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VORONOTA-CADSCORE(1) User Commands VORONOTA-CADSCORE(1)

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:

string * input target structure file in PDB or mmCIF format
string * input model structure file in PDB format
string input atoms filtering query parameters
flag to filter model residues by the set of target residue IDs
string output text file with residue scores
string output target PDB file with residue scores as B-factors
string output model PDB file with residue scores as B-factors
number residue scores smoothing window size, default is 0
string contacts query parameters
flag to consider only inter-chain contacts
string contacts query code, possible codes are AA, AS, SS, AM, MM, MS
flag to output global scores for all query codes, one line per code
string path to cache directory
flag to output header before result line
flag to display help message and exit

Advanced options:

flag to consider just residue numbers and ignore residue names
falg to enable site-based scoring
flag to handle multiple models in PDB file as an assembly
input text file with renaming rules for chains
flag to automatically rearrange chain names for higher scores
string output file with chain names rearrangement
number number of layers to for per-residue scoring, default is 0
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} ]
February 2021 voronota-cadscore 1.22.3149