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.