.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH PLIPCMD "1" "November 2016" "plipcmd 1.3.3+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 ...]) [\-o OUTPATH]
.IP
[\-v] [\-p] [\-x] [\-t] [\-y] [\-\-maxthreads MAXTHREADS]
[\-\-breakcomposite] [\-\-altlocation] [\-\-debug] [\-\-nofix]
[\-\-peptides PEPTIDES [PEPTIDES ...] | \fB\-\-intra\fR INTRA] [\-\-keepmod]
.PP
Protein\-Ligand Interaction Profiler (PLIP) v1.3.3 is 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 proteinligand interaction profiler. Nucl. Acids Res. (1 July 2015) 43 (W1):
W443\-W447. doi: 10.1093/nar/gkv315
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.HP
\fB\-f\fR INPUT [INPUT ...], \fB\-\-file\fR INPUT [INPUT ...]
.HP
\fB\-i\fR PDBID [PDBID ...], \fB\-\-input\fR PDBID [PDBID ...]
.HP
\fB\-o\fR OUTPATH, \fB\-\-out\fR OUTPATH
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Set verbose 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 into with covalent
bonds but treat them as single ligandsfot the
analysis.
.TP
\fB\-\-altlocation\fR
Also consider alternate locations for atoms (e.g.
alternate conformations).
.TP
\fB\-\-debug\fR
Turn on DEBUG mode with extended log.
.TP
\fB\-\-nofix\fR
Turns off fixing of PDB files.
.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