### Version Option Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Example of using the --version flag to display the pyKVFinder version.

```bash
$ pyKVFinder --version
```

--------------------------------

### Help Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Examples of using the -h or --help flags to display the help message.

```bash
$ pyKVFinder -h
```

```bash
$ pyKVFinder --help
```

--------------------------------

### Output Directory Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Examples of using the -O or --output_directory flags to specify the output directory.

```bash
$ pyKVFinder (<.pdb> | <.xyz>) -O <str>
```

```bash
$ pyKVFinder (<.pdb> | <.xyz>) --output_directory <str>
```

--------------------------------

### Grid Spacing Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Examples of using the -s or --step flags to set the grid spacing in Angstroms.

```bash
$ pyKVFinder (<.pdb> | <.xyz>) -s <float>
```

```bash
$ pyKVFinder (<.pdb> | <.xyz>) --step <float>
```

--------------------------------

### Cavity Detection Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/package/tutorial/index.rst.txt

Example of detecting cavities using pyKVFinder.detect and displaying the number of cavities and the cavity grid.

```python
>>> ncav_la, cavities_la = pyKVFinder.detect(atomic, vertices, latomic=latomic, ligand_cutoff=ligand_cutoff)
>>> ncav_la
2
>>> cavities_la
array([[[-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1],
        ...,
        [-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1]],

       ...,

       [[-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1],
        ...,
        [-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1],
        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
```

--------------------------------

### Base Name Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Examples of using the -b or --base_name flags to specify a prefix for output files.

```bash
$ pyKVFinder (<.pdb> | <.xyz>) -b <str>
```

```bash
$ pyKVFinder (<.pdb> | <.xyz>) --base_name <str>
```

--------------------------------

### Summary installation commands

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/pymol/index.rst.txt

A consolidated set of commands for setting up the environment, installing PyMOL, pyKVFinder, and launching PyMOL.

```bash
conda create -n pymol python=3.10
conda activate pymol
conda install -c conda-forge -c schrodinger pymol-bundle
pip install pyKVFinder
pymol
```

--------------------------------

### Depth Characterization Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Examples of using the -D or --depth flags to characterize the depth of detected cavities.

```bash
$ pyKVFinder (<.pdb> | <.xyz>) -D
```

```bash
$ pyKVFinder (<.pdb> | <.xyz>) --depth
```

--------------------------------

### Probe In Size Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/cli/index.rst.txt

Examples of using the -i or --probe_in flags to set the Probe In size in Angstroms.

```bash
$ pyKVFinder (<.pdb> | <.xyz>) -i <float>
```

```bash
$ pyKVFinder (<.pdb> | <.xyz>) --probe_in <float>
```

--------------------------------

### Build Documentation

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/INSTRUCTIONS.rst

Command to build the pyKVFinder documentation as a GitHub page.

```bash
make html
```

--------------------------------

### Example Usage

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/package/api_reference/get_vertices_from_file.html

Demonstrates how to read a box configuration file and use it with pyKVFinder to get grid vertices and atomic information.

```python
>>> import os
>>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
>>> with open(fn, 'r') as f:
...     print(f.read())
[box]
p1 = [3.11, 7.34, 1.59]
p2 = [11.51, 7.34, 1.59]
p3 = [3.11, 10.74, 1.59]
p4 = [3.11, 7.34, 6.19]

>>> from pyKVFinder import get_vertices_from_file
>>> vertices, atomic = pyKVFinder.get_vertices_from_file(fn, atomic)
```

--------------------------------

### Example Usage

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/source/package/api_reference/get_vertices.md

With the atomic data read with `read_pdb` or `read_xyz`, we can get the coordinates of 3D grid vertices (origin, X-axis, Y-axis, Z-axis):

```python
from pyKVFinder import get_vertices
vertices = get_vertices(atomic)
vertices
array([[-19.911, -32.125, -30.806],
    [ 40.188, -32.125, -30.806],
    [-19.911,  43.446, -30.806],
    [-19.911, -32.125,  27.352]])
```

--------------------------------

### Standard and Full Workflows with Box Configuration

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/package/tutorial/index.rst.txt

Demonstrates how to run the standard and full pyKVFinder workflows using a custom box configuration file.

```python
>>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
>>> # Box configuration filepath
>>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
>>> # Standard workflow
>>> results = pyKVFinder.run_workflow(pdb, box=fn)
>>> # Full workflow
>>> results = pyKVFinder.run_workflow(pdb, box=fn, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
```

