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