options:

-h, --help

show this help message and exit

-f, --file INPUT [INPUT ...]

Set input file, '-' reads from stdin

-i, --input PDBID [PDBID ...]

-o, --out OUTPATH

-O, --stdout

Write to stdout instead of file

--rawstring

Use Python raw strings for stdin

-v, --verbose

Turn on verbose mode

-q, --quiet

Turn on quiet mode

-s, --silent

Turn on silent 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).

--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

Treat nucleic acids as part of the receptor structure (together with any present protein) instead of as a ligand.

--name OUTPUTFILENAME

Set a filename for the report TXT and XML files. Will only work when processing single structures.

--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.

--residues RESIDUES [RESIDUES ...]

Allows to specify which residues of the chain(s) should be considered as peptide ligands. Give single residues (separated with comma) or ranges (with dash) or both, for several chains separate selections with one space

--keepmod

Keep modified residues as ligands

--nohydro

Do not add polar hydrogens in case your structure already contains hydrogens.

--model MODEL

Model number to be used for multi-model structures.

--chains CHAINS

Specify chains as receptor/ligand groups, e.g., '[['A'], ['B']]'. Use format [['A'], ['B', 'C']] to define A as receptor, and B, C as ligands.