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} ]

voronota-cadscore 1.22.3149                       February 2021                             VORONOTA-CADSCORE(1)