Compute

Field of points properties

get_fop_inputs(atoms_frame, pocket_selection, subpex_config, *args, **kwargs)

Generates a dictionary of inputs for field of points (FoP) calculations.

This function selects atoms from the provided MDAnalysis AtomGroup according to the given pocket selection string and the Subpex configuration. It returns a dictionary containing the positions of protein atoms, pocket C-alpha atoms, pocket radius, resolution, and pocket center.

PARAMETER	DESCRIPTION
atoms_frame	An MDAnalysis AtomGroup object containing the atoms of the molecular structure. TYPE: AtomGroup
pocket_selection	A string specifying the selection criteria for pocket atoms. This string should follow the MDAnalysis selection syntax. TYPE: str | None
subpex_config	The Subpex configuration object containing parameters for pocket radius, resolution, and center. TYPE: SubpexConfig
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
MutableMapping[str, Any]	A dictionary with the following keys: protein: Positions of protein atoms. pocket_c_alphas: Positions of pocket C-alpha atoms. radius: Radius of the pocket. resolution: Resolution of the pocket. center: Center of the pocket.

RAISES	DESCRIPTION
ValueError	If the pocket selection string is None or if the pocket center is None.

Example

atoms_frame = u.select_atoms("protein")
pocket_selection = "resid 50-60"
subpex_config = SubpexConfig(...)
inputs = get_fop_inputs(atoms_frame, pocket_selection, subpex_config)

get_fop_volume(fop, resolution, *args, **kwargs)

Computes the volume of a field of points (FoP) based on the given resolution.

This function calculates the volume occupied by a field of points by assuming that each point occupies a cubic space defined by the resolution.

PARAMETER	DESCRIPTION
fop	A sequence of sequences containing XYZ coordinates for each point. TYPE: Sequence[Sequence[float]]
resolution	The resolution of the field of points in Angstroms. TYPE: float
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
float	The volume of the field of points as a float.

Example

fop = [[0.0, 0.0, 0.0], [1.0, 1.0, 1.0], [2.0, 2.0, 2.0]]
resolution = 1.0
volume = get_fop_volume(fop, resolution)