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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} ]