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} ]

                                                                              VORONOTA-VOROMQA(1)