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

Set verbose 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).

--debug

Turn on DEBUG mode with extended log.

--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