NAME

voronota-voromqa - implementation of VoroMQA method using Voronota

DESCRIPTION

'voronota-voromqa' script is an implementation of VoroMQA method using Voronota.

--input | -i: string * input structure file in PDB format
--input-filter-query: string input atoms filtering query parameters
--output-atom-scores: string output text file with atom scores
--output-atom-scores-pdb: string output PDB file with atom scores as B-factors
--output-residue-scores: string output text file with residue scores
--output-residue-scores-pdb: string output PDB file with residue scores as B-factors
--output-residue-scores-plot: string output PNG image file with residue scores plot, requires R
--help | -h: flag to display help message and exit

--cache-dir: string path to cache directory
--smoothing-window: number residue scores smoothing window size, default is 5
--atoms-query: string atoms query parameters to define selection
--contacts-query: string contacts query parameters to define selection
--output-selected-scores: string output text file with selected atom scores
--reference-sequence: string sequence file or string for residue renumbering
--output-sequence-alignment: string output text file with sequence alignment
--multiple-models: flag to handle multiple models in PDB file

: {input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]