Gets sine and cossine of the grid rotation angles from a list of vertices coordinates. Parameters ---------- vertices : numpy.ndarray

Detects biomolecular cavities. Cavity points that belongs to the same cavity are assigned with an integer in the grid. Parameters --

Reads PDB file into numpy.ndarrays. Parameters ---------- fn : Union[str, pathlib.Path] A path to PDB file. vdw : Dict[str, D

Export cavitiy (H) and surface (HA) points to PDB-formatted file with a variable (B; optional) in B-factor column, and hydropathy to PDB-forma

Read cavities and receptor inside a 3D grid. Parameters ---------- cavity : Union[str, pathlib.Path] A path to a PDB file of cavi

Writes file paths and cavity characterization to TOML-formatted file. Parameters ---------- fn : Union[str, pathlib.Path] A path

Reads van der Waals radii from .dat file. Parameters ---------- fn : Optional[Union[str, pathlib.Path]], optional A path to a van

Fill the 3D grid with the molecule as the van der Waals surface representation. Parameters ---------- step : float, optional

Get cavity label, eg 2, 3, and so on, based on the cavity name. Naming convention: - KAA-KZZ -> 2-677 - Kaa-Kzz -> 678-1353 Paramete

Select cavities in the 3D grid by cavity labels. Parameters ---------- cavities : numpy.ndarray Cavity points in the 3D grid (cav

Gets 3D grid vertices from box configuration file or parKVFinder parameters file, selects atoms inside custom 3D grid, define sine and cosine

Hydropathy characterization of the detected cavities. Map a target hydrophobicity scale per surface point and calculate average hydropathy of det

Gets dimensions of 3D grid from vertices. Parameters ---------- vertices : numpy.ndarray | list[list[float]] A numpy.ndarray or a

Constitutional characterization (interface residues) of the detected cavities. Parameters ---------- cavities : numpy.ndarray

Gets 3D grid vertices. Parameters ---------- atomic : numpy.ndarray | list[list[str | float | int]] A numpy array with atomic dat

Get cavity name, eg KAA, KAB, and so on, based on the index. Naming convention: - 0-675 -> KAA ... KZZ - 676-1351 -> Kaa ... Kzz P

Reads XYZ file into numpy.ndarrays. Parameters ---------- fn : Union[str, pathlib.Path] A path to XYZ file. vdw : Dict[str, D

Characterization of the depth of the detected cavities, including depth per cavity point and maximum and average depths of detected cavities.

Fill the 3D grid with the molecule as the van der Waals surface representation. Parameters ---------- step : float, optional

Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations. Returns -----

Processes arrays of volumes and areas. Parameters ---------- raw_volume : numpy.ndarray A numpy.ndarray of volumes. raw_area

Calculate frequencies of residues and class of residues (R1, R2, R3, R4 and R5) for detected cavities. Parameters ---------- residues

* Function: dgrid * --------------- * * Fill double grid with 0.0 * * grid: empty 3D grid * size: number of voxels * */

* Function: fill * -------------- * * Insert atoms with a probe addition inside a 3D grid * * grid: 3D grid * nx: x grid units * ny: y grid uni

* Function: igrid * --------------- * * Fill integer grid with 1 * * grid: empty 3D grid * size: number of voxels * */

* Function: ses * -------------- * * Adjust surface representation to Solvent Excluded Surface (SES) * * grid: 3D grid * nx: x grid units * ny:

Spatial characterization (volume and area) of the detected cavities. Parameters ---------- cavities : numpy.ndarray Cavity points

Automatically define the padding based on molecule coordinates, probe size, grid spacing and atom radii. Returns ------- padd

Export molecule points (H) to a PDB-formatted file. Parameters ---------- fn : Union[str, pathlib.Path], optional

* Function: cluster * ----------------- * * Cluster consecutive cavity points together * * grid: cavities 3D grid * nx: x grid units * ny: y gr

* Function: _fill_receptor * ------------------------ * * Insert atoms with a SES or SAS representation into a 3D grid * * grid: 3D grid * nx: x

Get opening label, eg 2, 3, and so on, based on the opening name. Naming convention: - OAA-OZZ -> 2-677 - Oaa-Ozz -> 678-1353 Parame

Get opening name, eg OAA, OAB, and so on, based on the index. Naming convention: - 0-675 -> OAA ... OZZ - 676-1351 -> Oaa ... Ozz

Gets 3D grid vertices from box coordinates. Parameters ---------- box : dict[str, list[float]] A dictionary with xyz coordinates

Gets xyz coordinates of 3D grid vertices. Parameters ---------- args (argparse.Namespace) Arguments passes by argparser CLI.

Processes arrays of maximum and average depths. Parameters ---------- raw_max_depth : numpy.ndarray A numpy.ndarray of maximum de

Processes array of average hydropathy. Parameters ---------- raw_avg_hydropathy : numpy.ndarray A numpy.ndarray of average hydrop

Processes raw list of residues from _constitutional to a list of residue information per cavity name. Parameters ---------- raw : lis

Refresh the list of objects in the given widget. Parameters ---------- widget : QComboBox The widget to refresh.

Show the cavity file colored by descriptors (default, depth, hydropathy). Parameters ---------- cavity_pdb : str The name of

Plot bar charts of calculated frequencies (residues and classes of residues) for each detected cavity in a target PDF file. Parameters --

Plot bar charts of frequencies (residues and classes of residues) in a PDF file. Parameters ---------- pdf : Union[st

Writes file paths and cavity characterization to TOML-formatted file Parameters ---------- fn : Union[str, pathlib.P

* Function: DFS * ------------- * * Recursive DFS algorithm * * grid: cavities 3D grid * nx: x grid units * ny: y grid units * nz: z grid unit