ProtoCaller.Parametrise package

This package is responsible for parametrising molecules to a particular force field. So far, ProtoCaller only supports automatic parametrisation via AmberTools (antechamber and tleap). Proteins, ligands, water molecules and simple hard anions and cations can be readily parametrised using Ambertools. However, cofactors and transition metal complexes are not trivial to parametrise automatically and as such support for these systems is currently limited.

The most important elements in this module are the Params class, which is a simple, yet needed by ProtoCaller class, which describes the desired force fields and the parametriseFile() function, which handles the actual parametrisaton.

Module contents

class ProtoCaller.Parametrise.Params(protein_ff='ff14SB', ligand_ff='gaff', water_ff='tip3p')

Bases: object

A simple class which contains force field names for different molecule types.

Parameters

  • protein_ff (str) – Initialises the protein force field.

  • ligand_ff (str) – Initialises the ligand force field.

  • water_ff (str) – Initialises the water / simple ion force field.

property ligand_ff

The ligand force field.

property protein_ff

The protein force field.

property water_ff

The water / simple ion force field.

property water_points

How many points the water model has.

ProtoCaller.Parametrise.parametriseAndLoadBSS(params, *args, **kwargs)

Calls parametriseFile and loads the files into BioSimSpace.

Parameters

  • params (ProtoCaller.Parametrise.Params) – Force field parameters.

  • args – Positional arguments to be passed to parametriseFile.

  • kwargs – Keyword arguments to be passed to parametriseFile.

Returns

system – The loaded parametrised files as a BioSimSpace System.

Return type

BioSimSpace.system

ProtoCaller.Parametrise.parametriseAndLoadPmd(params, *args, **kwargs)

Calls parametriseFile and loads the files into ParmEd.

Parameters

  • params (ProtoCaller.Parametrise.Params) – Force field parameters.

  • args – Positional arguments to be passed to parametriseFile.

  • kwargs – Keyword arguments to be passed to parametriseFile.

Returns

system – The loaded parametrised files as a ParmEd Structure.

Return type

parmed.structure.Structure

ProtoCaller.Parametrise.parametriseFile(params, filename, molecule_type, fix_charge=True, id=None, *args, **kwargs)

Parametrises an input file according to a force field.

Parameters

  • params (ProtoCaller.Parametrise.Params) – Force field parameters.

  • filename (str) – Name of the input file.

  • molecule_type (str) – The type of the molecule. One of: “protein”, “ligand”, “cofactor”, “water”, “simple_anion”, “complex_anion”, “simple_cation”, “complex_cation”.

  • fix_charge (bool) – Whether to enforce integer net charge.

  • id (str) – The name of the molecule. Default: equal to molecule_type.

  • args – Positional arguments to be passed to the relevant wrapper.

  • kwargs – Keyword arguments to be passed to the relevant wrapper.

Returns

files – The output parametrised file(s). If there is more than one file, the first one is always the topology file and the second one - the coordinate file.

Return type

[str]