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]  [--residues  RESIDUES  [RESIDUES ...]]
              [--keepmod] [--nohydro] [--model MODEL] [--chains CHAINS]

       The Protein-Ligand Interaction Profiler (PLIP) Version 2.4.0 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

   options:
       -h, --help
              show this help message and exit

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

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

       -o, --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, --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.

       --residues RESIDUES [RESIDUES ...]
              Allows  to  specify  which  residues of the chain(s) should be considered as peptide ligands. Give
              single residues (separated with comma) or ranges (with dash) or both, for several chains  separate
              selections with one space

       --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.

       --chains CHAINS
              Specify  chains  as receptor/ligand groups, e.g., '[['A'], ['B']]'. Use format [['A'], ['B', 'C']]
              to define A as receptor, and B, C as ligands.

plipcmd 2.4.0+dfsg-2                              January 2025                                        PLIPCMD(1)