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VORONOTA-CADSCORE(1) |
User Commands |
VORONOTA-CADSCORE(1) |
NAME¶
voronota-cadscore - implementation of CAD-score method using Voronota
DESCRIPTION¶
'voronota-cadscore' script is an implementation of CAD-score method using
Voronota.
Basic options:¶
- --input-target | -t
- string * input target structure file in PDB format
- --input-model | -m
- string * input model structure file in PDB format
- --input-filter-query
- string input atoms filtering query parameters
- --output-residue-scores
- string output text file with residue scores
- --output-residue-scores-pdb-t
- string output target PDB file with residue scores as B-factors
- --output-residue-scores-pdb-m
- string output model PDB file with residue scores as B-factors
- --smoothing-window
- number residue scores smoothing window size, default is 0
- --contacts-query
- string contacts query parameters
- --contacts-query-inter-chain
- flag to consider only inter-chain contacts
- --contacts-query-by-code
- string contacts query code, possible codes are AA, AS, SS, AM, MM, MS
- --use-all-query-codes
- flag to output global scores for all query codes, one line per code
- --cache-dir
- string path to cache directory
- --output-header
- flag to output header before result line
- --help | -h
- flag to display help message and exit
Advanced options:¶
- --ignore-residue-names
- flag to consider just residue numbers and ignore residue names
- --enable-site-based-scoring
- falg to enable site-based scoring
- --multiple-models
- flag to handle multiple models in PDB file
- --remap-chains
- flag to automatically rearrange chain names for higher scores
- --remap-chains-output
- string output file with chain names rearrangement
- --old-regime
- flag to calculate areas as in pre-Voronota CAD-score
Standard output (one line):¶
- {target file path} {model file path} {query code} {number of residues}
{global score} {target total area} {corresponding model total area} [
{site-based number of residues} {site-based global score} {site-based
target total area} {corresponding site-based model total area} ]