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.

$ pyKVFinder
Usage: pyKVFinder [-h] [-v] [--version] [-b <str>] [-O <str>]
                  [--nthreads <int>] [-d <str>] [-s <float>] [-i <float>]
                  [-o <float>] [-V <float>] [-R <float>] [-S <str>]
                  [--ignore_backbone] [-D] [--plot_frequencies]
                  [--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle,
                  MoonFleming, RadzickaWolfenden, WimleyWhite, ZhaoLondon, <.toml>}]]
                  [-B <.toml>] [-L (<.pdb> | <.xyz>)] [--ligand_cutoff <float>]
                  (<.pdb> | <.xyz>)

Positional arguments

The positional arguments are:

(<.pdb> | <.xyz>): A path to a target PDB or XYZ file.
```
$ pyKVFinder <.pdb>
```

Optional arguments

The optional arguments are:

-h or --help: Show help message.
```
$ pyKVFinder -h
$ pyKVFinder --help
```
--version: Display pyKVFinder version.
```
$ pyKVFinder --version
```
-v or --verbose: Print extra information to standard output.
```
$ pyKVFinder <.pdb> --verbose
```
Default:

False
-b <str> or --base_name <str>: A prefix for output files.
```
$ pyKVFinder <.pdb> -b <str>
$ pyKVFinder <.pdb> --base_name <str>
```
Default:

Prefix of target PDB file (<.pdb>)
-O <str> or --output_directory <str>: A path to a directory for output files.
```
$ pyKVFinder <.pdb> -O <str>
$ pyKVFinder <.pdb> --output_directory <str>
```
Default:

Current working directory
--nthreads <int>: Number of threads to apply in parallel routines.
```
$ pyKVFinder <.pdb> --nthreads <int>
```
Default:

os.cpu_count() - 1

Detection and characterization

The arguments for adjusting biomolecular detection are:

-d <str> or --dictionary <str>: A path to a van der Waals radii file (see template).
```
$ pyKVFinder <.pdb> -d <str>
$ pyKVFinder <.pdb> --dictionary <str>
```
Default:

vdw.dat

-s <float> or --step <float>: Grid spacing (A).

$ pyKVFinder <.pdb> -s <float>
$ pyKVFinder <.pdb> --step <float>

Default:: 0.6

-i <float> or --probe_in <float>: Probe In size (A).

$ pyKVFinder <.pdb> -i <float>
$ pyKVFinder <.pdb> --probe_in <float>

Default:: 1.4

-o <float> or --probe_out <float>: Probe Out size (A).

$ pyKVFinder <.pdb> -o <float>
$ pyKVFinder <.pdb> --probe_out <float>

Default:: 4.0

-V <float> or --volume_cutoff <float>: Cavities volume filter (A3).

$ pyKVFinder <.pdb> -V <float>
$ pyKVFinder <.pdb> --volume_cutoff <float>

Default:: 5.0

-R <float> or --removal_distance <float>: Length to be removed from the cavity-bulk frontier (A).
```
$ pyKVFinder <.pdb> -R <float>
$ pyKVFinder <.pdb> --removal_distance <float>
```
Default:

2.4
-S <str> or --surface <str>: A surface representation. Options are: SES and SAS. SES specifies solvent excluded surface and SAS specifies solvent accessible surface.
```
$ pyKVFinder <.pdb> -S <str>
$ pyKVFinder <.pdb> --surface <str>
```
Default:

SES
--ignore_backbone: Ignore backbone contacts to cavity when defining interface residues.
```
$ 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.
```
$ 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.
```
$ 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.
```
$ 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.
```
$ 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).
```
$ 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]).
```
$ 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.
```
$ pyKVFinder <.pdb> -L <.pdb>
$ pyKVFinder <.pdb> --ligand <.pdb>
```
Default:

None
--ligand_cutoff <float>: A radius value to limit a space around the defined ligand.
```
$ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff <float>
```
Default:

5.0