aquaduct.geom.pocket module

get_spc(sp, window=None)[source]
Parameters

  • sp – Single path like object or Generic path.

  • window (tuple) – Optional frames window.

Return type

numpy.ndarray

Returns

Coordinates of path; to be used in pocket calculation.

find_minmax(spaths, pbar=None)[source]
Parameters

  • spaths (list) – List of single like path objects.

  • pbar – Optional progress object providing next() method.

Return type

2 element tuple of numpy.ndarray each of shape (3,)

Returns

Minimal and maximal boundaries of coordinates used in pocket calulations of spaths.

find_minmax_map(spaths, pbar=None, map_fun=None)[source]
Parameters

  • spaths (list) – List of single like path objects.

  • pbar – Optional progress object providing next() method.

Return type

2 element tuple of numpy.ndarray each of shape (3,)

Returns

Minimal and maximal boundaries of coordinates used in pocket calulations of spaths.

find_edges(spaths, grid_size=1.0, pbar=None, map_fun=None)[source]
Parameters

  • spaths (list) – List of single like path objects.

  • grid_size (float) – Size of grid cell in A.

  • pbar – Optional progress object providing next() method.

Return type

list of numpy.ndarrays

Returns

Edges of bins of grid spanning all submited paths.

distribution(spaths, grid_size=1.0, edges=None, window=None, pbar=None, map_fun=None)[source]
Parameters

  • spaths (list) – List of single like path objects.

  • grid_size (float) – Size of grid cell in A.

  • of numpy.ndarrays edges (list) – Edges of bins of grid spanning all submited paths.

  • window (tuple) – Optional frames window.

  • pbar – Optional progress object providing next() method.

System Message: WARNING/2 (/home/kara/Desktop/AQ/aqua-duct/src/aquaduct/geom/pocket.py:docstring of aquaduct.geom.pocket.distribution, line 6)

Field list ends without a blank line; unexpected unindent.

:rtype tuple of numpy.ndarrays :return: Coordinates of pocket and number of points.

outer_inner(H, threshold=None)[source]
Parameters

  • H (numpy.ndarray) – Pocket distribution.

  • threshold (float) – Percent value of max density which will be used to partition pocket into inner and outer.

Returns

Indices of outer and inner pocket.

Return type

tuple of numpy.ndarray

sphere_density_raw(trajs, mol_name, centers, radius, pool, window=None, pbar=None)[source]

Calculate density of sphere with specified radius and with center in each point.

Parameters

  • trajs (class:aquaduct.sandwich.ReaderTraj) – Collection of trajectory readers

  • mol_name (str) – Name of molecule which amount will be calculated around points.

  • radius (float) – Radius of selection for each point.

  • centers (Iterator) – Points of path

  • pool (Preconfigured Pool instance) – Preconfigured Pool instance

Returns

Density for each center.

Return type

numpy.ndarray