Compute

Compute properties of pockets.

get_pocket_jaccard(fop_ref, fop_frame, resolution)

Calculates the Jaccard distance between two fields of points (FoPs).

The Jaccard distance measures the dissimilarity between two sets of points based on their intersection and union, considering a specific resolution for point proximity.

PARAMETER	DESCRIPTION
fop_ref	Reference field of points. TYPE: Sequence[Sequence[float]]
fop_frame	Field of points from the current frame. TYPE: Sequence[Sequence[float]]
resolution	Resolution for determining point proximity. TYPE: float

RETURNS	DESCRIPTION
float	The Jaccard distance between the reference and current field of points.

Examples:

>>> fop_ref = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]
>>> fop_frame = [[1.1, 2.1, 3.1], [4.1, 5.1, 6.1]]
>>> jaccard = get_pocket_jaccard(fop_ref, fop_frame, 0.5)
>>> print(f"Jaccard Distance: {jaccard:.2f}")

get_pocket_jaccard_convenience(atoms_frame, subpex_config, atoms_ref=None, *args, **kwargs)

A convenience wrapper around get_pocket_jaccard using a simulation frame.

This function simplifies the calculation of the Jaccard distance between a reference frame and a given trajectory frame using the subpex configuration.

PARAMETER	DESCRIPTION
atoms_frame	Trajectory frame to analyze. TYPE: AtomGroup
subpex_config	SuPEx configuration containing selection strings and other parameters. TYPE: SubpexConfig
atoms_ref	Reference frame for comparison, must be provided if not None. TYPE: AtomGroup | None DEFAULT: None
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
float	The Jaccard distance between the reference and current field of points.

Examples:

>>> u = mda.Universe("topology.pdb", "trajectory.dcd")
>>> frame = u.select_atoms("protein")
>>> ref = u.select_atoms("protein").positions
>>> config = SubpexConfig(pocket=PocketConfig(selection_str="protein"))
>>> jaccard = get_pocket_jaccard_convenience(frame, config, ref)
>>> print(f"Pocket Jaccard Distance: {jaccard:.2f}")

get_pocket_rmsd(atoms_ref, atoms_frame)

Calculates the root-mean-square deviation (RMSD) between two sets of atomic coordinates.

This function computes the RMSD between a reference structure and a current frame, assuming each atom has an equal mass of one. RMSD is a measure of the average distance between atoms of superimposed proteins.

PARAMETER	DESCRIPTION
atoms_ref	Atomic coordinates of the reference structure. TYPE: NDArray[float64]
atoms_frame	Atomic coordinates of the current frame. TYPE: NDArray[float64]

RETURNS	DESCRIPTION
float	The RMSD between the reference and current frame.

Example

atoms_ref = np.array([[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]) atoms_frame = np.array([[1.1, 2.1, 3.1], [4.1, 5.1, 6.1]]) rmsd = get_pocket_rmsd(atoms_ref, atoms_frame) print(f"RMSD: {rmsd:.2f}")

get_pocket_rmsd_convenience(atoms_frame, subpex_config, atoms_ref=None, *args, **kwargs)

A convenience wrapper around get_pocket_rmsd using a simulation frame.

This function simplifies the calculation of the RMSD between a reference frame and a given trajectory frame using the subpex configuration.

PARAMETER	DESCRIPTION
atoms_frame	Trajectory frame to analyze. TYPE: AtomGroup
subpex_config	SuPEx configuration containing selection strings and other parameters. TYPE: SubpexConfig
atoms_ref	Reference frame for comparison, must be provided if not None. TYPE: AtomGroup | None DEFAULT: None
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
float	The RMSD between the reference and current frame.

RAISES	DESCRIPTION
ValueError	If atoms_ref is None.

Example

u = mda.Universe("topology.pdb", "trajectory.dcd") frame = u.select_atoms("protein") ref = u.select_atoms("protein").positions config = SubpexConfig(pocket=PocketConfig(selection_str="protein")) rmsd = get_pocket_rmsd_convenience(frame, config, ref) print(f"Pocket RMSD: {rmsd:.2f}")

get_pocket_rog(fop, *args, **kwargs)

Calculates the radius of gyration for a field of points (FOP).

The radius of gyration is a measure of the compactness of a set of points, assuming a uniform mass distribution.

PARAMETER	DESCRIPTION
fop	The field of points defining the pocket shape. TYPE: Sequence[Sequence[float]]
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
float	The radius of gyration of the pocket.

Example

fop = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] rog = get_pocket_rog(fop) print(f"Radius of Gyration: {rog:.2f}")

get_pocket_rog_convenience(atoms_frame, subpex_config, atoms_ref=None, *args, **kwargs)

A convenience wrapper around get_pocket_rog using a simulation frame.

This function simplifies the calculation of the radius of gyration for a pocket from a given trajectory frame using the subpex configuration.

PARAMETER	DESCRIPTION
atoms_frame	Trajectory frame to analyze. TYPE: AtomGroup
subpex_config	SuPEx configuration containing selection strings and other parameters. TYPE: SubpexConfig
atoms_ref	Reference frame for comparison, must be provided if not None. TYPE: AtomGroup | None DEFAULT: None
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
float	The radius of gyration of the pocket.

Examples:

>>> u = mda.Universe("topology.pdb", "trajectory.dcd")
>>> frame = u.select_atoms("protein")
>>> config = SubpexConfig(pocket=PocketConfig(selection_str="protein"))
>>> rog = get_pocket_rog_convenience(frame, config)
>>> print(f"Radius of Gyration: {rog:.2f}")

get_pocket_volume_convenience(atoms_frame, subpex_config, atoms_ref=None, *args, **kwargs)

This function simplifies the calculation of the volume of a pocket from a given trajectory frame. It wraps around the lower-level get_fop_volume function, abstracting away some of the complexity and inputs.

PARAMETER	DESCRIPTION
atoms_frame	Trajectory frame to analyze. TYPE: AtomGroup
subpex_config	SuPEx configuration containing selection strings and other parameters. TYPE: SubpexConfig
atoms_ref	Reference frame for comparison, defaults to None. TYPE: AtomGroup | None DEFAULT: None
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
float	The calculated volume of the pocket.

Example

u = mda.Universe("topology.pdb", "trajectory.dcd") frame = u.select_atoms("protein") config = SubpexConfig(pocket=PocketConfig(selection_str="protein")) volume = get_pocket_volume_convenience(frame, config) print(f"Pocket volume: {volume:.2f}")