[med-svn] [python-csb] 04/05: Add manpages for csb tools
Andreas Tille
tille at debian.org
Mon Nov 13 11:39:50 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-csb.
commit 11a1a7a043c956e77a75b61c92f872cce149eb65
Author: Andreas Tille <tille at debian.org>
Date: Mon Nov 13 12:33:53 2017 +0100
Add manpages for csb tools
---
debian/changelog | 1 +
debian/createmanpages | 76 +++++++++++++++++++++++++++++++++++++++++++++
debian/csb.manpages | 1 +
debian/mans/csb-bfit.1 | 50 +++++++++++++++++++++++++++++
debian/mans/csb-bfite.1 | 41 ++++++++++++++++++++++++
debian/mans/csb-buildhmm.1 | 55 ++++++++++++++++++++++++++++++++
debian/mans/csb-csfrag.1 | 48 ++++++++++++++++++++++++++++
debian/mans/csb-embd.1 | 38 +++++++++++++++++++++++
debian/mans/csb-hhfrag.1 | 71 ++++++++++++++++++++++++++++++++++++++++++
debian/mans/csb-hhsearch.1 | 28 +++++++++++++++++
debian/mans/csb-precision.1 | 48 ++++++++++++++++++++++++++++
debian/mans/csb-promix.1 | 28 +++++++++++++++++
debian/mans/csb-test.1 | 43 +++++++++++++++++++++++++
13 files changed, 528 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index de3b231..fb02aa7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,7 @@ python-csb (1.2.5+dfsg-1) UNRELEASED; urgency=medium
* Fix reading UTF-8 encoded files
* Build-Depends: python-setuptools
* Add csb binary package with user executable tools
+ * Add manpages for csb tools
-- Andreas Tille <tille at debian.org> Mon, 13 Nov 2017 08:21:31 +0100
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..106780f
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,76 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=csb-bfit
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-bfite
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-buildhmm
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='build an HMM from a FASTA sequence' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-csfrag
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='build a dynamic library of analogous fragments' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-embd
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='Sharpening of EM maps by non-negative blind deconvolution' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-hhfrag
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='build a dynamic variable-length fragment library for protein structure' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-hhsearch
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='Python bindings for the HHsearch program' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-precision
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='measure the precision and coverage of a fragment library' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-promix
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='find a mixture of rigid segments or a mixture of conformers in a protein structure ensemble' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=csb-test
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='CSB Test Runner Console' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/csb.manpages b/debian/csb.manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/csb.manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/csb-bfit.1 b/debian/mans/csb-bfit.1
new file mode 100644
index 0000000..8b338c2
--- /dev/null
+++ b/debian/mans/csb-bfit.1
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-BFIT "1" "November 2017" "csb-bfit 1.2.5" "User Commands"
+.SH NAME
+csb-bfit \- models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions
+.SH DESCRIPTION
+usage: csb\-bfit [\-h] [\-c CHAIN1] [\-d CHAIN2] [\-s {student,k}] [\-a ALIGNMENT]
+.IP
+[\-o OUTFILE] [\-n NITER] [\-\-em]
+pdb1 pdb2
+.PP
+Python application for robust structure superposition of two structures. bfit
+models non\-rigid displacements in protein ensembles with outlier\-tolerant
+probability distributions.
+.SS "positional arguments:"
+.TP
+pdb1
+full path to the first structure
+.TP
+pdb2
+full path to the second structure
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-c\fR CHAIN1, \fB\-\-chain1\fR CHAIN1
+Chain of the first structure (default=A)
+.TP
+\fB\-d\fR CHAIN2, \fB\-\-chain2\fR CHAIN2
+Chain of the second structure (default=A)
+.TP
+\fB\-s\fR {student,k}, \fB\-\-scalemixture\fR {student,k}
+Scale mixture distribution (default=student)
+.TP
+\fB\-a\fR ALIGNMENT, \fB\-\-alignment\fR ALIGNMENT
+Alignment in fasta format defining equivalent
+positions Assumes that chain1 is the first sequence of
+the alignment and chain2 the second sequence
+.TP
+\fB\-o\fR OUTFILE, \fB\-\-outfile\fR OUTFILE
+file to which the rotated second structure will be
+written (default=bfit.pdb)
+.TP
+\fB\-n\fR NITER, \fB\-\-niter\fR NITER
+Number of optimization steps (default=200)
+.TP
+\fB\-\-em\fR
+Use the EM algorithm for optimsation (default=False)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-bfite.1 b/debian/mans/csb-bfite.1
new file mode 100644
index 0000000..93e6f53
--- /dev/null
+++ b/debian/mans/csb-bfite.1
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-BFITE "1" "November 2017" "csb-bfite 1.2.5" "User Commands"
+.SH NAME
+csb-bfite \- models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions
+.SH DESCRIPTION
+usage: csb\-bfite [\-h] [\-c CHAIN] [\-s {student,k}] [\-a ALIGNMENT] [\-o OUTFILE]
+.IP
+[\-n NITER]
+pdb
+.PP
+Python application for robust structure superposition of an ensemble of
+structures. bfite models non\-rigid displacements in protein ensembles with
+outlier\-tolerant probability distributions.
