[med-svn] r2060 - trunk/packages/pdb2pqr/trunk/debian
hauro-guest at alioth.debian.org
hauro-guest at alioth.debian.org
Sun Jun 15 18:53:49 UTC 2008
Author: hauro-guest
Date: 2008-06-15 18:53:48 +0000 (Sun, 15 Jun 2008)
New Revision: 2060
Added:
trunk/packages/pdb2pqr/trunk/debian/propka.1.xml
trunk/packages/pdb2pqr/trunk/debian/psize.1.xml
Modified:
trunk/packages/pdb2pqr/trunk/debian/changelog
trunk/packages/pdb2pqr/trunk/debian/rules
Log:
Added manpages for psize(1) and propka(1)
Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog 2008-06-15 18:52:07 UTC (rev 2059)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog 2008-06-15 18:53:48 UTC (rev 2060)
@@ -7,11 +7,11 @@
[ Manuel Prinz ]
* Updated Standards-Version to 3.8.0
- * Wrote man page for pdb2pqr(1)
+ * Wrote man page for pdb2pqr(1), psize(1) and propka(1)
* Added binary package for propka (Closes: #420734)
* Moved API documentation to pdb2pqr-doc package
- -- Manuel Prinz <debian at pinguinkiste.de> Thu, 12 Jun 2008 14:28:50 +0200
+ -- Manuel Prinz <debian at pinguinkiste.de> Sun, 15 Jun 2008 20:54:10 +0200
pdb2pqr (1.3.0-1) experimental; urgency=low
Added: trunk/packages/pdb2pqr/trunk/debian/propka.1.xml
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.1.xml (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/propka.1.xml 2008-06-15 18:53:48 UTC (rev 2060)
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+<!ENTITY propka "<command>propka</command>">
+]>
+<refentry>
+ <refentryinfo>
+ <title>PROPKA Manual</title>
+ <!-- "date" should be the date of the latest change -->
+ <date>2008-06-15</date>
+ <productname>propka</productname>
+ <authorgroup>
+ <author>
+ <firstname>Manuel</firstname><surname>Prinz</surname>
+ <contrib>Wrote this manpage for the Debian System.</contrib>
+ <address><email>debian at pinguinkiste.de</email></address>
+ </author>
+ </authorgroup>
+ <copyright><year>2008</year><holder>Manuel Prinz</holder></copyright>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>propka</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>propka</refname>
+ <refpurpose>Protonate <acronym>PDB</acronym> files based on pKa</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>propka</command>
+ <arg choice="plain"><option><filename>PROPKATMP1</filename></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ &propka; is a able to protonate a structure in <acronym>PDB</acronym> format to a given pKa value. The file to use has to be named <filename>PROPKATMP1</filename> in the directory where propka is run.</para>
+ <para>&propka; will generate two output files named <filename>PROPKATMP2</filename> and <filename>PROPKATMP3</filename>. <filename>PROPKATMP2</filename> contains the resulting structure in <acronym>PDB</acronym> format. <filename>PROPKATMP3</filename> contains a summary of the &propka; run.</para>
+ </refsect1>
+ <refsect1 id="citing">
+ <title>CITING PROPKA</title>
+ <para>Please acknowledge your use of &propka; by citing:</para>
+ <para>Hui Li, Andrew D. Robertson, and Jan H. Jensen: Very Fast Empirical Prediction and Interpretation of Protein pKa Values, Proteins, 2005, 61, 704-721.</para>
+ </refsect1>
+ <refsect1 id="webservice">
+ <title>WEB SERVICE</title>
+ <para>PropKa can be used via a web interface at <ulink url="http://propka.ki.ku.dk/">http://propka.ki.ku.dk/</ulink>.</para>
+ </refsect1>
+ <refsect1 id="seealso">
+ <title>SEE ALSO</title>
+ <para><citerefentry><refentrytitle>pdb2pqr</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
+ </refsect1>
+</refentry>
Added: trunk/packages/pdb2pqr/trunk/debian/psize.1.xml
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/psize.1.xml (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/psize.1.xml 2008-06-15 18:53:48 UTC (rev 2060)
@@ -0,0 +1,113 @@
+<?xml version="1.0"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+<!ENTITY psize "<command>psize</command>">
+]>
+<refentry>
+ <refentryinfo>
+ <title>PDB2PQR Manual</title>
+ <!-- "date" should be the date of the latest change -->
+ <date>2008-06-04</date>
+ <productname>psize</productname>
+ <authorgroup>
+ <author>
+ <firstname>Manuel</firstname><surname>Prinz</surname>
+ <contrib>Wrote this manpage for the Debian System.</contrib>
+ <address><email>debian at pinguinkiste.de</email></address>
+ </author>
+ </authorgroup>
