PLIPCMD

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.