waterEntropy.recipes package

Submodules

waterEntropy.recipes.bulk_water module

These functions calculate orientational entropy from labelled coordination shells of bulk water

waterEntropy.recipes.bulk_water.get_bulk_water_orient_entropy(system, start: int, end: int, step: int, temperature=298)

For a given system, containing the topology and coordinates of molecules, find the bulk water and calculate their orientational entropy if there is a solute atom in the solvent coordination shell.

Parameters:

• system – mdanalysis instance of atoms in a frame

• start – starting frame number

• end – end frame number

• step – steps between frames

waterEntropy.recipes.forces_torques module

Get the rotated mass-weighted forces and inertia-weighted torques from transformed atom positons and forces and save these as covariance matrices in a Covariances class instance.

waterEntropy.recipes.forces_torques.get_forces_torques(covariances: CovarianceCollection, molecule, nearest: str, system)

Calculate the covariance matrices of molecules and populate these in the covariances instance. Molecules are grouped based on the molecule name and the name of the molecule that is nearest to it.

Parameters:

• covariances – instance of CovarianceCollection class

• molecule – MDAnalysis instance of a molecule

• nearest – name of nearest molecule

• system – MDAnalysis instance of whole system

waterEntropy.recipes.interfacial_solvent module

These functions calculate orientational entropy from labelled coordination shells

waterEntropy.recipes.interfacial_solvent._entropy_per_step(args)

For a given system, containing the topology and coordinates of molecules, find the interfacial water molecules around solutes and calculate their orientational entropy if there is a solute atom in the solvent coordination shell.

Parameters:

args – tuple of variables containing frame index and MDA system frame.

waterEntropy.recipes.interfacial_solvent.find_interfacial_solvent(solutes, system, shells: ShellCollection)

For a given set of solute molecules, find the RAD shells for each UA in the molecules, if a solvent molecule is in the RAD shell, then save the solvent atom index to a list. A solvent is defined as molecule that constitutes a single UA. These solvent molecule are defined as interfacial molecules.

Parameters:

• solutes – mdanalysis instance of a selection of atoms in solute molecules that are greater than one UA

• system – mdanalysis instance of atoms in a frame

• shells – ShellCollection instance

waterEntropy.recipes.interfacial_solvent.get_interfacial_shells(system, start: int, end: int, step: int)

For a given system, containing the topology and coordinates of molecules, find the interfacial water molecules around solutes and calculate their orientational entropy if there is a solute atom in the solvent coordination shell.

Parameters:

• system – mdanalysis instance of atoms in a frame

• start – starting frame number

• end – end frame number

• step – steps between frames

waterEntropy.recipes.interfacial_solvent.get_interfacial_water_orient_entropy(system, start: int, end: int, step: int, temperature=298, parallel=False, client=None)

For a given system, containing the topology and coordinates of molecules, find the interfacial water molecules around solutes and calculate their orientational entropy if there is a solute atom in the solvent coordination shell. This method is a common calling function for the serial and parallel implementation and should be the calling point into those functions. Defaults to serial.

Parameters:

• system – mdanalysis instance of atoms in a frame

• start – starting frame number

• end – end frame number

• step – steps between frames

• parallel – set to True to run the parallel calculation

• client – dask client instance if custom cluster layout required

waterEntropy.recipes.interfacial_solvent.print_frame_solvent_dicts(frame_solvent_indices: dict)

Print the interfacial solvent for each analysed frame

Parameters:

frame_solvent_indices – dictionary containing solvent indices in the first shell of solute atoms over each frame analysed

waterEntropy.recipes.interfacial_solvent.print_frame_solvent_shells(frame_solvent_shells: dict)

Print the interfacial solvent for each analysed frame

Parameters:

frame_solvent_indices – dictionary containing solvent indices in the first shell of solute atoms over each frame analysed

waterEntropy.recipes.interfacial_solvent.save_solvent_indices(frame: int, atom_idx: int, nearest_resid: int, nearest_resname: str, frame_solvent_indices: dict)

Save the solvent indices at interfaces per frame into a dictionary

Parameters:

• frame – frame number of analysed frame

• atom_idx – solvent atom index

• nearest_resid – residue of number of nearest solute molecule

• nearest_resname – residue name of nearest solute molecule

• frame_solvent_indices – the dictionary to populate

waterEntropy.recipes.interfacial_solvent.save_solvent_shells(frame: int, atom_idx: int, shell_indices: list, frame_solvent_shells: dict)

Save the solvent indices at interfaces per frame into a dictionary

Parameters:

• frame – frame number of analysed frame

• atom_idx – solvent atom index

• nearest_resid – residue of number of nearest solute molecule

• nearest_resname – residue name of nearest solute molecule

• frame_solvent_indices – the dictionary to populate

Module contents

waterEntropy: calculate water entropy near heterogeneous interfaces