.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH VORONOTA-VOROMQA "1" "October 2022" "voronota-voromqa 1.22.3149" "User Commands"
.SH NAME
voronota-voromqa \- manual page for voronota-voromqa 1.22.3149
.SH DESCRIPTION
\&'voronota\-voromqa' script is an implementation of VoroMQA method using Voronota.
.SS "Basic options:"
.TP
\fB\-\-input\fR | \fB\-i\fR
string      input structure file in PDB or mmCIF format
.TP
\fB\-\-input\-filter\-query\fR
string      input atoms filtering query parameters
.TP
\fB\-\-output\-atom\-scores\fR
string      output text file with atom scores
.TP
\fB\-\-output\-atom\-scores\-pdb\fR
string      output PDB file with atom scores as B\-factors
.TP
\fB\-\-output\-residue\-scores\fR
string      output text file with residue scores
.TP
\fB\-\-output\-residue\-scores\-pdb\fR
string      output PDB file with residue scores as B\-factors
.TP
\fB\-\-output\-residue\-scores\-plot\fR
string      output PNG image file with residue scores plot, requires R
.TP
\fB\-\-help\fR | \fB\-h\fR
flag to display help message and exit
.SS "Advanced options:"
.TP
\fB\-\-cache\-dir\fR
string      path to cache directory
.TP
\fB\-\-smoothing\-window\fR
number      residue scores smoothing window size, default is 5
.TP
\fB\-\-atoms\-query\fR
string      atoms query parameters to define selection
.TP
\fB\-\-contacts\-query\fR
string      contacts query parameters to define selection
.TP
\fB\-\-output\-selected\-scores\fR
string      output text file with selected atom scores
.TP
\fB\-\-reference\-sequence\fR
string      sequence file or string for residue renumbering
.TP
\fB\-\-output\-sequence\-alignment\fR
string      output text file with sequence alignment
.TP
\fB\-\-print\-header\fR
flag to print output header
.TP
\fB\-\-multiple\-models\fR
flag to handle multiple models in PDB file
.TP
\fB\-\-score\-inter\-chain\fR
flag to output inter\-chain interface scores
.TP
\fB\-\-list\-all\-options\fR
flag to display list of all command line options and exit
.SS "Standard output (one line):"
.IP
{input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]