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.
Submodules¶
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]