* Function: _area * --------------- * * Calculate area of cavities * * surface: surface points 3D grid * nx: x grid units * ny: y grid units *

Clean the results tab. This method is called before loading the results of pyKVFinder into PyMOL. It will clear the lists in the resu

Draw box in PyMOL interface. Parameters ---------- min_x : QDoubleSpinBox The minimum x value of the box

* Function: _export * ----------------- * * Export cavities to PDB file with depth as B-factor and hydropathy as Q-factor * * fn: cavity pdb file

Get the parameters from the GUI. This method is called when the user clicks the 'Run pyKVFinder' button in the GUI. It will return a

Gets 3D grid vertices based on a list of residues (name and chain) and a padding value. Parameters ---------- box : dict[str, list[fl

Load a molecule file into PyMOL. Parameters ---------- filename : str The path to the molecule file. pymolname : str

Extracts ATOM and HETATM information of PDB line. Parameters ---------- line : str A line of a valid PDB file vdw : Dict[str,

Reads xyz coordinates and labels of a cavities file into numpy.ndarray. Parameters ---------- cavity : Union[str, pathlib.Path] A

Restore the results tab to the default values. This method is called when the user clicks the 'Restore Defaults' button in the GUI.

Open a dialog to select a file. Callback for the "Browse ..." buttons. Parameters ---------- caption : str The caption for t

Define the 3D grid for the target molecule. Parameters ---------- padding : float, optional The length to add to

Show the selected cavities in Volume and Area lists. Surface cavity points are colored in red and remaining points are colored in blue.

Show the selected cavities colored by depth in Max Depth and Avg Depth lists. Parameters ---------- widget1 : QListWidget Th

Set the default values for the widgets in the GUI. This method is called when the plugin is started.

* Function: _volume * ----------------- * * Calculate volume of cavities * * cavities: cavities 3D grid * nx: x grid units * ny: y grid units

Exports cavities and characterization to PDB-formatted files, writes file paths and characterization to a TOML-formatted file, and opt

* Function: filter * ---------------- * * Adjust cavities to a search box * * grid: cavities 3D grid * nx: x grid units * ny: y grid units * n

* Function: filter_noise * ---------------------- * * Removes cavities points (1) surrounded by biomolecule (0) or medium (-1) * points * * grid

* Function: get_hydrophobicity_value * ---------------------------------- * * Get hydrophobicity scale value for a target residue name * * resnam

Get _grid attribute.

* Function: remove_cavity * ----------------------- * * Untag cavity that does not reach volume cutoff * * grid: cavities 3D grid * nx: x grid u

Run pyKVFinder with the current parameters. This method is called when the user clicks the 'Run pyKVFinder' button in the GUI. After

* Function: subtract * ------------------ * * Compare Probe In and Probe Out 3D grids to define biomolecular cavities * * PI: Probe In 3D grid *

* Function: _constitutional * ------------------------- * * Constitutional characterization (interface residues) of the detected cavities * * cav

Create a box file (box.<basename>.pdb) with the parameters from the GUI. Returns ------- dict The box pa

Delete box object, disable 'Delete Box' and 'Redraw Box' buttons and enable 'Draw Box' button. Parameters ----------

* Function: _depth * ---------------- * * Characterization of the depth of the detected cavities. Calculate depth per * cavity point and maximum a

* Function: _detect * ----------------- * * Detect and cluster cavities * * PI: 3D grid * size: number of voxels in 3D grid * nx: x grid units

* Function: _detect_ladj * ---------------------- * * Detect and cluster cavities with ligand adjustment * * PI: 3D grid * size: number of voxel

* Function: _export_openings * -------------------------- * * Export openings to PDB file * * fn: openings PDB filename * openings: openings 3D

* Function: _fill_cavity * ---------------------- * * Insert cavities inside a 3D grid * * grid: 3D grid * nx: x grid units * ny: y grid units

* Function: _filter_pdb * --------------------- * * Select pdb atoms inside the 3D grid (box adjustment mode) * * nx: x grid units * ny: y grid

Display help information about the box operations.

* Function: _hydropathy * --------------------- * * Hydropathy characterization of the detected cavities. Map a hydrophobicity * scale per surface

Initialize the graphical user interface of the plugin.

Load a area file into PyMOL. Parameters ---------- results : dict The results from the pyKVFinder calculation. widget :

Load a avg_depth file into PyMOL. Parameters ---------- results : dict The results from the pyKVFinder calculation. widg

Load a avg_hydropathy file into PyMOL. Parameters ---------- results : dict The results from the pyKVFinder calculation.

Load a cavity file into PyMOL. Parameters ---------- filename : str The path to the cavity file. pymolname : str

Load the file information into the results tab. This method is called after running pyKVFinder. It will load the file information int

Load a max_depth file into PyMOL. Parameters ---------- results : dict The results from the pyKVFinder calculation. widg

Load a residues file into PyMOL. Parameters ---------- results : dict The results from the pyKVFinder calculation. widge

Load the results of pyKVFinder into PyMOL. This method is called after running pyKVFinder. It will load the cavities and the results

Load a volume file into PyMOL. Parameters ---------- results : dict The results from the pyKVFinder calculation. widget

* Function: _openings * ------------------- * * Cavity openings characterization of the detected cavities * * openings: openings 3D grid * size:

* Function: _openings_in_cavities * ------------------------------- * * Cluster consecutive cavity points together * * o2c: empty array with open

Prepare the plugin to run pyKVFinder. This method is called when the user clicks the 'Run pyKVFinder' button in the GUI. It will chec

Processes arrays of openings' areas. Parameters ---------- raw_openings : numpy.ndarray A numpy.ndarray of openings' areas. o

Redraw box in PyMOL interface. If selection is provided, the box will be drawn around the selected residues. If no selection is provi

Open a dialog to select the base directory for the output files. Callback |for the "Browse ..." button.

Create box coordinates, enable 'Delete Box' and 'Redraw Box' buttons and call _draw_box function. Parameters -------

Show the selected cavities colored by hydropathy in Avg Hydropathy list. Parameters ---------- results : dict The results fr

Show the residues for the selected cavity. Parameters ---------- results : dict The results from the pyKVFinder calculation.

* Function: _spatial * ----------------- * * Spatial characterization (volume and area) of the detected cavities * * cavities: cavities 3D grid

Writes parameters used in cavity detection and characterization of pyKVFinder to TOML-formatted file. Parameters ---------- args : ar

* Function: adjust * ---------------- * * Adjust cavities to a radius around a ligand atoms * * grid: cavities 3D grid * nx: x grid units * ny:

Defines pyKVFinder argument parser. Parameters ---------- None Returns ------- parser : argparse.ArgumentParser pyKV

* Function: check_protein_neighbours * ---------------------------------- * * Checks if a cavity point on the grid is next to a protein point (0 or

* Function: check_unclustered_neighbours * -------------------------------------- * * Checks if a cavity point on the grid is next to a unclustered

* Function: check_voxel_class * --------------------------- * * Identify voxel class of surface voxel and return class weight * * surface: surfac

* Function: create * ---------------- * * Create a res node * * pos: atom index in xyzr array (coordinates and radii of pdb) * * returns: res n

* Function: define_boundary_points * -------------------------------- * * Identify cavity-bulk boundary points based on neighboring points * * ca

* Function: define_surface_points * ------------------------------- * * Identify surface points based on neighboring points * * cavities: cavitie