ProtoCaller.Ensemble package¶

This package is the core of ProtoCaller. Here you will find the Ligand class, which is used to handle ligand protonation and parametrisation, the Protein class, which handles the complicated and multi-faceted process of protein preparation, the Perturbation and PerturbationList classes, which handle ligand mapping and ligand alignment and finally the Ensemble class, which bundles all of the above together to enable high-throughput parametrised input file generation.

Some good uses of these classes have been demonstrated in the Examples section.

Submodules¶

Module contents¶

class ProtoCaller.Ensemble.Ensemble(engine='GROMACS', box_length_complex=9, box_length_morph=4, ion_conc=0.154, shell=0, neutralise=True, centre=True, protein_ff='ff14SB', ligand_ff='gaff', water_ff='tip3p', protein=None, ligand_ref=None, morphs=None, workdir=None)¶

Bases: object

The main class responsible for handling batches of complexes in ProtoCaller.

Parameters

engine (str) – Initialises the engine.
box_length_complex (float, iterable) – Initialises box_length_complex.
box_length_morph (float, iterable) – Initialises box_length_morph.
ion_conc (float) – Initialises ion_conc.
shell (float) – Initialises shell.
neutralise (bool) – Initialises neutralise.
centre (bool) – Initialises centre.
protein_ff (str) – The protein force field. Used to initialise params.
ligand_ff (str) – The ligand force field. Used to initialise params.
water_ff (str) – The water / simple ion force field. Used to initialise params.
protein (ProtoCaller.Ensemble.Protein.Protein) – Initialises protein.
ligand_ref (str or ProtoCaller.Ensemble.Ligand.Ligand or None or False) – Initialises protein.ligand_ref.
morphs (ProtoCaller.Ensemble.PerturbationList.PerturbationList or [ProtoCaller.Ensemble.Perturbation.Perturbation] or [[ProtoCaller.Ensemble.Ligand.Ligand, ProtoCaller.Ensemble.Ligand.Ligand]]) – Initialises morphs.
workdir (str) – Initialises workdir.

workdir¶

The working directory of the ensemble.

Type: ProtoCaller.Utils.fileio.Dir

engine¶

The engine for which the input files are created. One of: “GROMACS”.

Type: str

box_length_complex¶

Size of the solvated complex box in nm. Cubic shape is assumed.

Type: float, iterable

box_length_morph¶

Size of the solvated morph box in nm. Cubic shape is assumed.

Type: float, iterable

shell¶

Places a layer of water of the specified thickness in nm around the solute.

Type: float

neutralise¶

Whether to add counterions to neutralise the system.

Type: bool

ion_conc¶

Ion concentration of NaCl in mol/L.

Type: float

centre¶

Whether to centre the system.

Type: bool

params¶

Force field parameters.

Type: ProtoCaller.Parametrise.Params

protein¶

The common protein.

Type: ProtoCaller.Ensemble.Protein

morphs¶

A list of all perturbations.

Type: ProtoCaller.Ensemble.PerturbationList.PerturbationList

systems_prep¶

The prepared systems.

Type: dict

prepareComplexes(replica_temps=None, scale_dummy_bonds=1, dummy_bond_smarts='[*]~[*]', intermediate_files=False, store_complexes=False, output_files=True)¶

Batch prepares all complexes with an option to output files for REST(2).

Parameters

replica_temps ([float] or None) – A list of replica temperatures. Everything is normalised with respect to the lowest temperature. None means only output the normal files.
scale_dummy_bonds (float) – Sets the dummy bond length distance as a fraction of the real bond length distance.
dummy_bond_smarts (str) – SMARTS string which indicates which dummy bonds are to be affected by scale_dummy_bonds.
intermediate_files (bool) – Whether to store all intermediate files.
store_complexes (bool) – Whether to store the final complexes as a dictionary of BioSimSpace System objects.
output_files (bool) – Whether to write output files immediately or later via saveSystems.

saveSystems(systems=None)¶

Saves all systems.

Parameters: systems (dict or None) – Input systems to be saved. None means use self.systems_prep.