[med-svn] [Git][med-team/pdb2pqr][master] 5 commits: Removing dependency on xmlto and outdated manpages (will be built using help2man).
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Wed Feb 23 13:16:15 GMT 2022
Andrius Merkys pushed to branch master at Debian Med / pdb2pqr
Commits:
1305c081 by Andrius Merkys at 2022-02-23T06:57:37-05:00
Removing dependency on xmlto and outdated manpages (will be built using help2man).
- - - - -
e4e99bb7 by Andrius Merkys at 2022-02-23T06:58:56-05:00
Does not depend on openbabel anymore.
- - - - -
4af989fc by Andrius Merkys at 2022-02-23T08:05:47-05:00
Creating manpages using help2man.
- - - - -
157df156 by Andrius Merkys at 2022-02-23T08:14:49-05:00
Providing a symlink to old executable name, pdb2pqr.
- - - - -
faaa68ce by Andrius Merkys at 2022-02-23T08:15:59-05:00
Adjusting dependencies of pdb2pqr.
- - - - -
7 changed files:
- + debian/clean
- debian/control
- − debian/pdb2pqr.1.xml
- + debian/pdb2pqr.links
- + debian/pdb2pqr.manpages
- − debian/psize.1.xml
- debian/rules
Changes:
=====================================
debian/clean
=====================================
@@ -0,0 +1,3 @@
+dx2cube.1
+inputgen.1
+pdb2pqr30.1
=====================================
debian/control
=====================================
@@ -8,8 +8,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 12),
dh-python,
dh-sequence-sphinxdoc,
- xmlto,
- openbabel,
+ help2man,
python3-dev,
python3-numpy,
python3-pandas <!nocheck>,
@@ -26,11 +25,11 @@ Rules-Requires-Root: no
Package: pdb2pqr
Architecture: all
-Depends: ${shlibs:Depends},
+Depends: python3-numpy,
+ python3-networkx,
+ python3-pdb2pqr,
${misc:Depends},
- ${python3:Depends},
- python3-numpy,
- python3-networkx
+ ${python3:Depends}
Suggests: apbs
Enhances: autodocktools
Description: Preparation of protein structures for electrostatics calculations
=====================================
debian/pdb2pqr.1.xml deleted
=====================================
@@ -1,229 +0,0 @@
-<?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 aligned 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="citing">
- <title>CITING PDB2PQR</title>
- <para>Please acknowledge your use of &pdb2pqr; by citing:</para>
- <para>Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).</para>
- </refsect1>
- <refsect1 id="seealso">
- <title>SEE ALSO</title>
- <para><citerefentry><refentrytitle>psize</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
- </refsect1>
-</refentry>
=====================================
debian/pdb2pqr.links
=====================================
@@ -0,0 +1,2 @@
+usr/bin/pdb2pqr30 usr/bin/pdb2pqr
+usr/share/man/man1/pdb2pqr30.1.gz usr/share/man/man1/pdb2pqr.1.gz
=====================================
debian/pdb2pqr.manpages
=====================================
@@ -0,0 +1,3 @@
+dx2cube.1
+inputgen.1
+pdb2pqr30.1
=====================================
debian/psize.1.xml deleted
=====================================
@@ -1,113 +0,0 @@
-<?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; derives information from <acronym>PQR</acronym> files to preprare the models of proteins and chemicals for electrostatics calculations. The tool calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics calculation.</para>
- <para>The calculation of this information can be influenced by giving constraints 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>
=====================================
debian/rules
=====================================
@@ -1,5 +1,6 @@
#!/usr/bin/make -f
-# -*- mode: makefile; coding: utf-8 -*-
+
+include /usr/share/dpkg/pkg-info.mk
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
@@ -20,6 +21,12 @@ override_dh_auto_build:
dh_auto_build
PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html
+override_dh_installman:
+ PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string $(DEB_VERSION_UPSTREAM) > dx2cube.1
+ PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string $(DEB_VERSION_UPSTREAM) > inputgen.1
+ PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string $(DEB_VERSION_UPSTREAM) > pdb2pqr30.1
+ dh_installman
+
override_dh_installchangelogs_hide:
dh_installchangelogs ChangeLog.md
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0
--
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/d0bc9318aade2fd9f88843c66b36f0b975e2684b...faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0
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