+ <copyright><year>2008</year><holder>Manuel Prinz</holder></copyright>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>psize</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>psize</refname>
+ <refpurpose>Get dimensions and other information from <acronym>PQR</acronym> files</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>psize</command>
+ <arg choice="opt"><option>--cfact=<replaceable>value</replaceable></option></arg>
+ <arg choice="opt"><option>--fadd=<replaceable>value</replaceable></option></arg>
+ <arg choice="opt"><option>--space=<replaceable>value</replaceable></option></arg>
+ <arg choice="opt"><option>--gememfac=<replaceable>value</replaceable></option></arg>
+ <arg choice="opt"><option>--gememceil=<replaceable>value</replaceable></option></arg>
+ <arg choice="opt"><option>--ofrac=<replaceable>value</replaceable></option></arg>
+ <arg choice="opt"><option>--redfac=<replaceable>value</replaceable></option></arg>
+ <arg choice="req"><option><replaceable>pqrfile</replaceable></option></arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>psize</command>
+ <group choice="req">
+ <arg choice="plain"><option>--help</option></arg>
+ <arg choice="plain"><option>-h</option></arg>
+ </group>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ &psize; is able to calculate dimensions and other information from <acronym>PQR</acronym> files. This information can be used to perform electrostatics calculations. It includes dimensions for coarse and fine grids, grid spacings, box size and an estimation of the memory required to perform an electrostatics calculation.</para>
+ <para>The calculation of this information can be influenced by giving contraints to &psize; as parameters.</para>
+ </refsect1>
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <para>&psize; accepts the following options:</para>
+ <variablelist>
+ <varlistentry>
+ <term><option>--help</option></term>
+ <term><option>-h</option></term>
+ <listitem>
+ <para>Print a help message and exit.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--cfact=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Factor by which to expand the molecule dimensions to get the coarse grid dimensions</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--fadd=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Amount to add to the molecule dimensions to get the fine grid dimensions.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--space=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Desired fine mesh resolution.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--gememfac=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Number of bytes per grid point required for sequential <acronym>MG</acronym> calculation.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--gememceil=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Maximum <acronym>MB</acronym> allowed for sequential <acronym>MG</acronym> calculation. Adjust this to force the script to perform faster calculations (which require more parallelism).</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--ofrac=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Overlap factor between mesh partitions.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--redfac=<replaceable class="option">value</replaceable></option></term>
+ <listitem>
+ <para>Maximum factor by which a domain dimension can be reduced during focusing.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="seealso">
+ <title>SEE ALSO</title>
+ <para><citerefentry><refentrytitle>apbs</refentrytitle><manvolnum>1</manvolnum></citerefentry>, <citerefentry><refentrytitle>pdb2pqr</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
+ </refsect1>
+</refentry>
Modified: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules 2008-06-15 18:52:07 UTC (rev 2059)
+++ trunk/packages/pdb2pqr/trunk/debian/rules 2008-06-15 18:53:48 UTC (rev 2060)
@@ -38,10 +38,14 @@
done
# Generate and install manpages
xmlto -o $(CURDIR)/debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
+ xmlto -o $(CURDIR)/debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
binary-fixup/pdb2pqr::
DH_PYCENTRAL=nomove dh_pycentral -ppdb2pqr
+install/propka::
+ xmlto -o $(CURDIR)/debian/propka/usr/share/man/man1/ man debian/propka.1.xml
+
# Clean files that are not removed in upstream's "distclean" target
# (Reported upstream, fixed in SVN, will be in next release (>1.3.0))
clean::
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