VORONOTA-CADSCORE

NAME

voronota-cadscore - manual page for voronota-cadscore 1.22.3149

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 or mmCIF format

--input-model | -m

string * input model structure file in PDB format

--input-filter-query

string input atoms filtering query parameters

--filter-model-by-target

flag to filter model residues by the set of target residue IDs

--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 as an assembly

--input-model-chains-renaming

input text file with renaming rules for chains

--remap-chains

flag to automatically rearrange chain names for higher scores

--remap-chains-output

string output file with chain names rearrangement

--neighborhood-depth

number number of layers to for per-residue scoring, default is 0

--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} ]