+.SS "positional arguments:"
+.TP
+pdb
+full path to the ensemble
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-c\fR CHAIN, \fB\-\-chain\fR CHAIN
+Chain (default=A)
+.TP
+\fB\-s\fR {student,k}, \fB\-\-scalemixture\fR {student,k}
+Scale mixture distribution (default=student)
+.TP
+\fB\-a\fR ALIGNMENT, \fB\-\-alignment\fR ALIGNMENT
+Alignment in fasta format defining equivalent
+positions Assumes that chain1 is the first sequence of
+the alignment and chain2 the second sequence
+.TP
+\fB\-o\fR OUTFILE, \fB\-\-outfile\fR OUTFILE
+file to which the rotated second structure will be
+written (default=bfit.pdb)
+.TP
+\fB\-n\fR NITER, \fB\-\-niter\fR NITER
+Number of optimization steps (default=200)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-buildhmm.1 b/debian/mans/csb-buildhmm.1
new file mode 100644
index 0000000..ee66a07
--- /dev/null
+++ b/debian/mans/csb-buildhmm.1
@@ -0,0 +1,55 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-BUILDHMM "1" "November 2017" "csb-buildhmm 1.2.5" "User Commands"
+.SH NAME
+csb-buildhmm \- build an HMM from a FASTA sequence
+.SH DESCRIPTION
+usage: csb\-buildhmm [\-h] \fB\-q\fR QUERY_ID [\-t TK_ROOT] [\-d DATABASE] [\-c TK_CONFIG]
+.TP
+[\-\-cpu CPU] [\-\-no\-ss] [\-\-no\-pseudo] [\-\-no\-calibration]
+query
+.PP
+Build an HMM from a FASTA sequence. This program is a proxy to
+hhblits/addss.pl and hhmake from the HHpred package. @note: assuming you have
+the full HHpred package installed and configured.
+.SS "positional arguments:"
+.TP
+query
+input sequence (FASTA or PDB file)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-q\fR QUERY_ID, \fB\-\-query\-id\fR QUERY_ID
+ID of the query, in PDB\-like format
+(accessionCHAIN).Used for naming the output files.
+Also, if the input is a PDB file with multiple chains,
+CHAIN is used to pull the required chain from the
+file.
+.TP
+\fB\-t\fR TK_ROOT, \fB\-\-tk\-root\fR TK_ROOT
+path to the ToolkitRoot folder in your HHsuite setup
+(default=/ebio/abt1_toolkit/share/wye)
+.TP
+\fB\-d\fR DATABASE, \fB\-\-database\fR DATABASE
+custom HHblits database; if not defined, toolkit's
+unirpto20 will be used
+.TP
+\fB\-c\fR TK_CONFIG, \fB\-\-tk\-config\fR TK_CONFIG
+path to a folder containing custom HHsuite configs
+(e.g. HHPaths.pm) (default=.)
+.TP
+\fB\-\-cpu\fR CPU
+maximum degree of parallelism (default=1)
+.TP
+\fB\-\-no\-ss\fR
+do not include secondary structure (default=False)
+.TP
+\fB\-\-no\-pseudo\fR
+do not add emission and transition pseudocounts
+(default=False)
+.TP
+\fB\-\-no\-calibration\fR
+do not calibrate the profile (default=False)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-csfrag.1 b/debian/mans/csb-csfrag.1
new file mode 100644
index 0000000..eb3bdb0
--- /dev/null
+++ b/debian/mans/csb-csfrag.1
@@ -0,0 +1,48 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-CSFRAG "1" "November 2017" "csb-csfrag 1.2.5" "User Commands"
+.SH NAME
+csb-csfrag \- build a dynamic library of analogous fragments
+.SH DESCRIPTION
+usage: csb\-csfrag [\-h] \fB\-d\fR DATABASE \fB\-s\fR SHIFTS [\-w WINDOW] [\-t TOP] [\-c CPU]
+.IP
+[\-v VERBOSITY] [\-o OUTPUT] [\-f]
+QUERY
+.PP
+CSfrag: build a dynamic library of analogous fragments, given a list of
+assigned chemical shifts.
