NAME

       csb-hhfrag - build a dynamic variable-length fragment library for protein structure

DESCRIPTION

       usage: csb-hhfrag [-h] [-H HHSEARCH] -d DATABASE [-m MIN] [-M MAX] [-s STEP]

              [-c   CPU]   [-g   GAP_FILLING]   [-F   FILTERED_FILLING]   [-f]   [--c-alpha]  [-t
              CONFIDENCE_THRESHOLD] [-v VERBOSITY] [-o OUTPUT] QUERY

       HHfrag: build a dynamic variable-length fragment library for protein structure  prediction
       with Rosetta AbInitio.

   positional arguments:
       QUERY  query profile HMM (e.g. created with csb.apps.buildhmm)

   optional arguments:
       -h, --help
              show this help message and exit

       -H HHSEARCH, --hhsearch HHSEARCH
              path to the HHsearch executable (default=hhsearch)

       -d DATABASE, --database DATABASE
              database directory (containing PDBS25.hhm)

       -m MIN, --min MIN
              minimum query segment length (default=6)

       -M MAX, --max MAX
              maximum query segment length (default=21)

       -s STEP, --step STEP
              query segmentation step (default=3)

       -c CPU, --cpu CPU
              maximum degree of parallelism (default=4)

       -g GAP_FILLING, --gap-filling GAP_FILLING
              path  to  a  fragment  file  (e.g. CSfrag or Rosetta NNmake), which will be used to
              complement lowconfidence regions (when specified,  a  hybrid  fragment  library  be
              produced)

       -F FILTERED_FILLING, --filtered-filling FILTERED_FILLING
              path  to a filtered fragment file (e.g. filtered CSfrag-ments), which will be mixed
              with the HHfrag-set and then filtered, resulting in a double-filtered library

       -f, --filtered-map
              make an additional filtered fragment map of centroids and  predict  torsion  angles
              (default=False)

       --c-alpha
              include also C-alpha vectors in the output (default=False)

       -t CONFIDENCE_THRESHOLD, --confidence-threshold CONFIDENCE_THRESHOLD
              confidence threshold for gap filling (default=0.7)

       -v VERBOSITY, --verbosity VERBOSITY
              verbosity level (default=2)

       -o OUTPUT, --output OUTPUT
              output directory (default=.)

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.