Utils.Symmetrizers.symmetrizer module¶

Description¶

This module defines the ParaMol.Utils.symmetrizer.symmetrizer.Symmetrizer .

class ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer(top_file)¶

Bases: object

ParaMol bse class that implements methods to symmetrize the ParaMol Force Field.

get_charge_symmetries(force_field_instance)¶

Method that gets the user-defined charge symmetries .

Parameters: force_field_instance (ParaMol.Force_field.force_field.ForceField) – Instance of the ParaMol ForceField (unsymmetrized) to respect AMBER symmetries.
Returns: force_field_instance (ParaMol.Force_field.force_field.ForceField) – Instance of the ParaMol ForceField symmetrized to respect AMBER symmetries.

get_symmetries(force_field_instance=None)¶

Method that gets symmetries with the aid of Parmed. User-defined charge symmetries require the passing of the force_field_instance argument.

Notes

Currently the implemented term types are: bonds, angles, torsions.

Parameters: force_field_instance (ParaMol.Force_field.force_field.ForceField) – Instance of the ParaMol ForceField (unsymmetrized).
Returns: dict, dict, dict, dict, dict – Dictionaries containing the symmetry group as keys and information about the parameters of that symmetry group as values.

save(output_file, format=None)¶

Method that writes the AMBER, GROMACS, CHARMM, and .mol2 files with the current force field parameters of the self._top_file instance.

Notes

In order to update the self._top_file instance with the optimal parameters, the method update_term_types_parameters should be run before this one.

Parameters

output_file (str) – Name of the output file (with the correct PARMED suffix)
format (str) – Format of the file as in Parmed. E.g. ‘amber’, ‘rst7’, etc…

Returns

None

symmetrize_force_field(force_field_instance)¶

Method that symmetrizes the ParaMol force field so that it respect atom-type symmetries.

Parameters: force_field_instance (ParaMol.Force_field.force_field.ForceField) – Instance of the ParaMol ForceField (unsymmetrized).
Returns: force_field_instance (ParaMol.Force_field.force_field.ForceField) – Instance of the ParaMol ForceField symmetrized to respect.

update_term_types_parameters(optimizable_parameters)¶

Method that updates the term type parameters in the Parmed AMBER topology object.

Notes

This method should be run before writing the AMBER topology file or AMBER .frcmod file.

Parameters: optimizable_parameters (list of ParaMol.Force_field.force_field_term_parameter.Parameter) – List that contains instances of ParaMol.Force_field.force_field_term_parameter.Parameter that are optimizable.
Returns: self._top_file – Instance of Parmed topology object.