.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.5.
.TH CSB-HHFRAG "1" "November 2017" "csb-hhfrag 1.2.5" "User Commands"
.SH NAME
csb-hhfrag \- build a dynamic variable-length fragment library for protein structure
.SH DESCRIPTION
usage: csb\-hhfrag [\-h] [\-H HHSEARCH] \fB\-d\fR DATABASE [\-m MIN] [\-M MAX] [\-s STEP]
.IP
[\-c CPU] [\-g GAP_FILLING] [\-F FILTERED_FILLING] [\-f]
[\-\-c\-alpha] [\-t CONFIDENCE_THRESHOLD] [\-v VERBOSITY]
[\-o OUTPUT]
QUERY
.PP
HHfrag: build a dynamic variable\-length fragment library for protein structure
prediction with Rosetta AbInitio.
.SS "positional arguments:"
.TP
QUERY
query profile HMM (e.g. created with
csb.apps.buildhmm)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-H\fR HHSEARCH, \fB\-\-hhsearch\fR HHSEARCH
path to the HHsearch executable (default=hhsearch)
.TP
\fB\-d\fR DATABASE, \fB\-\-database\fR DATABASE
database directory (containing PDBS25.hhm)
.TP
\fB\-m\fR MIN, \fB\-\-min\fR MIN
minimum query segment length (default=6)
.TP
\fB\-M\fR MAX, \fB\-\-max\fR MAX
maximum query segment length (default=21)
.TP
\fB\-s\fR STEP, \fB\-\-step\fR STEP
query segmentation step (default=3)
.TP
\fB\-c\fR CPU, \fB\-\-cpu\fR CPU
maximum degree of parallelism (default=4)
.TP
\fB\-g\fR GAP_FILLING, \fB\-\-gap\-filling\fR 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)
.TP
\fB\-F\fR FILTERED_FILLING, \fB\-\-filtered\-filling\fR 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
.TP
\fB\-f\fR, \fB\-\-filtered\-map\fR
make an additional filtered fragment map of centroids
and predict torsion angles (default=False)
.TP
\fB\-\-c\-alpha\fR
include also C\-alpha vectors in the output
(default=False)
.TP
\fB\-t\fR CONFIDENCE_THRESHOLD, \fB\-\-confidence\-threshold\fR CONFIDENCE_THRESHOLD
confidence threshold for gap filling (default=0.7)
.TP
\fB\-v\fR VERBOSITY, \fB\-\-verbosity\fR VERBOSITY
verbosity level (default=2)
.TP
\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
output directory (default=.)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.