+.SS "positional arguments:"
+.TP
+QUERY
+query sequence (FASTA file)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-d\fR DATABASE, \fB\-\-database\fR DATABASE
+PDBS25 database directory (containing PDBS25cs.scs)
+.TP
+\fB\-s\fR SHIFTS, \fB\-\-shifts\fR SHIFTS
+assigned chemical shifts table (NMR STAR file
+fragment)
+.TP
+\fB\-w\fR WINDOW, \fB\-\-window\fR WINDOW
+sliding window size (default=8)
+.TP
+\fB\-t\fR TOP, \fB\-\-top\fR TOP
+maximum number per starting position (default=25)
+.TP
+\fB\-c\fR CPU, \fB\-\-cpu\fR CPU
+maximum degree of parallelism (default=4)
+.TP
+\fB\-v\fR VERBOSITY, \fB\-\-verbosity\fR VERBOSITY
+verbosity level (default=1)
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output directory (default=.)
+.TP
+\fB\-f\fR, \fB\-\-filtered\-map\fR
+make an additional filtered fragment map of centroids
+(default=False)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-embd.1 b/debian/mans/csb-embd.1
new file mode 100644
index 0000000..08a09b8
--- /dev/null
+++ b/debian/mans/csb-embd.1
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-EMBD "1" "November 2017" "csb-embd 1.2.5" "User Commands"
+.SH NAME
+csb-embd \- Sharpening of EM maps by non-negative blind deconvolution
+.SH DESCRIPTION
+usage: csb\-embd [\-h] [\-s PSF_SIZE] [\-o OUTPUT] [\-i ITERATIONS]
+.IP
+[\-f OUTPUT_FREQUENCY] [\-v]
+mapfile
+.PP
+Sharpening of EM maps by non\-negative blind deconvolution. For details see:
+Hirsch M, Schoelkopf B and Habeck M (2010) A New Algorithm for Improving the
+Resolution of Cryo\-EM Density Maps.
+.SS "positional arguments:"
+.TP
+mapfile
+Input Cryo EM file in CCP4 MRC format
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-s\fR PSF_SIZE, \fB\-\-psf\-size\fR PSF_SIZE
+size of the point spread function (default=15)
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output directory of the sharpened maps (default=.)
+.TP
+\fB\-i\fR ITERATIONS, \fB\-\-iterations\fR ITERATIONS
+number of iterations (default=1000)
+.TP
+\fB\-f\fR OUTPUT_FREQUENCY, \fB\-\-output\-frequency\fR OUTPUT_FREQUENCY
+create a map file each f iterations (default=50)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+verbose mode (default=False)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-hhfrag.1 b/debian/mans/csb-hhfrag.1
new file mode 100644
index 0000000..4756996
--- /dev/null
+++ b/debian/mans/csb-hhfrag.1
@@ -0,0 +1,71 @@
+.\" 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.
diff --git a/debian/mans/csb-hhsearch.1 b/debian/mans/csb-hhsearch.1
new file mode 100644
index 0000000..82d7105
--- /dev/null
+++ b/debian/mans/csb-hhsearch.1
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-HHSEARCH "1" "November 2017" "csb-hhsearch 1.2.5" "User Commands"
+.SH NAME
+csb-hhsearch \- Python bindings for the HHsearch program
+.SH DESCRIPTION
+usage: csb\-hhsearch [\-h] [\-b BINARY] [\-c CPU] \fB\-d\fR DATABASE query [query ...]
+.PP
+Python bindings for the HHsearch program. Capable of executing multiple
+HHsearch jobs in parallel.
+.SS "positional arguments:"
+.TP
+query
+query HMM file(s)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-b\fR BINARY, \fB\-\-binary\fR BINARY
+full path to the HHsearch binary (default=hhsearch)
+.TP
+\fB\-c\fR CPU, \fB\-\-cpu\fR CPU
+maximum degree of parallelism (default=4)
+.TP
+\fB\-d\fR DATABASE, \fB\-\-database\fR DATABASE
+the subject (database) HMM file
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-precision.1 b/debian/mans/csb-precision.1
new file mode 100644
index 0000000..538e2a6
--- /dev/null
+++ b/debian/mans/csb-precision.1
@@ -0,0 +1,48 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-PRECISION "1" "November 2017" "csb-precision 1.2.5" "User Commands"
+.SH NAME
+csb-precision \- measure the precision and coverage of a fragment library
+.SH DESCRIPTION
+usage: csb\-precision [\-h] \fB\-p\fR PDB \fB\-n\fR NATIVE [\-c CHAIN] [\-t TOP] [\-C CPU]
+.TP
+[\-r RMSD] [\-o OUTPUT] [\-s]
+library
+.PP
+Measure the precision and coverage of a fragment library stored in Rosetta
+NNmake format.
