Gridmesh

GridMesh(box, res)

A class representing a box of equidistant points.

Initialize the class.

PARAMETER	DESCRIPTION
box	A numpy array representing two 3D points, (min_x, min_y, min_z) and (max_x, max_y, max_z), that define a box. TYPE: NDArray[float64]
res	The space between the points of the box, in the X, Y, and Z direction. TYPE: float

points = np.array(list(zip(x.ravel(), y.ravel(), z.ravel())))

write_pdbs = write_pdbs()

__delete_limited_points(pt_indices)

A support function

__keep_limited_points(pt_indices)

A support function

__snap_float(val, res)

Snaps an arbitrary point to the nearest grid point.

PARAMETER	DESCRIPTION
val	A numpy array corresponding to a 3D point. TYPE: NDArray[float64]
res	The resolution (distance in the X, Y, and Z directions between adjacent points) of the grid. TYPE: float

RETURNS	DESCRIPTION
NDArray[float64]	A numpy array corresponding to a 3D point near val that is on a nearby grid point.

__unique_points()

Identifies unique points (rows) in an array of points.

PARAMETER	DESCRIPTION
a	A nx3 np.array representing 3D points.

RETURNS	DESCRIPTION
	A nx2 np.array containing the 3D points that are unique.

expand_around_existing_points(num_pts, reso)

Add points to the current box that surround existing points, essentially increasing the resolution of the box.

PARAMETER	DESCRIPTION
num_pts	An int, the number of points to place on each side of the existing points, in the X, Y, and Z directions.
res	The distance between adjacent added points.

filter_isolated_points_until_no_change(reso, number_of_neighbors)

Keep removing points that don't have enough neighbors, until no such points exist.

PARAMETER	DESCRIPTION
res	The distance between adjacent points.
number_of_neighbors	The minimum number of permissible neighbors.

remove_all_points_close_to_other_points(other_points, dist_cutoff, config)

Removes all points in this box that come within the points specified in a numpy array

PARAMETER	DESCRIPTION
other_points	A numpy array containing the other points. TYPE: NDArray[float64]
dist_cutoff	A float, the cutoff distance to use in determining whether or not box points will be removed. TYPE: float
config	Configuration object containing n_cores. TYPE: PocketVolumeConfig

remove_points_outside_convex_hull(hull, config)

Removes box points that are outside a convex hull.

PARAMETER	DESCRIPTION
hull	The convex hull.
config	Configuration object containing n_cores.

separate_out_pockets()

Separate the points according to the pocket they belong to. Determined by looking at patches of contiguous points.

RETURNS	DESCRIPTION
list[NDArray[float64]]	A list of point arrays, each array corresponding to the points of a separate pocket.

to_pdb(let='X')

Converts the points in this box into a PDB representation.

PARAMETER	DESCRIPTION
let	An optional string, the chain ID to use. "X" by default. DEFAULT: 'X'

RETURNS	DESCRIPTION
	A PDB-formatted string.

TaskGetClosePoints

Bases: RayTaskGeneral

A class to identify box points that are near other, user-specified points.

process_item(item)

Identifies indices of box points close to other points.

PARAMETER	DESCRIPTION
item	A tuple containing: - box_of_pts_distance_tree: KDTree of box points. - dist_cutoff: The cutoff distance. - other_points: Numpy array of other points. TYPE: tuple[KDTree, float, NDArray[float64]]

RETURNS	DESCRIPTION
NDArray[float64]	A numpy array of unique indices of box points that are within dist_cutoff.

TaskRemovePointsOutsideHull

Bases: RayTaskGeneral

A class to remove points outside a convex hull using multiple processors.

process_item(item)

Removes points outside the convex hull.

PARAMETER	DESCRIPTION
item	A tuple containing: - hull: The convex hull object. - some_points: A numpy array of points to be tested. TYPE: tuple[Any, NDArray[float64]]

RETURNS	DESCRIPTION
NDArray[float64]	A numpy array of points that are inside the convex hull.