.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PLIPCMD "1" "December 2020" "plipcmd 2.1.7+dfsg-1" "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) 2.1.6is a command\-line based
tool to analyze interactions in a protein\-ligand complex. If you are using
PLIP in your work, please cite: Salentin,S. et al. PLIP: fully automated
protein\-ligand interaction profiler. Nucl. Acids Res. (1 July 2015) 43 (W1):
W443\-W447. doi:10.1093/nar/gkv315Supported and maintained by: PharmAI GmbH
(2020) \- www.pharm.ai \- hello@pharm.ai
.SS "optional arguments:"
.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
Uses the DNA instead of the protein as a receptor for
interactions.
.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.