qmmmrebind.parameterize.ParameterizeHost

class qmmmrebind.parameterize.ParameterizeHost(xyz_file='host_qm_coords.xyz', coordinate_file='host_qm_coordinates.txt', unprocessed_hessian_file='host_qm_unprocessed_hessian.txt', bond_list_file='host_qm_bond_list.txt', angle_list_file='host_qm_angle_list.txt', hessian_file='host_qm_hessian.txt', atom_names_file='host_qm_atom_names.txt', bond_parameter_file='host_qm_bonds.txt', angle_parameter_file='host_qm_angles.txt', charge_parameter_file='host_qm_surround_charges.txt', host_qm_pdb='host_qm.pdb', functional='B3LYP', basis_set='6-31G')[source]

A class used to obtain force field parameters for the QM region of the receptor (bond, angle and charge parameters) from QM calculations.

This class contain methods to process the output files of the Gaussian QM output files (.chk, .fchk and .log files). Methods in the class extract the unprocessed hessian matrix from the Gaussian QM calculations, processes it and uses the Modified Seminario Method to ontain the bond and angle parameters. The class also extracts the QM charges from the log file.

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Variables

  • xyz_file (str, optional) – XYZ file for ligand coordinates obtained from its corresponding formatted checkpoint file.

  • coordinate_file (str, optional) – Text file containing the receptor coordinates (extracted from the formatted checkpoint file).

  • unprocessed_hessian_file (str, optional) – Unprocessed hessian matrix of the receptor obtained from the formatted checkpoint file.

  • bond_list_file (str, optional) – Text file containing the bond information of the receptor extracted from the log file.

  • angle_list_file (str, optional) – Text file containing the angle information of the receptor extracted from the log file.

  • hessian_file (str, optional) – Processed hessian matrix of the receptor.

  • atom_names_file (str, optional) – Text file containing the list of atom names from the fchk file.

  • bond_parameter_file (str, optional) – Text file containing the bond parameters for the receptor obtained using the Modified Seminario method.

  • angle_parameter_file (str, optional) – Text file containing the angle parameters of the receptor.

  • charge_parameter_file (str, optional) – Text file containing the QM charges of the receptor.

  • host_qm_pdb (str, optional) – PDB file for the receptor’s QM region.

  • functional (str, optional) – Exchange/Correlation or hybrid functional to use in the Gaussian QM calculation.

  • basis_set (str, optional) – Basis set to use for the Gaussian QM calculation.

__init__(xyz_file='host_qm_coords.xyz', coordinate_file='host_qm_coordinates.txt', unprocessed_hessian_file='host_qm_unprocessed_hessian.txt', bond_list_file='host_qm_bond_list.txt', angle_list_file='host_qm_angle_list.txt', hessian_file='host_qm_hessian.txt', atom_names_file='host_qm_atom_names.txt', bond_parameter_file='host_qm_bonds.txt', angle_parameter_file='host_qm_angles.txt', charge_parameter_file='host_qm_surround_charges.txt', host_qm_pdb='host_qm.pdb', functional='B3LYP', basis_set='6-31G')[source]

Methods

__init__([xyz_file, coordinate_file, ...])

get_atom_names()

Saves a list of atom names from the formatted checkpoint file.

get_bond_angle_params()

Saves the bond and angle parameter files obtained from the formatted checkpoint file.

get_bond_angles()

Saves a text file containing bonds and angles from the gaussian log file.

get_charges()

Saves the atomic charges in a text file obtained from the Gaussian log file.

get_hessian()

Extracts hessian matrix from the unprocessed hessian matrix and saves into a new file.

get_unprocessed_hessian()

Saves a text file of the unprocessed hessian matrix from the formatted checkpoint file.

get_xyz()

Saves XYZ file from the formatted checkpoint file.