csb-hhfrag1
Build a dynamic variable-length fragment library for protein structure
Overview
usage: csb-hhfrag [-h] [-H HHSEARCH] -d DATABASE [-m MIN] [-M MAX] [-s STEP]
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[-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
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-H HHSEARCH, --hhsearch HHSEARCH -
path to the HHsearch executable (default=hhsearch)
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-d DATABASE, --database DATABASE -
database directory (containing PDBS25.hhm)
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-m MIN, --min MIN -
minimum query segment length (default=6)
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-M MAX, --max MAX -
maximum query segment length (default=21)
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-s STEP, --step STEP -
query segmentation step (default=3)
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-c CPU, --cpu CPU -
maximum degree of parallelism (default=4)
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-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)
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-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
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-f, --filtered-map -
make an additional filtered fragment map of centroids and predict torsion angles (default=False)
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--c-alpha -
include also C-alpha vectors in the output (default=False)
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-t CONFIDENCE_THRESHOLD, --confidence-threshold CONFIDENCE_THRESHOLD -
confidence threshold for gap filling (default=0.7)
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-v VERBOSITY, --verbosity VERBOSITY -
verbosity level (default=2)
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-o OUTPUT, --output OUTPUT -
output directory (default=.)