init

`all = ['SphericalRegion', 'RectangularRegion', 'collect_regions', '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.

`RectangularRegion(center, lengths)` ¶

Bases: Region

A 3D rectangular region defined by its center and dimensions.

This class represents a rectangular box in 3D space, capable of generating a grid of points that fill the box.

Initialize a rectangular region.

PARAMETER	DESCRIPTION
`center` ¶	The x, y, and z coordinates of the center of the box. TYPE: `list[float]`
`lengths` ¶	The lengths of the box along the x, y, and z axes. TYPE: `list[float]`

`center = np.array(center)` ¶

A list of three floats representing the x, y, and z coordinates of the box's center, in Angstroms.

`lengths = np.array(lengths)` ¶

A list of three floats representing the lengths of the box along the x, y, and z axes, in Angstroms.

`str()` ¶

Returns a string representation of the rectangular region.

`get_points(res)` ¶

Generates a grid of points filling the rectangular region.

PARAMETER	DESCRIPTION
`res` ¶	The resolution of the grid, defining the spacing between points.

RETURNS	DESCRIPTION
	A numpy array of shape (n, 3), where each row is a [x, y, z]
	coordinate representing a point within the rectangular region.

`SphericalRegion(center, radius)` ¶

Bases: Region

A 3D spherical region defined by a center and a radius.

This class represents a sphere in 3D space, capable of generating a grid of points that fill the sphere. Points outside the sphere boundary are excluded.

Initialize a spherical region.

PARAMETER	DESCRIPTION
`center` ¶	The x, y, and z coordinates of the center of the sphere. TYPE: `list[float]`
`radius` ¶	The radius of the sphere in Angstroms. TYPE: `float`

`center = np.array(center)` ¶

x, y, and z coordinates in Angstroms of the center.

`radius = radius` ¶

Sphere radius in Angstroms.

`str()` ¶

Returns a string representation of the spherical region.

`get_points(res)` ¶

Generates a grid of points filling the spherical region.

PARAMETER	DESCRIPTION
`res` ¶	The resolution of the grid, defining the spacing between points. TYPE: `float`

RETURNS	DESCRIPTION
`NDArray[float64]`	A numpy array of shape (n, 3), where each row is a [x, y, z]
`NDArray[float64]`	coordinate representing a point within the spherical region.

`collect_regions(spherical_configs, rectangular_configs)` ¶

Creates a collection of 3D regions from spherical and rectangular configurations.

This function takes configurations for spherical and rectangular regions, instantiates the respective region objects, and returns a combined list of these regions. Empty or invalid configurations are skipped.

PARAMETER	DESCRIPTION
`spherical_configs` ¶	A list of dictionaries, each specifying a spherical region. Each dictionary must have: `"center"` (`list[float]`): The x, y, and z coordinates of the sphere's center. `"radius"` (`float`): The radius of the sphere. If `None`, no spherical regions are added. TYPE: `list[dict[str, list[float] \| float]] \| None`
`rectangular_configs` ¶	A list of dictionaries, each specifying a rectangular region. Each dictionary must have: `"center"` (`list[float]`): The x, y, and z coordinates of the box's center. `"lengths"` (`list[float]`): The lengths of the box along the x, y, and z axes. If `None`, no rectangular regions are added. TYPE: `list[dict[str, list[float]]] \| None`

RETURNS	DESCRIPTION
`list[SphericalRegion \| RectangularRegion]`	A list containing `SphericalRegion` and `RectangularRegion` objects created based on the provided configurations.

Example

>>> spherical_configs = [
...     {"center": [0.0, 0.0, 0.0], "radius": 5.0},
...     {"center": [10.0, 10.0, 10.0], "radius": 3.0},
... ]
>>> rectangular_configs = [
...     {"center": [0.0, 0.0, 0.0], "lengths": [10.0, 5.0, 2.0]}
... ]
>>> regions = collect_regions(spherical_configs, rectangular_configs)
>>> for region in regions:
...     print(region)
sphere at (0.0, 0.0, 0.0), radius = 5.0
sphere at (10.0, 10.0, 10.0), radius = 3.0
box centered at (0.0, 0.0, 0.0) with dimensions (10.0, 5.0, 2.0)

init

__all__ = ['SphericalRegion', 'RectangularRegion', 'collect_regions', 'GridMesh'] ¶

GridMesh(box, res) ¶

box ¶

res ¶

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

write_pdbs = write_pdbs() ¶

__delete_limited_points(pt_indices) ¶

__keep_limited_points(pt_indices) ¶

__snap_float(val, res) ¶

val ¶

res ¶

__unique_points() ¶

a ¶

expand_around_existing_points(num_pts, reso) ¶

num_pts ¶

res ¶

filter_isolated_points_until_no_change(reso, number_of_neighbors) ¶

res ¶

number_of_neighbors ¶

remove_all_points_close_to_other_points(other_points, dist_cutoff, config) ¶

other_points ¶

dist_cutoff ¶

config ¶

remove_points_outside_convex_hull(hull, config) ¶

hull ¶

config ¶

separate_out_pockets() ¶

to_pdb(let='X') ¶

let ¶

RectangularRegion(center, lengths) ¶

center ¶

lengths ¶

center = np.array(center) ¶

lengths = np.array(lengths) ¶

__str__() ¶

get_points(res) ¶

res ¶

SphericalRegion(center, radius) ¶

center ¶

radius ¶

center = np.array(center) ¶

radius = radius ¶

__str__() ¶

get_points(res) ¶

res ¶

collect_regions(spherical_configs, rectangular_configs) ¶

spherical_configs ¶

rectangular_configs ¶

`all = ['SphericalRegion', 'RectangularRegion', 'collect_regions', 'GridMesh']` ¶

`GridMesh(box, res)` ¶

`box` ¶

`res` ¶

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

`write_pdbs = write_pdbs()` ¶

`__delete_limited_points(pt_indices)` ¶

`__keep_limited_points(pt_indices)` ¶

`__snap_float(val, res)` ¶

`val` ¶

`res` ¶

`__unique_points()` ¶

`a` ¶

`expand_around_existing_points(num_pts, reso)` ¶

`num_pts` ¶

`res` ¶

`filter_isolated_points_until_no_change(reso, number_of_neighbors)` ¶

`res` ¶

`number_of_neighbors` ¶

`remove_all_points_close_to_other_points(other_points, dist_cutoff, config)` ¶

`other_points` ¶

`dist_cutoff` ¶

`config` ¶

`remove_points_outside_convex_hull(hull, config)` ¶

`hull` ¶

`config` ¶

`separate_out_pockets()` ¶

`to_pdb(let='X')` ¶

`let` ¶

`RectangularRegion(center, lengths)` ¶

`center` ¶

`lengths` ¶

`center = np.array(center)` ¶

`lengths = np.array(lengths)` ¶

`str()` ¶

`get_points(res)` ¶

`res` ¶

`SphericalRegion(center, radius)` ¶

`center` ¶

`radius` ¶

`center = np.array(center)` ¶

`radius = radius` ¶

`str()` ¶

`get_points(res)` ¶

`res` ¶

`collect_regions(spherical_configs, rectangular_configs)` ¶

`spherical_configs` ¶

`rectangular_configs` ¶