[med-svn] r2042 - trunk/packages/pdb2pqr/trunk/debian
hauro-guest at alioth.debian.org
hauro-guest at alioth.debian.org
Wed Jun 11 23:00:44 UTC 2008
Author: hauro-guest
Date: 2008-06-11 23:00:43 +0000 (Wed, 11 Jun 2008)
New Revision: 2042
Added:
trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.1.xml
Modified:
trunk/packages/pdb2pqr/trunk/debian/changelog
trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs
trunk/packages/pdb2pqr/trunk/debian/rules
Log:
Added pdb2pqr(1) man page. More to follow.
Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog 2008-06-11 22:24:09 UTC (rev 2041)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog 2008-06-11 23:00:43 UTC (rev 2042)
@@ -6,12 +6,11 @@
* Disabled adv-tests to allow package build process without
internet access.
- [ Manuel ]
- * Various improvements for lintian-cleanliness and beyond
- - wrote man pages
- - package names as prefix in debian/*
+ [ Manuel Prinz ]
+ * Updated Standards-Version to 3.8.0
+ * Wrote man page for pdb2pqr(1)
- -- Manuel Prinz <debian at pinguinkiste.de> Sat, 07 Jun 2008 22:03:19 +0200
+ -- Manuel Prinz <debian at pinguinkiste.de> Thu, 12 Jun 2008 00:57:25 +0200
pdb2pqr (1.3.0-1) experimental; urgency=low
Added: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.1.xml
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.1.xml (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.1.xml 2008-06-11 23:00:43 UTC (rev 2042)
@@ -0,0 +1,224 @@
+<?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 pdb2pqr "<command>pdb2pqr</command>">
+]>
+<refentry>
+ <refentryinfo>
+ <title>PDB2PQR Manual</title>
+ <!-- "date" should be the date of the latest change -->
+ <date>2008-06-04</date>
+ <productname>pdb2pqr</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>pdb2pqr</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>pdb2pqr</refname>
+ <refpurpose>Generate <acronym>PQR</acronym> files for use in electrostatics calculations</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>pdb2pqr</command>
+ <arg choice="opt"><option>--nodebump</option></arg>
+ <arg choice="opt"><option>--noopt</option></arg>
+ <arg choice="opt"><option>--chain</option></arg>
+ <arg choice="opt"><option>--assign-only</option></arg>
+ <arg choice="opt"><option>--clean</option></arg>
+ <arg choice="opt"><option>--ffout=<replaceable>name</replaceable></option></arg>
+ <arg choice="opt"><option>--with-ph=<replaceable>ph</replaceable></option></arg>
+ <arg choice="opt"><option>--apbs-input</option></arg>
+ <arg choice="opt"><option>--ligand=<replaceable>path</replaceable></option></arg>
+ <group choice="opt">
+ <arg><option>--verbose</option></arg>
+ <arg><option>-v</option></arg>
+ </group>
+ <arg choice="plain"><option>--ff=<replaceable class="option">forcefield</replaceable></option></arg>
+ <arg choice="plain"><option><replaceable>path</replaceable></option></arg>
+ <arg choice="plain"><option><replaceable>output-path</replaceable></option></arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>pdb2pqr</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>
+ &pdb2pqr; automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for converting protein files in <acronym>PDB</acronym> format (<replaceable>path</replaceable>) to <acronym>PQR</acronym> format (<replaceable>output-path</replaceable>). These tasks include:</para>
+ <itemizedlist>
+ <listitem><para>Adding a limited number of missing heavy atoms to biomolecular structures</para></listitem>
+ <listitem><para>Determining side-chain pKas</para></listitem>
+ <listitem><para>Placing missing hydrogens</para></listitem>
+ <listitem><para>Optimizing the protein for favorable hydrogen bonding</para></listitem>
+ <listitem><para>Assigning charge and radius parameters from a variety of force fields</para></listitem>
+ </itemizedlist>
+ </refsect1>
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <para>&pdb2pqr; accepts the following options:</para>
+ <variablelist>
+ <varlistentry>
+ <term><option>--ff=<replaceable class="option">forcefield</replaceable></option></term>
+ <listitem>
+ <para>The <replaceable class="option">forcefield</replaceable> to use. Current values are <option>amber</option>, <option>charm</option>, <option>parse</option> and <option>tyl06</option>.</para>
+ </listitem>
+ </varlistentry>
+ <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>--nodebump</option></term>
+ <listitem>
+ <para>Do not perform debumping operation.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--noopt</option></term>
+ <listitem>
+ <para>Do not perform hydrogen optimization.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--chain</option></term>
+ <listitem>
+ <para>Keep the chain ID in the output PQR file.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--assign-only</option></term>