+.SS "positional arguments:"
+.TP
+library
+Fragment library file in Rosetta NNmake format
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-p\fR PDB, \fB\-\-pdb\fR PDB
+the PDB database (a directory containing all PDB
+files)
+.TP
+\fB\-n\fR NATIVE, \fB\-\-native\fR NATIVE
+native structure of the target (PDB file)
+.TP
+\fB\-c\fR CHAIN, \fB\-\-chain\fR CHAIN
+chain identifier (if not specified, the first chain)
+.TP
+\fB\-t\fR TOP, \fB\-\-top\fR TOP
+read top N fragments per position (default=25)
+.TP
+\fB\-C\fR CPU, \fB\-\-cpu\fR CPU
+maximum degree of parallelism (default=4)
+.TP
+\fB\-r\fR RMSD, \fB\-\-rmsd\fR RMSD
+RMSD cutoff for precision and coverage (default=1.5)
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output directory (default=.)
+.TP
+\fB\-s\fR, \fB\-\-save\-structures\fR
+create a PDB file for each fragment, superimposed over
+the native (default=False)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-promix.1 b/debian/mans/csb-promix.1
new file mode 100644
index 0000000..e645b7e
--- /dev/null
+++ b/debian/mans/csb-promix.1
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-PROMIX "1" "November 2017" "csb-promix 1.2.5" "User Commands"
+.SH NAME
+csb-promix \- find a mixture of rigid segments or a mixture of conformers in a protein structure ensemble
+.SH DESCRIPTION
+usage: csb\-promix [\-h] [\-K COMPONENTS] [\-t {segments,conformers}] infile
+.PP
+ProMix: Take a protein structure ensemble and find a mixture of rigid segments
+or a mixture of conformers. Writes K copies of the ensemble (for segments) or
+K subsets of the ensemble (for conformers) as PDB files, each superposed on
+different components. Reference: Hirsch M, Habeck M. \- Bioinformatics. 2008
+Oct 1;24(19):2184\-92
+.SS "positional arguments:"
+.TP
+infile
+input PDB file
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-K\fR COMPONENTS, \fB\-\-components\fR COMPONENTS
+Number of components (default=\-1)
+.TP
+\fB\-t\fR {segments,conformers}, \fB\-\-type\fR {segments,conformers}
+Type of mixture (default=segments)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/csb-test.1 b/debian/mans/csb-test.1
new file mode 100644
index 0000000..867616d
--- /dev/null
+++ b/debian/mans/csb-test.1
@@ -0,0 +1,43 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CSB-TEST "1" "November 2017" "csb-test 1.2.5" "User Commands"
+.SH NAME
+csb-test \- CSB Test Runner Console
+.SH DESCRIPTION
+usage: csb\-test [\-h] [\-t {unit,functional,custom,any,regression}]
+.IP
+[\-v VERBOSITY] [\-u] [\-g GENERATED_RESOURCES]
+[namespaces [namespaces ...]]
+.PP
+CSB Test Runner Console.
+.SS "positional arguments:"
+.TP
+namespaces
+An optional list of CSB test dotted namespaces, from
+which to load tests. '__main__' and '.' are
+interpreted as the current module. If a namespace ends
+with an asterisk '.*', all sub\-packages will be
+scanned as well. Examples: "csb.test.cases.bio.*"
+"csb.test.cases.bio.io" "csb.test.cases.bio.utils"
+".")
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-t\fR {unit,functional,custom,any,regression}, \fB\-\-type\fR {unit,functional,custom,any,regression}
+Type of tests to load from each namespace
+(default=any)
+.TP
+\fB\-v\fR VERBOSITY, \fB\-\-verbosity\fR VERBOSITY
+Verbosity level passed to unittest.TextTestRunner
+(default=1).
+.TP
+\fB\-u\fR, \fB\-\-update\-files\fR
+Force update of the test pickles in
+\fI\,/usr/lib/python3/dist\-packages/csb/test/data\/\fP
+.TP
+\fB\-g\fR GENERATED_RESOURCES, \fB\-\-generated\-resources\fR GENERATED_RESOURCES
+Generate, store and load additional test resources in
+this directory (default=/usr/lib/python3/distpackages/csb/test/data)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
--
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