--------------------------------

### Get vertices from atomic data

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/package/api_reference/get_vertices.html

Example of how to use the get_vertices function with atomic data read from a PDB or XYZ file.

```python
from pyKVFinder import get_vertices
vertices = get_vertices(atomic)
print(vertices)
```

--------------------------------

### Example Usage

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_modules/pyKVFinder/grid/geometry.html

Demonstrates how to define a box configuration file and use it with pyKVFinder to get grid vertices and select atoms within the custom box.

```python
import tomlkit
from pyKVFinder._pyKVFinder import _filter_pdb

# Check arguments types
if type(fn) not in [str, pathlib.Path]:
    raise TypeError("`fn` must be a string or a pathlib.Path.")
if type(atomic) not in [numpy.ndarray, list]:
    raise TypeError("`atomic` must be a list or a numpy.ndarray.")
elif len(numpy.asarray(atomic).shape) != 2:
    raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
elif numpy.asarray(atomic).shape[1] != 8:
    raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
if type(step) not in [float, int]:
    raise TypeError("`step` must be a positive real number.")
elif step <= 0.0:
    raise ValueError("`step` must be a positive real number.")
if type(probe_in) not in [float, int]:
    raise TypeError("`probe_in` must be a non-negative real number.")
elif probe_in < 0.0:
    raise ValueError("`probe_in` must be a non-negative real number.")
if type(probe_out) not in [float, int]:
    raise TypeError("`probe_out` must be a non-negative real number.")
elif probe_out < 0.0:
    raise ValueError("`probe_out` must be a non-negative real number.")
```

--------------------------------

### Standard Workflow Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/source/package/tutorial/index.md

This snippet demonstrates a standard workflow for analyzing protein data, likely involving frequency calculations.

```python
>>> results.frequencies
{'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
```

--------------------------------

### Full Workflow Execution

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/package/tutorial/index.rst.txt

Demonstrates running the full cavity detection workflow with characterizations for depth and hydropathy.

```python
>>> results = pyKVFinder.run_workflow(pdb, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
```

--------------------------------

### get_vertices function

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_modules/pyKVFinder/grid/geometry.html

Gets 3D grid vertices. This function calculates the origin and axes for a 3D grid based on atomic data, probe size, and step size. It includes detailed parameter descriptions, return values, potential exceptions, and a usage example.

```python
import os
import pathlib

import numpy

[["docs"]](../../../package/api_reference/get_vertices.html#pyKVFinder.get_vertices)
def get_vertices(
    atomic: numpy.ndarray | list[list[str | float | int]],
    probe_out: float | int = 4.0,
    step: float | int = 0.6,
) -> numpy.ndarray:
    """Gets 3D grid vertices.

    Parameters
    ----------
    atomic : numpy.ndarray | list[list[str | float | int]]
        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
        and radius) for each atom.
    probe_out : float | int, optional
        Probe Out size (A), by default 4.0.
    step : float | int, optional
        Grid spacing (A), by default 0.6.

    Returns
    -------
    vertices : numpy.ndarray
        A numpy.ndarray with xyz vertices coordinates
        (origin, X-axis, Y-axis, Z-axis).

    Raises
    ------
    TypeError
        `atomic` must be a list or a numpy.ndarray.
    ValueError
        `atomic` has incorrect shape. It must be (n, 8).
    TypeError
        `probe_out` must be a non-negative real number.
    ValueError
        `probe_out` must be a non-negative real number.
    TypeError
        `step` must be a positive real number.
    ValueError
        `step` must be a positive real number.

    See Also
    --------
    read_pdb
    read_xyz
    detect
    constitutional
    hydropathy
    export

    Example
    -------
    With the atomic data read with `read_pdb` or `read_xyz`, we can get the coordinates of 3D grid vertices (origin, X-axis, Y-axis, Z-axis):

    >>> from pyKVFinder import get_vertices
    >>> vertices = get_vertices(atomic)
    >>> vertices
    array([[-19.911, -32.125, -30.806],
        [ 40.188, -32.125, -30.806],
        [-19.911,  43.446, -30.806],
        [-19.911, -32.125,  27.352]])
    """
    # Check arguments types
    if type(atomic) not in [numpy.ndarray, list]:
        raise TypeError("`atomic` must be a list or a numpy.ndarray.")
    elif len(numpy.asarray(atomic).shape) != 2:
        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
    elif numpy.asarray(atomic).shape[1] != 8:
        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
    if type(probe_out) not in [int, float, numpy.float64]:
        raise TypeError("`probe_out` must be a non-negative real number.")
    elif probe_out < 0.0:
        raise ValueError("`probe_out` must be a non-negative real number.")
    if type(step) not in [int, float, numpy.float64]:
        raise TypeError("`step` must be a positive real number.")
    elif step <= 0.0:
        raise ValueError("`step` must be a positive real number.")

    # Convert atomic type
    if isinstance(atomic, list):
        atomic = numpy.asarray(atomic)

    # Extract xyzr from atomic
    xyzr = atomic[:, 4:].astype(numpy.float64)

    # Prepare vertices
    P1 = numpy.min(xyzr[:, 0:3], axis=0) - probe_out - step
    xmax, ymax, zmax = numpy.max(xyzr[:, 0:3], axis=0) + probe_out + step
    P2 = numpy.array([xmax, P1[1], P1[2]])
    P3 = numpy.array([P1[0], ymax, P1[2]])
    P4 = numpy.array([P1[0], P1[1], zmax])

    # Pack vertices
    vertices = numpy.array([P1, P2, P3, P4])

    return vertices
```