+ <listitem>
+ <para>Only assigns charges to add atoms, debump, or optimize.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--clean</option></term>
+ <listitem>
+ <para>Do no optimization, atom addition, or parameter assignment, just return
+ the original <acronym>PDB</acronym> file in alligned format.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--ffout=<replaceable>name</replaceable></option></term>
+ <listitem>
+ <para>Instead of using the standard caninical naming scheme for
+ residue and atom names, use the names from the given forcefield.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--with-ph=<replaceable>ph</replaceable></option></term>
+ <listitem>
+ <para>Use <command>propka</command> to calculate pKas and apply
+ them to the molecule given the pH value. Actual PropKa results will
+ be output to <filename><replaceable>output-path</replaceable>.propka</filename>.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--apbs-input</option></term>
+ <listitem>
+ <para>Create an APBS input file based on the generated
+ PQR file. Also create a Python pickle for using these
+ parameters in other programs.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--ligand=<replaceable>path</replaceable></option></term>
+ <listitem>
+ <para>Calculate the parameters for the ligand in MOL2 format at
+ the given <replaceable>path</replaceable>. Pdb2pka must be compiled.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--verbose</option></term>
+ <term><option>-v</option></term>
+ <listitem>
+ <para>Print additional information to screen.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="extensions">
+ <title>EXTENSIONS</title>
+ <para>Extensions add functionality to PDB2PQR and are called by passing a parameter
+ to &pdb2pqr;. They put their results into files located in <replaceable>output-path</replaceable>.</para>
+ <para>The following extensions can be used by &pdb2pqr;:</para>
+ <variablelist>
+ <varlistentry>
+ <term><option>--phi</option></term>
+ <listitem>
+ <para>Print the per-residue backbone phi angle to
+ <filename><replaceable>output-path</replaceable>.phi</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--psi</option></term>
+ <listitem>
+ <para>Print the per-residue backbone psi angle to
+ <filename><replaceable>output-path</replaceable>.phi</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--hbond</option></term>
+ <listitem>
+ <para>Print a list of hygrogen bonds to
+ <filename><replaceable>output-path</replaceable>.hbond</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--chi</option></term>
+ <listitem>
+ <para>Print the per-residue backbone chi angle to
+ <filename><replaceable>output-path</replaceable>.chi</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--contact</option></term>
+ <listitem>
+ <para>Print a list of contacts to
+ <filename><replaceable>output-path</replaceable>.con</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--hbondwhatif</option></term>
+ <listitem>
+ <para>Print a list of hydrogen bonds to
+ <filename><replaceable>output-path</replaceable>.hbo</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--salt</option></term>
+ <listitem>
+ <para>Print a list of salt bridges to
+ <filename><replaceable>output-path</replaceable>.salt</filename>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>--rama</option></term>
+ <listitem>
+ <para>Print the per-residue phi and psi angles to
+ <filename><replaceable>outpath-path</replaceable>.rama</filename>.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="seealso">
+ <title>SEE ALSO</title>
+ <para><citerefentry><refentrytitle>psize</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
+ </refsect1>
+</refentry>
Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2008-06-11 22:24:09 UTC (rev 2041)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2008-06-11 23:00:43 UTC (rev 2042)
@@ -2,6 +2,7 @@
/usr/lib/pdb2pqr/pdb2pka/substruct
/usr/lib/pdb2pqr/propka
/usr/share/doc/pdb2pqr
+/usr/share/man/man1
/usr/share/pdb2pqr/dat
/usr/share/pdb2pqr/extensions
/usr/share/pdb2pqr/pdb2pka/ligandclean
Modified: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules 2008-06-11 22:24:09 UTC (rev 2041)
+++ trunk/packages/pdb2pqr/trunk/debian/rules 2008-06-11 23:00:43 UTC (rev 2042)
@@ -35,6 +35,8 @@
>$(CURDIR)/debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \
chmod 0755 $(CURDIR)/debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \
done
+# Generate and install manpages
+ xmlto -o $(CURDIR)/debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
binary-strip/pdb2pqr::
DH_PYCENTRAL=nomove dh_pycentral -ppdb2pqr
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