CAD-score-LT version 0.9

'cadscore-lt' calculates CAD-score (Contact Area Difference score).

Options:
    --targets | -t                                   string     input file or directory paths for target (reference) structure files
    --models | -m                                    string     input file or directory paths for model structure files
    --processors                                     number     maximum number of OpenMP threads to use, default is 2 if OpenMP is enabled, 1 if disabled
    --recursive-directory-search                                flag to search directories recursively
    --include-heteroatoms                                       flag to include heteroatoms when reading input in PDB or mmCIF format
    --read-inputs-as-assemblies                                 flag to join multiple models into an assembly when reading a file in PDB or mmCIF format
    --radii-config-file                              string     input file path for reading atom radii assignment rules
    --probe                                          number     rolling probe radius, default is 1.4
    --restrict-raw-input                             string     selection expression to restrict input atoms before any chain renaming or residue renumbering
    --reference-sequences-file                       string     input file path for reference sequences in FASTA format
    --reference-stoichiometry                        numbers    list of stoichiometry values to apply when mapping chains to reference sequences
    --restrict-processed-input                       string     selection expression to restrict input atoms after all chain renaming and residue renumbering
    --save-processed-inputs-mmcif                               flag to save processed input structures in mmCIF format to the output directory
    --save-processed-inputs-pdb                                 flag to save processed input structures in PDB format to the output directory
    --save-sequence-alignments                                  flag to save best alignments with reference sequences into a file in the output directory
    --quit-before-scoring                                       flag to exit before scoring but after all the input processing and saving
    --subselect-contacts                             string     selection expression to restrict contact area descriptors to score, default is '[-min-sep 1]'
    --subselect-atoms                                string     selection expression to restrict atom SAS and site area descriptors to score, default is '[]'
    --conflate-atom-types                                       flag to conflate known equivalent atom types
    --conflation-config-file                         string     input file path for reading atom name conflation rules
    --scoring-types                                  strings    scoring types ('contacts', 'SAS', 'sites'), default is 'contacts'
    --scoring-levels                                 strings    scoring levels ('atom', 'residue', 'chain'), default is 'residue'
    --local-output-formats                           strings    list of formats (can include 'table', 'pdb', 'mmcif', 'contactmap', 'graphics-pymol', 'graphics-chimera')
    --local-output-levels                            strings    list of output levels (can include 'atom', 'residue', 'chain'), default is 'residue'
    --consider-residue-names                                    flag to include residue names in residue and atom identifiers, making mapping more strict
    --binarize-areas                                            flag to binarize (convert to 0 or 1) all area values before scoring
    --remap-chains                                              flag to automatically rename chains in models to maximize residue-residue contacts global score
    --max-chains-to-fully-permute                    number     limit of chain combinations to chech exhaustively when remapping chains, default is 200
    --clustering-thresholds                          numbers    clustering thresholds for Taylor-Butina-like clustering if in all-to-all comparison mode
    --max-renaming-cache-size                        number     max number of contact sets to cache when doing comparisons to multiple targets, default is 400
    --print-paths-in-output                                     flag to print file paths instead of file base names in output
    --output-with-f1                                            flag to output area-based F1 scores along with CAD-scores
    --output-with-areas                                         flag to output all recorded types of areas in tables of global and local scores
    --output-with-identities                                    flag to output identity percentages (for input atoms, residues, chains) along with CAD-scores
    --compact-output                                            flag to reduce size of output global scores table without removing rows
    --extremely-compact-output                                  flag to reduce size of output global scores by writing them as an integer matrix
    --output-global-scores                           string     path to output table of global scores, default is '_stdout' to print to standard output 
    --output-dir                                     string     path to output directory for all result files
    --help | -h                                                 flag to print help info to stderr and exit

Standard output stream:
    Global scores

Standard error output stream:
    Error messages

Usage examples:

    cadscore-lt -t ./target.pdb -m ./model1.pdb ./model2.pdb

    cadscore-lt -t ./target.pdb -m ./model1.pdb ./model2.pdb --subselect-contacts '[-inter-chain]'


