Provided by: plip_1.3.5+dfsg-1_all 
NAME
plipcmd - Protein-Ligand Interaction Profiler (PLIP)
DESCRIPTION
usage: PLIP [-h] (-f INPUT [INPUT ...] | -i PDBID [PDBID ...]) [-o OUTPATH]
[-v] [-p] [-x] [-t] [-y] [--maxthreads MAXTHREADS] [--breakcomposite] [--altlocation] [--debug]
[--nofix] [--dnareceptor] [--peptides PEPTIDES [PEPTIDES ...] | --intra INTRA] [--keepmod]
Protein-Ligand Interaction Profiler (PLIP) v1.3.4 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.
--dnareceptor
Uses the DNA instead of the protein as a receptor for interactions.
--peptides PEPTIDES [PEPTIDES ...], --inter PEPTIDES [PEPTIDES ...]
Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts
--intra INTRA
Allows to define one chain to analyze intra-chain contacts.
--keepmod
Keep modified residues as ligands