PLIPCMD(1)

💖 PLIPCMD 💖

okay bestie, welcome to the plipcmd glow-up — section 1 of the User Commands manual, the Protein-Ligand Interaction Profiler, aka the tool that looks at your protein-ligand complex and tells you exactly which atoms are being cute with each other. no cap.

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✨ NAME ✨

plipcmd — Protein-Ligand Interaction Profiler (PLIP) 🌸

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🦋 DESCRIPTION 🦋

so the actual invocation vibe is this, and yes it's a whole mouthful, we love her for it:

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 🫶

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🎀 options 🎀

the full menu, bestie, every single one, no skips:

• -h, --help — show this help message and exit 🙈
• -i, --input PDBID [PDBID ...]
• -f, --file INPUT [INPUT ...] — Set input file, '-' reads from stdin
• -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.

💀 heads up bestie: -i, --input and -o, --out got no description in the original, so I'm not gonna invent one. they're just there, being mysterious, main character energy. 👑

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okay that's the whole page, you ate that 🍓 this was plipcmd version 2.4.0+dfsg-4, dated April 2025, and that's on periodt. 💜✨