bionic (1) csb-hhfrag.1.gz

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.