.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH VORONOTA-CADSCORE "1" "October 2022" "voronota-cadscore 1.22.3149" "User Commands"
.SH NAME
voronota-cadscore \- manual page for voronota-cadscore 1.22.3149
.SH DESCRIPTION
\&'voronota\-cadscore' script is an implementation of CAD\-score method using Voronota.
.SS "Basic options:"
.TP
\fB\-\-input\-target\fR | \fB\-t\fR
string   *  input target structure file in PDB or mmCIF format
.TP
\fB\-\-input\-model\fR | \fB\-m\fR
string   *  input model structure file in PDB format
.TP
\fB\-\-input\-filter\-query\fR
string      input atoms filtering query parameters
.TP
\fB\-\-filter\-model\-by\-target\fR
flag to filter model residues by the set of target residue IDs
.TP
\fB\-\-output\-residue\-scores\fR
string      output text file with residue scores
.TP
\fB\-\-output\-residue\-scores\-pdb\-t\fR
string      output target PDB file with residue scores as B\-factors
.TP
\fB\-\-output\-residue\-scores\-pdb\-m\fR
string      output model PDB file with residue scores as B\-factors
.TP
\fB\-\-smoothing\-window\fR
number      residue scores smoothing window size, default is 0
.TP
\fB\-\-contacts\-query\fR
string      contacts query parameters
.TP
\fB\-\-contacts\-query\-inter\-chain\fR
flag to consider only inter\-chain contacts
.TP
\fB\-\-contacts\-query\-by\-code\fR
string      contacts query code, possible codes are AA, AS, SS, AM, MM, MS
.TP
\fB\-\-use\-all\-query\-codes\fR
flag to output global scores for all query codes, one line per code
.TP
\fB\-\-cache\-dir\fR
string      path to cache directory
.TP
\fB\-\-output\-header\fR
flag to output header before result line
.TP
\fB\-\-help\fR | \fB\-h\fR
flag to display help message and exit
.SS "Advanced options:"
.TP
\fB\-\-ignore\-residue\-names\fR
flag to consider just residue numbers and ignore residue names
.TP
\fB\-\-enable\-site\-based\-scoring\fR
falg to enable site\-based scoring
.TP
\fB\-\-multiple\-models\fR
flag to handle multiple models in PDB file as an assembly
.TP
\fB\-\-input\-model\-chains\-renaming\fR
input text file with renaming rules for chains
.TP
\fB\-\-remap\-chains\fR
flag to automatically rearrange chain names for higher scores
.TP
\fB\-\-remap\-chains\-output\fR
string      output file with chain names rearrangement
.TP
\fB\-\-neighborhood\-depth\fR
number      number of layers to for per\-residue scoring, default is 0
.TP
\fB\-\-old\-regime\fR
flag to calculate areas as in pre\-Voronota CAD\-score
.SS "Standard output (one line):"
.IP
{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} ]