VORONOTA-VOROMQA

NAME

voronota-voromqa - manual page for voronota-voromqa 1.22.3149

DESCRIPTION

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

Basic options:

--input | -i

string input structure file in PDB or mmCIF 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

--print-header

flag to print output header

--multiple-models

flag to handle multiple models in PDB file

--score-inter-chain

flag to output inter-chain interface scores

--list-all-options

flag to display list of all command line options and exit

Standard output (one line):

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