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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} ]