.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH PLIPCMD "1" "January 2024" "plipcmd 2.3.0+dfsg-2" "User Commands"
.SH NAME
plipcmd \- Protein-Ligand Interaction Profiler (PLIP)
.SH DESCRIPTION
usage: PLIP [\-h] (\fB\-f\fR INPUT [INPUT ...] | \fB\-i\fR PDBID [PDBID ...])
.IP
[\-o OUTPATH | \fB\-O]\fR [\-\-rawstring] [\-v] [\-q] [\-s] [\-p] [\-x] [\-t] [\-y]
[\-\-maxthreads MAXTHREADS] [\-\-breakcomposite] [\-\-altlocation]
[\-\-nofix] [\-\-nofixfile] [\-\-nopdbcanmap] [\-\-dnareceptor]
[\-\-name OUTPUTFILENAME] [\-\-peptides PEPTIDES [PEPTIDES ...] |
\fB\-\-intra\fR INTRA] [\-\-keepmod] [\-\-nohydro] [\-\-model MODEL]
.PP
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
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-f\fR INPUT [INPUT ...], \fB\-\-file\fR INPUT [INPUT ...]
Set input file, '\-' reads from stdin
.HP
\fB\-i\fR PDBID [PDBID ...], \fB\-\-input\fR PDBID [PDBID ...]
.HP
\fB\-o\fR OUTPATH, \fB\-\-out\fR OUTPATH
.TP
\fB\-O\fR, \fB\-\-stdout\fR
Write to stdout instead of file
.TP
\fB\-\-rawstring\fR
Use Python raw strings for stdin
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Turn on verbose mode
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Turn on quiet mode
.TP
\fB\-s\fR, \fB\-\-silent\fR
Turn on silent mode
.TP
\fB\-p\fR, \fB\-\-pics\fR
Additional pictures
.TP
\fB\-x\fR, \fB\-\-xml\fR
Generate report file in XML format
.TP
\fB\-t\fR, \fB\-\-txt\fR
Generate report file in TXT (RST) format
.TP
\fB\-y\fR, \fB\-\-pymol\fR
Additional PyMOL session files
.TP
\fB\-\-maxthreads\fR MAXTHREADS
Set maximum number of main threads (number of binding
sites processed simultaneously).If not set, PLIP uses
all available CPUs if possible.
.TP
\fB\-\-breakcomposite\fR
Don't combine ligand fragments with covalent bonds but
treat them as single ligands for the analysis.
.TP
\fB\-\-altlocation\fR
Also consider alternate locations for atoms (e.g.
alternate conformations).
.TP
\fB\-\-nofix\fR
Turns off fixing of PDB files.
.TP
\fB\-\-nofixfile\fR
Turns off writing files for fixed PDB files.
.TP
\fB\-\-nopdbcanmap\fR
Turns off calculation of mapping between canonical and
PDB atom order for ligands.
.TP
\fB\-\-dnareceptor\fR
Treat nucleic acids as part of the receptor structure
(together with any present protein) instead of as a
ligand.
.TP
\fB\-\-name\fR OUTPUTFILENAME
Set a filename for the report TXT and XML files. Will
only work when processing single structures.
.TP
\fB\-\-peptides\fR PEPTIDES [PEPTIDES ...], \fB\-\-inter\fR PEPTIDES [PEPTIDES ...]
Allows to define one or multiple chains as peptide
ligands or to detect inter\-chain contacts
.TP
\fB\-\-intra\fR INTRA
Allows to define one chain to analyze intra\-chain
contacts.
.TP
\fB\-\-keepmod\fR
Keep modified residues as ligands
.TP
\fB\-\-nohydro\fR
Do not add polar hydrogens in case your structure
already contains hydrogens.
.TP
\fB\-\-model\fR MODEL
Model number to be used for multi\-model structures.