oracular (1) plipcmd.1.gz

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 2.3.0 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 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.