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VORONOTA-VOROMQA(1) User Commands VORONOTA-VOROMQA(1)

NAME

voronota-voromqa - implementation of VoroMQA method using Voronota

DESCRIPTION

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

Basic options:

--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

Advanced options:

--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

Standard output (one line):

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