--------------------------------

### Frequencies Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_modules/pyKVFinder/utils.html

An example of the frequencies data structure.

```python
frequencies = {
    'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']],
    'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']],
    'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']],
    'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']],
    'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']],
    'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']],
    'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']],
    'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']],
    'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']],
    'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']],
    'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']],
    'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']],
    'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']],
    'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']],
    'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']],
    'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']],
    'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']],
    'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]
}

```

--------------------------------

### Help Option Examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/plugins/cli/index.html

Examples of how to display the help message using the -h or --help flags.

```bash
$ pyKVFinder \-h
$ pyKVFinder \--help
```

--------------------------------

### Install latest release

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/README.md

Installs the latest release of pyKVFinder from PyPI.

```bash
pip install pyKVFinder
```

--------------------------------

### Install Python Modules

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/plugins/PyMOL-pyKVFinder-Tools/INSTALLATION.md

Installs the necessary Python modules (pyKVFinder, toml, pyqt5) required for the plugin, specifically for PyMOL v3 which uses Python 3.

```bash
# PyMOL v3 (python 3)
$ pip3 install pyKVFinder toml pyqt5
```

--------------------------------

### Install developmental version

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/README.md

Installs the latest developmental version of pyKVFinder from GitHub.

```bash
git clone https://github.com/LBC-LNBio/pyKVFinder.git
pip install -e pyKVFinder
```

--------------------------------

### Calculate Frequencies Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_modules/pyKVFinder/utils.html

Example of how to calculate residue and class frequencies for detected cavities.

```python
from pyKVFinder import calculate_frequencies
residues
{'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']]}
frequencies = calculate_frequencies(residues)
frequencies
```

--------------------------------

### Standard Workflow Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/package/api_reference/run_workflow.html

This example demonstrates the standard workflow for cavity detection using pyKVFinder, including spatial and constitutional characterization.

```python
import os
import pyKVFinder
pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
results = pyKVFinder.run_workflow(pdb)
print(results)
print(results.cavities)
print(results.surface)
print(results.ncav)
print(results.volume)
print(results.area)
print(results.residues)
```

--------------------------------

### Loading data from target structure

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/source/package/tutorial/index.md

Example of loading a PDB file using `pyKVFinder.read_pdb` and the resulting NumPy array.

```python
>>> import os
>>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
>>> atomic = pyKVFinder.read_pdb(pdb)
>>> atomic
array([['13', 'E', 'GLU', ..., '-15.642', '-14.858', '1.824'],
     ['13', 'E', 'GLU', ..., '-14.62', '-15.897', '1.908'],
     ['13', 'E', 'GLU', ..., '-13.357', '-15.508', '1.908'],
     ...,
     ['350', 'E', 'PHE', ..., '18.878', '-9.885', '1.908'],
     ['350', 'E', 'PHE', ..., '17.624', '-9.558', '1.908'],
     ['350', 'E', 'PHE', ..., '19.234', '-13.442', '1.69']],
    dtype='<U32')
```

