diff --git a/mosdef_dihedral_fit/utils/file_read_and_write.py b/mosdef_dihedral_fit/utils/file_read_and_write.py index 0830992..a5a21bf 100755 --- a/mosdef_dihedral_fit/utils/file_read_and_write.py +++ b/mosdef_dihedral_fit/utils/file_read_and_write.py @@ -479,35 +479,35 @@ def get_final_gaussian_output_file_data( Returns ------- - | list of: - | all_dihedral_angle_degrees_list: list (nested list) - | This is the list of the optimized Gaussian dihedral angles (degrees) with the - | specific angles removed per the 'qm_log_file_dict' list - | (value) input. This is a nested list, with an inner list for every - | Gaussian log file or 'qm_log_file_dict' (key). - | all_energy_hartree_list: list (nested list) - | This is the list of the optimized Gaussian energies with the specific energies - | (hartree) removed per the 'qm_log_file_dict' list - | (value) input. This is a nested list, with an inner list for every - | Gaussian log file or 'qm_log_file_dict' (key). - | all_coordinates_ang_list: list (nested list) - | This is the list of the optimized Gaussian energies with the specific energies - | (hartree) removed per the 'qm_log_file_dict' list - | (value) input. This is a nested list, with an inner list for every - | Gaussian log file or 'qm_log_file_dict' (key). - | element_names_list: list - | This is the list of the Gaussian element names per the - | 'qm_log_file_dict' list (value) input. - | The list length is dependant on the number of elements in the Gaussian log file - | These values are confirmed to be the same for all entered Gaussian log files. - | number_of_atoms: int - | This is the number of atoms in the Gaussian - | 'qm_log_file_dict' list (value) input. - | These values are confirmed to be the same for all entered Gaussian log files. - | manual_dihedral_atom_numbers_list: list, list of four (4) int (example: [3,2,1,5]) - | This is a list of the dihedral atom numbers in order that were used for the dihedral - | fit. This information needs to be correct and in order to produce correct results. - | The values must be the same in all the combined files. + list of: + | all_dihedral_angle_degrees_list: list (nested list) + | This is the list of the optimized Gaussian dihedral angles (degrees) with the + | specific angles removed per the 'qm_log_file_dict' list + | (value) input. This is a nested list, with an inner list for every + | Gaussian log file or 'qm_log_file_dict' (key). + | all_energy_hartree_list: list (nested list) + | This is the list of the optimized Gaussian energies with the specific energies + | (hartree) removed per the 'qm_log_file_dict' list + | (value) input. This is a nested list, with an inner list for every + | Gaussian log file or 'qm_log_file_dict' (key). + | all_coordinates_ang_list: list (nested list) + | This is the list of the optimized Gaussian energies with the specific energies + | (hartree) removed per the 'qm_log_file_dict' list + | (value) input. This is a nested list, with an inner list for every + | Gaussian log file or 'qm_log_file_dict' (key). + | element_names_list: list + | This is the list of the Gaussian element names per the + | 'qm_log_file_dict' list (value) input. + | The list length is dependant on the number of elements in the Gaussian log file + | These values are confirmed to be the same for all entered Gaussian log files. + | number_of_atoms: int + | This is the number of atoms in the Gaussian + | 'qm_log_file_dict' list (value) input. + | These values are confirmed to be the same for all entered Gaussian log files. + | manual_dihedral_atom_numbers_list: list, list of four (4) int (example: [3,2,1,5]) + | This is a list of the dihedral atom numbers in order that were used for the dihedral + | fit. This information needs to be correct and in order to produce correct results. + | The values must be the same in all the combined files. """ if not isinstance(qm_log_file_dict, dict): raise TypeError( @@ -763,35 +763,36 @@ def get_gaussian_log_file_data( Returns ------- - all_dihedral_angle_degrees_list: list (nested list of str) - This is the list of the optimized Gaussian dihedral angles (degrees) with the - specific angles removed per the 'qm_log_file_dict' list - (value) input. This is a nested list, with an inner list for every - Gaussian log file or 'qm_log_file_dict' (key). - all_energy_hartree_list: list (nested list of str) - This is the list of the optimized Gaussian energies with the specific energies - (hartree) removed per the 'qm_log_file_dict' list - (value) input. This is a nested list, with an inner list for every - Gaussian log file or 'qm_log_file_dict' (key). - all_coordinates_ang_list: list (nested list of float) - This is the list of the optimized Gaussian energies with the specific energies - (hartree) removed per the 'qm_log_file_dict' list - (value) input. This is a nested list, with an inner list for every - Gaussian log file or 'qm_log_file_dict' (key). - element_names_list: list of str - This is the list of the Gaussian element names per the - 'qm_log_file_dict' list (value) input. - The list length is dependant on the number of elements in the Gaussian log file - These values are confirmed to be the same for all entered Gaussian log files. - number_of_atoms: int - This is the number of atoms in the Gaussian - 'qm_log_file_dict' list (value) input. - These values are confirmed to be the same for all entered Gaussian log files. - dihedral_atom_numbers_list: list of 4 int - This is the list of the dihedral atom numbers used in the Gaussian - dihedral scan, which are taken from the Gaussian - 'qm_log_file_dict' list (value) input. - These values are confirmed to be the same for all entered Gaussian log files. + list of: + | all_dihedral_angle_degrees_list: list (nested list of str) + | This is the list of the optimized Gaussian dihedral angles (degrees) with the + | specific angles removed per the 'qm_log_file_dict' list + | (value) input. This is a nested list, with an inner list for every + | Gaussian log file or 'qm_log_file_dict' (key). + | all_energy_hartree_list: list (nested list of str) + | This is the list of the optimized Gaussian energies with the specific energies + | (hartree) removed per the 'qm_log_file_dict' list + | (value) input. This is a nested list, with an inner list for every + | Gaussian log file or 'qm_log_file_dict' (key). + | all_coordinates_ang_list: list (nested list of float) + | This is the list of the optimized Gaussian energies with the specific energies + | (hartree) removed per the 'qm_log_file_dict' list + | (value) input. This is a nested list, with an inner list for every + | Gaussian log file or 'qm_log_file_dict' (key). + | element_names_list: list of str + | This is the list of the Gaussian element names per the + | 'qm_log_file_dict' list (value) input. + | The list length is dependant on the number of elements in the Gaussian log file + | These values are confirmed to be the same for all entered Gaussian log files. + | number_of_atoms: int + | This is the number of atoms in the Gaussian + | 'qm_log_file_dict' list (value) input. + | These values are confirmed to be the same for all entered Gaussian log files. + | dihedral_atom_numbers_list: list of 4 int + | This is the list of the dihedral atom numbers used in the Gaussian + | dihedral scan, which are taken from the Gaussian + | 'qm_log_file_dict' list (value) input. + | These values are confirmed to be the same for all entered Gaussian log files. """ if not isinstance(qm_log_file_dict, dict): raise TypeError(