* Function: estimate_average_hydropathy * ------------------------------------- * * Calculate average hydropathy of detected cavities. * * avgh:

* Function: estimate_depth * ------------------------ * * Calculate depth of each cavity point and maximum and average depth of * cavities * * c

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

* Function: filter_boundary * ------------------------- * * Inspect cavities 3D grid and mark detected cavity-bulk boundary points * * cavities:

* Function: filter_openings * ------------------------- * * Inspect openings 3D grid and mark detected openings points * * openings: openings 3D

* Function: filter_surface * ------------------------ * * Inspect cavities 3D grid and mark detected surface points on a surface 3D * grid * * c

* Function: insert * ---------------- * * Insert res node in linked list * * res: pointer to linked list head * new: res node * */

* Function: interface * ------------------- * * Retrieve interface residues surrounding cavities * * cavities: cavities 3D grid * nx: x grid uni

* Function: project_hydropathy * --------------------------- * * Map a hydrophobicity scale per surface point of detected cavities. * * hydropath

* Function: remove_boundary * ------------------------- * * Inspect cavities 3D grid and unmark detected cavity-bulk boundary points * * cavities

* Function: remove_enclosed_cavity * -------------------------------- * * Cluster consecutive cavity points together * * openings: openings 3D gr

Initialize the Molecule object with molecule, radii, model, nthreads and verbose. Parameters ---------- molecule : Union[str,

Add an entry to the PyMOL "Plugin" menu. This function is called when the plugin is loaded by PyMOL.

Checks if x is a acceptable option for hydropathy argument. Parameters ---------- x : Any Option to be checked. Returns

Checks if x is a .pdb or .xyz extension and returns its abspath. Parameters ---------- x : Any Option to be checked. Returns

Checks if x is a float. Parameters ---------- x : Any Variable to be checked. Returns ------- x : float A va

Checks if x is in range (0.0, 2.0]. Parameters ---------- x : Any Grid spacing (A). Returns ------- x : float

Get the surface selection from the GUI. This method is called when the user selects a surface type in the GUI.

Get _atomic attribute.

* Function: cgrid * --------------- * * Fill char grid with '\0' * * grid: empty 3D grid * size: number of voxels * */

pyKVFinder Command Line Interface (CLI). Parameters ---------- None Returns ------- None Example ------- Usage:

Exit the plugin. This method is called when the user clicks the 'Exit' button in the GUI.

Get _dim attribute

Export opening points (H) to a PDB-formatted file. Parameters ---------- fn : str | pathlib.Path | None A path to PDB file for wr

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

Model the surface of the input. This method is called when the user clicks the 'Model Surface' button in the GUI. It will model the s

Get _molecule attribute.

Get grid units in X-axis.

Get grid units in Y-axis.

Get grid units in Z-axis.

Identify openings of the detected cavities and calculate their areas. Parameters ---------- cavities : numpy.ndarray Cavity point

Get origin of the 3D grid.

Get X-axis max of the 3D grid.

Get Y-axis max of the 3D grid.

Get Z-axis max of the 3D grid.

Get _padding attribute.

Preview the molecular surface in the 3D grid. Example ------- With the molecular surface modelled by ``Molecule.vdw()`` or ``

Get _probe attribute.

Get _radii attribute.

Get _representation attribute.

Restore the default values for the widgets in the GUI. This method is called when the user clicks the 'Restore Defaults' button in th

Get _rotation attribute.

Open our custom dialog. If it is already open, bring it to the front.

Detects and characterizes cavities (volume, area, depth [optional], hydropathy [optional] and interface residues). Parameters ----------