table of contents
| VORONOTA-VOROMQA(1) | User Commands | VORONOTA-VOROMQA(1) |
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} ]
| October 2022 | voronota-voromqa 1.22.3149 |