Utils.gaussian_esp module

Description

This module defines the ParaMol.Utils.gaussian_esp.GaussianESP that contains function to extract an ESP potential from a gaussian output file so that it can be used as input for RESP calculations in ParaMol.

class ParaMol.Utils.gaussian_esp.GaussianESP(conformations=None, grids=None, esps=None)

Bases: object

static gaussian_read_log(log_file)

Method that reads the output of a gaussian ESP calculation.

Notes

Energy stored will be the last occurrence of “SCF Done:” in the gaussian log file.

Parameters

log_file (str) – Path to the Gaussian output file.

Returns

conformation, grid, esp, energy

read_log_files(files_names)

Method that reads multiple files that correspond to the output of a gaussian ESP calculation.

Parameters

files_names (str or list of str) – Path(s) to Gaussian output files.

Returns

  • conformations (np.array, shape=(n_conformations,n_atoms,3)) – Array with conformations.

  • grids (np.array, shape=(n_conformations,n_esp_point,3)) – Array with grid points.

  • esps (np.array, shape=(n_esp_points,3)) – Array with electrostatic potential values.

  • energies (np.array, shape=(n_conformations)) – Array with energies

write_esp_paramol_format()

Method that writes ESP files in ParaMol format.

Returns

True if everything run smoothly.