.. raw:: html
Command-line interface
In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.
.. code-block:: bash
$ pyKVFinder
Usage: pyKVFinder [-h] [-v] [--version] [-b ] [-O ]
[--nthreads ] [-d ] [-s ] [-i ]
[-o ] [-V ] [-R ] [-S ]
[--ignore_backbone] [-D] [--plot_frequencies]
[--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle,
MoonFleming, RadzickaWolfenden, WimleyWhite, ZhaoLondon, <.toml>}]]
[-B <.toml>] [-L (<.pdb> | <.xyz>)] [--ligand_cutoff ]
(<.pdb> | <.xyz>)
Positional arguments
--------------------
The positional arguments are:
* ``(<.pdb> | <.xyz>)``: A path to a target PDB or XYZ file.
.. code-block:: bash
$ pyKVFinder <.pdb>
Optional arguments
------------------
The optional arguments are:
* ``-h`` or ``--help``: Show help message.
.. code-block:: bash
$ pyKVFinder -h
$ pyKVFinder --help
* ``--version``: Display pyKVFinder version.
.. code-block:: bash
$ pyKVFinder --version
* ``-v`` or ``--verbose``: Print extra information to standard output.
.. code-block:: bash
$ pyKVFinder <.pdb> --verbose
:Default: ``False``
* ``-b `` or ``--base_name ``: A prefix for output files.
.. code-block:: bash
$ pyKVFinder <.pdb> -b
$ pyKVFinder <.pdb> --base_name
:Default: Prefix of target PDB file (<.pdb>)
* ``-O `` or ``--output_directory ``: A path to a directory for output files.
.. code-block:: bash
$ pyKVFinder <.pdb> -O
$ pyKVFinder <.pdb> --output_directory
:Default: Current working directory
* ``--nthreads ``: Number of threads to apply in parallel routines.
.. code-block:: bash
$ pyKVFinder <.pdb> --nthreads
:Default: ``os.cpu_count() - 1``
Detection and characterization
******************************
The arguments for adjusting biomolecular detection are:
* ``-d `` or ``--dictionary ``: A path to a van der Waals radii file (see template).
.. code-block:: bash
$ pyKVFinder <.pdb> -d
$ pyKVFinder <.pdb> --dictionary
:Default: ``vdw.dat``
* ``-s `` or ``--step ``: Grid spacing (A).
.. code-block:: bash
$ pyKVFinder <.pdb> -s
$ pyKVFinder <.pdb> --step
:Default: ``0.6``
* ``-i `` or ``--probe_in ``: Probe In size (A).
.. code-block:: bash
$ pyKVFinder <.pdb> -i
$ pyKVFinder <.pdb> --probe_in
:Default: ``1.4``
* ``-o `` or ``--probe_out ``: Probe Out size (A).
.. code-block:: bash
$ pyKVFinder <.pdb> -o
$ pyKVFinder <.pdb> --probe_out
:Default: ``4.0``
* ``-V `` or ``--volume_cutoff ``: Cavities volume filter (A3).
.. code-block:: bash
$ pyKVFinder <.pdb> -V
$ pyKVFinder <.pdb> --volume_cutoff
:Default: ``5.0``
* ``-R `` or ``--removal_distance ``: Length to be removed from the cavity-bulk frontier (A).
.. code-block:: bash
$ pyKVFinder <.pdb> -R
$ pyKVFinder <.pdb> --removal_distance
:Default: ``2.4``
* ``-S `` or ``--surface ``: A surface representation. Options are: ``SES`` and ``SAS``. SES specifies solvent excluded surface and SAS specifies solvent accessible surface.
.. code-block:: bash
$ pyKVFinder <.pdb> -S
$ pyKVFinder <.pdb> --surface
:Default: ``SES``
* ``--ignore_backbone``: Ignore backbone contacts to cavity when defining interface residues.
.. code-block:: bash
$ pyKVFinder <.pdb> --ignore_backbone
:Default: ``None``
Extra characterization
**********************
The parameters for additional characterization are:
* ``--D or --depth``: Characterize the depth of the detected cavities. This mode includes depth of each cavity point as the B-factor in the cavity PDB file and maximum and average depth of the detected cavities in the results file.
.. code-block:: bash
$ pyKVFinder <.pdb> -D
$ pyKVFinder <.pdb> --depth
:Default: ``None``
* ``--plot_frequencies``: Plot bar charts of calculated frequencies (residues and classes of residues) of the detected cavities in a PDF file. The classes of residues are aliphatic apolar (R1), aromatic (R2), polar uncharged (R3), negatively charged (R4), positively charged (R5) and non-standard (RX) residues.
.. code-block:: bash
$ pyKVFinder <.pdb> --plot_frequencies
:Default: ``None``
* ``--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, WimleyWhite, ZhaoLondon, <.toml>}]``: Characterize the hydropathy of the detected cavities. This mode maps a target hydrophobicity scale as B-factor at surface points of the detected cavities. Also, it calculates the average hydropathy of each detected cavity. The constant hydrophobicity scale is EisenbergWeiss.
.. code-block:: bash
$ pyKVFinder <.pdb> --hydropathy
In addition, the user can define one of the built-in hydrophobicity scale. The built-in hydrophobicity scales are: EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite and ZhaoLondon.
.. code-block:: bash
$ pyKVFinder <.pdb> --hydropathy EisenbergWeiss
$ pyKVFinder <.pdb> --hydropathy HessaHeijne
$ pyKVFinder <.pdb> --hydropathy KyteDoolittle
$ pyKVFinder <.pdb> --hydropathy MoonFleming
$ pyKVFinder <.pdb> --hydropathy RadzickaWolfenden
$ pyKVFinder <.pdb> --hydropathy WimleyWhite
$ pyKVFinder <.pdb> --hydropathy ZhaoLondon
Further, the user can also define a custom hydrophobicity scale file via a TOML-formatted file (see template).
.. code-block:: bash
$ pyKVFinder <.pdb> --hydropathy <.toml>
:Default: ``None``
:Constant: ``EisenbergWeiss``
Box adjusment
*************
The box adjustment argument is:
* ``-B <.toml>`` or ``--box <.toml>``: A path to TOML-formatted file with box parameters (see template). Adjust the 3D grid based on a list of residues (["resnum", "chain"]) and a padding or a set of four vertices (p1: origin, p2: X-axis max, p3: Y-axis max, p4: Z-axis max) with xyz coordinates ([x, y, z]).
.. code-block:: bash
$ pyKVFinder <.pdb> -B <.toml>
$ pyKVFinder <.pdb> --box <.toml>
:Default: ``None``
Ligand adjustment
*****************
The ligand adjustment arguments are:
* ``-L (<.pdb> | <.xyz>)`` or ``--ligand (<.pdb> | <.xyz>)``: A path to a ligand PDB or XYZ file to limit the cavities within a radius (ligand_cutoff) around it.
.. code-block:: bash
$ pyKVFinder <.pdb> -L <.pdb>
$ pyKVFinder <.pdb> --ligand <.pdb>
:Default: ``None``
* ``--ligand_cutoff ``: A radius value to limit a space around the defined ligand.
.. code-block:: bash
$ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff
:Default: ``5.0``