NAME

       plipcmd - Protein-Ligand Interaction Profiler (PLIP)

DESCRIPTION

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

              [-o  OUTPATH  |  -O] [--rawstring] [-v] [-q] [-s] [-p] [-x] [-t] [-y] [--maxthreads
              MAXTHREADS]    [--breakcomposite]    [--altlocation]    [--nofix]     [--nofixfile]
              [--nopdbcanmap]   [--dnareceptor]   [--name  OUTPUTFILENAME]  [--peptides  PEPTIDES
              [PEPTIDES ...] | --intra INTRA] [--keepmod] [--nohydro] [--model MODEL]

       The Protein-Ligand Interaction Profiler (PLIP) Version 2.2.2 is a command-line based  tool
       to  analyze  interactions in a protein-ligand complex. If you are using PLIP in your work,
       please cite: Adasme,M. et al.  PLIP  2021:  expanding  the  scope  of  the  protein-ligand
       interaction  profiler  to  DNA  and  RNA.  Nucl.   Acids Res. (05 May 2021), gkab294. doi:
       10.1093/nar/gkab294 Supported and maintained by: PharmAI GmbH (2020-2021) - www.pharm.ai -
       hello@pharm.ai

   optional arguments:
       -h, --help
              show this help message and exit

       -f INPUT [INPUT ...], --file INPUT [INPUT ...]
              Set input file, '-' reads from stdin

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

       -o OUTPATH, --out OUTPATH

       -O, --stdout
              Write to stdout instead of file

       --rawstring
              Use Python raw strings for stdin

       -v, --verbose
              Turn on verbose mode

       -q, --quiet
              Turn on quiet mode

       -s, --silent
              Turn on silent 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 with covalent bonds but treat them as single ligands
              for the analysis.

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

       --nofix
              Turns off fixing of PDB files.

       --nofixfile
              Turns off writing files for fixed PDB files.

       --nopdbcanmap
              Turns off calculation of mapping between canonical and PDB atom order for ligands.

       --dnareceptor
              Treat  nucleic  acids  as part of the receptor structure (together with any present
              protein) instead of as a ligand.

       --name OUTPUTFILENAME
              Set a filename for the report TXT and XML files. Will  only  work  when  processing
              single structures.

       --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

       --nohydro
              Do not add polar hydrogens in case your structure already contains hydrogens.

       --model MODEL
              Model number to be used for multi-model structures.