multiwfn3DAtomConnectivity(BaseFeaturizer):
"""Parent feature factory for the 3D atom connectivity Multiwfn features.
For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed
on 12.09.2025).
"""
connectivity_index_threshold: float
def __init__(self) -> None:
self.extraction_mode = "multi"
super().__init__()
[docs]
def calculate(self) -> None:
"""Calculate the Multiwfn connectivity features."""
# For the connectivity index, no electronic structure data is required. Therefore, it is
# calculated from the XYZ file.
# Generate the XYZ file and write it to the electronic_struc_n attribute for input
# to Multiwfn
self._write_input_file()
self._run_multiwfn()
self._read_output_file()
[docs]
def _run_multiwfn(self) -> None:
"""Run Multiwfn.
Returns
-------
None
"""
# Select other functions
multiwfn_commands: List[Union[str, int, float]]
multiwfn_commands = [100]
# Select connectivity index analysis
multiwfn_commands.append(9)
# Set threshold option
multiwfn_commands.append(self.connectivity_index_threshold)
# Exit program
multiwfn_commands.extend(["n", 0, "q"])
# Set up environment variables
environment_variables = {
var: getattr(self, var, None) for var in PROGRAM_ENVIRONMENT_VARIABLES["multiwfn"]
}
# Run Multiwfn
multiwfn_driver(
cmds=multiwfn_commands,
input_file_path=self.conformer_name + ".xyz",
output_file_name=f"{self.__class__.__name__}__{self.conformer_name}",
environment_variables=environment_variables,
namespace=self.conformer_name[::-1].split("__", 1)[-1][::-1],
)
[docs]
def _read_output_file(self) -> None:
"""Read the output file from Multiwfn and write the results to the ``results`` dictionary.
Returns
-------
None
"""
# Check if the output file exists
_opath = f"{self.__class__.__name__}__{self.conformer_name}.out"
if os.path.isfile(_opath) is False:
self._err = (
f"Multiwfn output file '{_opath}' not found; probably the calculation "
"did not run. Check your input"
)
return
# Open output file
with open(_opath, "r") as f:
multiwfn_output = f.readlines()
# Find the values and write them to the results dictionary
for line in multiwfn_output:
if "Sum of connectivity:" in line and "Sum of integer connectivity:" in line:
atom_idx = int(line.split()[0])
splitted = line.split(":")[1:]
con = float(splitted[0].split("Sum")[0])
int_con = int(splitted[-1])
self.results[atom_idx - 1] = {
"multiwfn3D-atom-connectivity_index": con,
"multiwfn3D-atom-connectivity_index_integer": int_con,
}
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class Multiwfn3DAtomConnectivityIndex(_Multiwfn3DAtomConnectivity):
"""Feature factory for the 3D atom feature "connectivity_index", calculated with multiwfn.
The index of this feature is 230 (see the ``list_atom_features()`` and
``list_bond_features()`` method). The corresponding configuration settings can be found
under "multiwfn.bond_analysis" in the _feature_config.toml file.
"""
def __init__(self) -> None:
super().__init__()
# This feature is automatically calculated in _Multiwfn3DAtomConnectivity
[docs]
class Multiwfn3DAtomConnectivityIndexInteger(_Multiwfn3DAtomConnectivity):
"""Feature factory for the 3D atom feature "connectivity_index_integer", calculated with
multiwfn.
The index of this feature is 231 (see the ``list_atom_features()`` and
``list_bond_features()`` method). The corresponding configuration settings can be found
under "multiwfn.bond_analysis" in the _feature_config.toml file.
"""
def __init__(self) -> None:
super().__init__()
# This feature is automatically calculated in _Multiwfn3DAtomConnectivity