DESCRIPTION

usage: PLIP [-h] (-f INPUT [INPUT ...] | -i PDBID [PDBID ...]) [-o OUTPATH]

[-v] [-p] [-x] [-t] [-y] [--maxthreads MAXTHREADS] [--breakcomposite] [--altlocation] [--debug] [--nofix]

Protein-Ligand Interaction Profiler (PLIP) v1.3.1 is a command-line based tool to analyze interactions in a protein-ligand complex. If you are using PLIP in your work, please cite: Salentin,S. et al. PLIP: fully automated proteinligand interaction profiler. Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315

optional arguments:

-h, --help

show this help message and exit

-f INPUT [INPUT ...], --file INPUT [INPUT ...]

-i PDBID [PDBID ...], --input PDBID [PDBID ...]

-o OUTPATH, --out OUTPATH

-v, --verbose

Set verbose mode

-p, --pics

Additional pictures

-x, --xml

Generate report file in XML format

-t, --txt

Generate report file in TXT (RST) format

-y, --pymol

Additional PyMOL session files

--maxthreads MAXTHREADS

Set maximum number of main threads (number of binding sites processed simultaneously).If not set, PLIP uses all available CPUs if possible.

--breakcomposite

Don't combine ligand fragments into with covalent bonds but treat them as single ligandsfot the analysis.

--altlocation

Also consider alternate locations for atoms (e.g. alternate conformations).

--debug

Turn on DEBUG mode with extended log.

--nofix

Turns off fixing of PDB files.