Detect

Detect pockets using a field of points.

get_fop_pocket(protein, pocket_c_alphas, center, resolution, radius, clustering_model=None, clustering_kwargs=None)

Calculate the field of points (FOP) for a pocket.

This function generates a field of points (FOP) representing the shape of a pocket using the provided protein and alpha carbon coordinates. It applies several processing steps including removing steric clashes and clustering.

PARAMETER	DESCRIPTION
protein	XYZ coordinates of protein atoms. TYPE: Sequence[Sequence[float]]
pocket_c_alphas	XYZ coordinates of all alpha carbons in the pocket. TYPE: Sequence[Sequence[float]]
center	XYZ center of the pocket. TYPE: Sequence[float]
resolution	Resolution for the FOP. TYPE: float
radius	Radius of sphere for FOP. TYPE: float
clustering_model	Scikit-learn clustering model class to use. TYPE: type | None DEFAULT: None
clustering_kwargs	Keyword arguments for clustering_model initialization. TYPE: MutableMapping[str, Any] | None DEFAULT: None

RETURNS	DESCRIPTION
Sequence[Sequence[float]]	Pocket shape as a field of points.

Example

protein_coords = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] alpha_carbons = [[1.1, 2.1, 3.1], [4.1, 5.1, 6.1]] center = [2.0, 3.0, 4.0] resolution = 0.5 radius = 5.0 fop = get_fop_pocket(protein_coords, alpha_carbons, center, resolution, radius) print(f"Field of Points: {fop}")

get_fop_pocket_convenience(atoms_frame, subpex_config, *args, **kwargs)

Convenience function for getting the FOP for a pocket.

This function simplifies the process of calculating the field of points (FOP) for a pocket using a simulation frame and the SuPEx configuration.

PARAMETER	DESCRIPTION
atoms_frame	Trajectory frame to analyze. TYPE: AtomGroup
subpex_config	SuPEx configuration containing selection strings and other parameters. TYPE: SubpexConfig
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: Any DEFAULT: {}

RETURNS	DESCRIPTION
Sequence[Sequence[float]]	Pocket shape as a field of points.

Example

u = mda.Universe("topology.pdb", "trajectory.dcd") frame = u.select_atoms("protein") config = SubpexConfig(pocket=PocketConfig(selection_str="protein")) fop = get_fop_pocket_convenience(frame, config) print(f"Field of Points: {fop}")

get_pocket_selection(u, center, radius, water_dist=6.7, water_resnames=['WAT', 'HOH', 'H2O'], selection_append='and (not name H*)')

Get the initial selection of the pocket based on the specified radius.

This function identifies the initial selection of pocket residues based on a user-specified radius, and optionally considers distance from water molecules as an approximation of surface residues.

PARAMETER	DESCRIPTION
universe	MDA universe containing the protein.
center	XYZ coordinates of the pocket center. TYPE: Sequence[float]
radius	Radius of the pocket to be considered. TYPE: float
water_dist	Constraint to use for proximity to calculate surface residues. TYPE: float DEFAULT: 6.7
water_resnames	Residue names for water molecules. TYPE: Sequence[str] DEFAULT: ['WAT', 'HOH', 'H2O']
selection_append	String to append to pocket selection. By default we exclude hydrogen atoms. TYPE: str DEFAULT: 'and (not name H*)'

RETURNS	DESCRIPTION
str	Selection string of the pocket as used in MDAnalysis.

Example

u = mda.Universe("topology.pdb", "trajectory.dcd") center = [10.0, 10.0, 10.0] radius = 5.0 selection = get_pocket_selection(u, center, radius) print(f"Pocket selection: {selection}")

Note

If water molecules are found within radius of the pocket center, we will try to limit the pocket residues to those near the surface. We approximate Residues are included if they are within water_dist away from any water molecule.

get_residues_in_pocket(u, center, radius, resnames)

Get residues within the pocket.

PARAMETER	DESCRIPTION
u	MDAnalysis universe containing the protein. TYPE: Universe
center	XYZ coordinates of the pocket center. TYPE: Sequence[float]
radius	Radius of the pocket to be considered. TYPE: float
resnames	Residue names for selection. TYPE: Sequence[str]

RETURNS	DESCRIPTION
AtomGroup	mda.AtomGroup: AtomGroup of residues within the pocket.