plipcmd - Protein-Ligand Interaction Profiler (PLIP)
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
- -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.