--------------------------------

### Install PyMOL Open-Source

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/pymol/index.rst.txt

Command to install the open-source version of PyMOL using conda.

```bash
conda install -c conda-forge pymol-open-source
```

--------------------------------

### Reading a PDB file for ligand adjustment

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/source/package/tutorial/index.md

This snippet demonstrates how to read a PDB file to obtain ligand atomic information, which can be used for ligand-guided cavity detection.

```python
>>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
>>> latomic = pyKVFinder.read_pdb(ligand)
>>> latomic
array([['351', 'E', 'ADN', "C5'", '11.087', '9.79', '2.052', '1.66'],
     ['351', 'E', 'ADN', "O5'", '11.545', '8.52', '1.545', '1.69'],
     ['351', 'E', 'ADN', "C4'", '10.688', '9.68', '3.523', '1.66'],
     ['351', 'E', 'ADN', "O4'", '9.714', '10.725', '3.81', '1.69'],
     ['351', 'E', 'ADN', "C3'", '9.973', '8.374', '3.903', '1.66'],
     ['351', 'E', 'ADN', "O3'", '10.879', '7.361', '4.304', '1.69'],
     ['351', 'E', 'ADN', "C2'", '9.115', '8.82', '5.059', '1.66'],
     ['351', 'E', 'ADN', "O2'", '9.887', '9.034', '6.232', '1.69'],
     ['351', 'E', 'ADN', "C1'", '8.625', '10.16', '4.5', '1.66'],
     ['351', 'E', 'ADN', 'N1', '3.499', '10.104', '4.402', '1.97'],
     ['351', 'E', 'ADN', 'C2', '4.376', '10.259', '5.387', '1.66'],
     ['351', 'E', 'ADN', 'N3', '5.705', '10.249', '5.351', '1.97'],
     ['351', 'E', 'ADN', 'C4', '6.136', '10.087', '4.094', '1.66'],
     ['351', 'E', 'ADN', 'C5', '5.353', '9.952', '2.974', '1.66'],
     ['351', 'E', 'ADN', 'C6', '3.957', '9.957', '3.146', '1.66'],
     ['351', 'E', 'ADN', 'N6', '3.083', '9.826', '2.142', '1.97'],
     ['351', 'E', 'ADN', 'N7', '6.146', '9.791', '1.843', '1.97'],
     ['351', 'E', 'ADN', 'C8', '7.374', '9.872', '2.291', '1.66'],
     ['351', 'E', 'ADN', 'N9', '7.444', '10.056', '3.646', '1.97']],
    dtype='<U32')
```

--------------------------------

### Install PyMOL v2.6

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/pymol/index.rst.txt

Command to install PyMOL version 2.6 using conda.

```bash
conda install -c conda-forge -c schrodinger pymol-bundle=2.6
```

--------------------------------

### Ligand adjustment command examples

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/plugins/cli/index.html

Examples demonstrating how to use the -L or --ligand and --ligand_cutoff arguments.

```bash
pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>)
```

```bash
pyKVFinder (<.pdb> | <.xyz>) --ligand (<.pdb> | <.xyz>)
```

```bash
pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>) --ligand_cutoff <float>
```

--------------------------------

### Install PyMOL v3.0

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/plugins/pymol/index.rst.txt

Command to install PyMOL version 3.0 using conda.

```bash
conda install -c conda-forge -c schrodinger pymol-bundle
```

--------------------------------

### Cavity Detection Parameters

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/package/tutorial/index.html

Example of setting default parameters for cavity detection.

```python
step = 0.6
probe_in = 1.4
probe_out = 4.0
removal_distance = 2.4
volume_cutoff = 5.0
surface = 'SES'
```

--------------------------------

### Constitutional Characterization Example

Source: https://github.com/lbc-lnbio/pykvfinder/blob/master/docs/_sources/package/tutorial/index.rst.txt

Example of performing constitutional characterization using pyKVFinder.constitutional to identify interface residues.

```python
>>> # Default ignore backbone contacts flag (ignore_backbone): False
>>> ignore_backbone = False
>>> residues = pyKVFinder.constitutional(cavities, atomic, vertices, step=step, probe_in=probe_in, ignore_backbone=ignore_backbone)
>>> residues
```