Tasks.resp_fitting module

Description

This module defines the ParaMol.Tasks.resp.RESPFitting class, which is a ParaMol task that performs fitting of the electrostatic potential.

class ParaMol.Tasks.resp_fitting.RESPFitting

Bases: ParaMol.Tasks.task.Task

ParaMol RESP fitting task.

static get_degenerate_hydrogen_indexes(rdkit_mol)

Method that determines the indices of the hydrogen atoms belonging to methyl or methylene groups.

Parameters

rdkit_mol – RDKit Molecule

Returns

hydrogen_indexes (list of int) – Tuple of tuples containing the indexes of the atoms forming rotatable (soft) bonds.

resp_solvers = ['EXPLICIT', 'SCIPY']
run_task(settings, systems, parameter_space=None, objective_function=None, optimizer=None, interface=None, solver='SCIPY', total_charge=None, restraint_hydrogens=True, constraint_tolerance=1e-06, rmsd_tol=1e-08, max_iter=10000)

Method that performs a RESP calculation.

Notes

Only one ParaMol system is supported at once.

Parameters

  • settings (dict) – Dictionary containing global ParaMol settings.

  • systems (list of ParaMol.System.system.ParaMolSystem) – List containing instances of ParaMol systems.

  • parameter_space (ParaMol.Parameter_space.parameter_space.ParameterSpace) – Instance of the parameter space.

  • objective_function (ParaMol.Objective_function.objective_function.ObjectiveFunction) – Instance of the objective function.

  • optimizer (one of the optimizers defined in the subpackage ParaMol.Optimizers) – Instance of the optimizer.

  • interface (ParaMol.Utils.interface.ParaMolInterface) – ParaMol system instance.

  • solver (str) – RESP solver. Options are “EXPLICTI” or “SCIPY” (default is “SCIPY”).

  • total_charge (int) – System’s total charge (default is None).

  • restraint_hydrogens (bool) – Flag that determines wheter or not hydrogens will be restrained when applying regularization.

  • constraint_tolerance (float) – Tolerance used to impose total charge or symmetry constraints. Only used if solver is “SCIPY” (default is 1e-6).

  • rmsd_tol (float) – RMSD convergence tolerance. Only used if solver is “explicit” (default is 1e-8).

  • max_iter (int) – Maximum number of iterations. Only used if solver is “explicit” (default is 10000).

Returns

systems, parameter_space, objective_function, optimizer