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]
The Protein-Ligand Interaction Profiler (PLIP)2.1.0-betais 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
optional arguments:
-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 stdout and stdin
-v, --verbose Turn on verbose mode
-q, --quiet Turn on quiet mode
-s, --silent Turn on silent mode
-p, --pics Additional pictures #添加渲染图片
-x, --xml Generate report filein XML format# 添加XML结果报告文件
-t, --txt Generate report filein TXT (RST)format# 添加TXT结果报告文件
-y, --pymol Additional PyMOL session files # 附加的PyMOL会话文件--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 Uses the DNA instead of the protein as a receptor for
interactions.
--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 incase your structure
already contains hydrogens.