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commit 11a1a7a043c956e77a75b61c92f872cce149eb65 Author: Andreas Tille <[email protected]> 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 <[email protected]> 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-csb.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
