[med-svn] r11414 - trunk/packages/pdb2pqr/trunk/debian
Manuel Prinz
manuel at alioth.debian.org
Thu Jun 21 14:21:40 UTC 2012
Author: manuel
Date: 2012-06-21 14:21:39 +0000 (Thu, 21 Jun 2012)
New Revision: 11414
Removed:
trunk/packages/pdb2pqr/trunk/debian/propka.dirs
trunk/packages/pdb2pqr/trunk/debian/propka.install
Modified:
trunk/packages/pdb2pqr/trunk/debian/README.Debian
trunk/packages/pdb2pqr/trunk/debian/changelog
trunk/packages/pdb2pqr/trunk/debian/compat
trunk/packages/pdb2pqr/trunk/debian/control
trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs
trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install
trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.links
trunk/packages/pdb2pqr/trunk/debian/rules
Log:
Merged propka and pdb2pqr packages
Modified: trunk/packages/pdb2pqr/trunk/debian/README.Debian
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian 2012-06-21 14:21:39 UTC (rev 11414)
@@ -1,11 +1,12 @@
PROPKA
======
-PDB2PQR can use PROPKA to protonate the structure it converts. If you want to
-use the propka binary as a stand-alone application, you have to install the
-"propka" package. This is not needed if you just want to run PROPKA during a
-PDB2PQR run.
+PDB2PQR can use PROPKA to protonate the structure it converts. PROPKA is
+packaged along with the PDB2PQR in this package.
+ -- Manuel Prinz Thu, 21 Jun 2012 15:57:01 +0200
+
+
Web Service
===========
Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog 2012-06-21 14:21:39 UTC (rev 11414)
@@ -4,13 +4,15 @@
* debian/upstream: Add publication information
[ Manuel Prinz ]
- * New upstream version
+ * New upstream version. Updated debian/copyright.
* Updated Standards-Version to 3.9.3. No changes needed.
* Changed Maintainer to Debian Med team.
* Pass -fPIC to CXXFLAGS. Thanks to Konstantinos Margaritis for the patch!
Closes: 654240. LP: 935357.
* Updated PROPKA packaging to new version. (It's written in Python now.)
* Added fix-hashbangs.patch.
+ * Merged pdb2pqr and propka packages as they are more interconnected since
+ this upstream version. Updated README.Debian accordingly.
-- Andreas Tille <tille at debian.org> Wed, 16 May 2012 09:32:56 +0200
Modified: trunk/packages/pdb2pqr/trunk/debian/compat
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/compat 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/compat 2012-06-21 14:21:39 UTC (rev 11414)
@@ -1 +1 @@
-7
+9
Modified: trunk/packages/pdb2pqr/trunk/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/control 2012-06-21 14:21:39 UTC (rev 11414)
@@ -5,9 +5,8 @@
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Manuel Prinz <manuel at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.0.50~), gfortran, swig, xmlto, openbabel,
- python-support, python-dev, python-numpy,
- autoconf, automake, libtool, autotools-dev
+Build-Depends: debhelper (>= 9), gfortran, swig, xmlto, openbabel,
+ autoconf, automake, libtool, autotools-dev, python-dev, python-numpy,
Standards-Version: 3.9.3
XS-Python-Version: 2.7
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/
@@ -20,6 +19,9 @@
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy
Suggests: apbs
Enhances: autodocktools
+Provides: propka
+Conflicts: propka
+Replaces: propka
Description: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
@@ -30,6 +32,11 @@
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
+ .
+ This package also includes PropKa, a tool to modify the protonation state of
+ protein structures in the Protein Data Bank (PDB) format to match a given pKa
+ value. It can also be used to refine NMR structures, which often yield
+ inaccurate pKa values for some residues.
Package: pdb2pqr-doc
Section: doc
@@ -40,18 +47,3 @@
Files containing protein structures tend to become large very quickly and
most users of this package will refrain from their installation, particularly
on larger clusters.
-
-Package: propka
-XB-Python-Version: ${python:Versions}
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
-Suggests: pdb2pqr
-Description: Modify the protonation state of protein structures
- PropKa is a tool to modify the protonation state of a protein structure
- in the Protein Data Bank (PDB) format to match a given pKa value.
- It can also be used to refine NMR structures, which often yield
- inaccurate pKa values for some residues.
- .
- The PROPKA method is described in Hui Li, Andrew D. Robertson, and
- Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of
- Protein pKa Values" Proteins, 2005, 61, 704-721
Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2012-06-21 14:21:39 UTC (rev 11414)
@@ -6,4 +6,5 @@
/usr/share/pdb2pqr/extensions
/usr/share/pdb2pqr/pdb2pka/ligandclean
/usr/share/pdb2pqr/pdb2pka/substruct
+/usr/share/pdb2pqr/propka30
/usr/share/pdb2pqr/src
Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install 2012-06-21 14:21:39 UTC (rev 11414)
@@ -7,6 +7,7 @@
pdb2pka/*.py usr/share/pdb2pqr/pdb2pka
pdb2pka/ligandclean/*.py usr/share/pdb2pqr/pdb2pka/ligandclean
pdb2pka/substruct/*.py usr/share/pdb2pqr/pdb2pka/substruct
+propka30/* usr/share/pdb2pqr/propka30/
# Binary parts
pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka
pdb2pka/substruct/Algorithms.so usr/lib/pdb2pqr/pdb2pka/substruct
Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.links
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.links 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.links 2012-06-21 14:21:39 UTC (rev 11414)
@@ -1,3 +1,3 @@
usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
-usr/lib/pdb2pqr/propka/_propkalib.so usr/share/pdb2pqr/propka/_propkalib.so
+#usr/lib/pdb2pqr/propka/_propkalib.so usr/share/pdb2pqr/propka/_propkalib.so
Deleted: trunk/packages/pdb2pqr/trunk/debian/propka.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.dirs 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/propka.dirs 2012-06-21 14:21:39 UTC (rev 11414)
@@ -1,2 +0,0 @@
-/usr/bin
-/usr/share/propka
Deleted: trunk/packages/pdb2pqr/trunk/debian/propka.install
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.install 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/propka.install 2012-06-21 14:21:39 UTC (rev 11414)
@@ -1 +0,0 @@
-propka30/* usr/share/propka
Modified: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules 2012-06-21 14:21:01 UTC (rev 11413)
+++ trunk/packages/pdb2pqr/trunk/debian/rules 2012-06-21 14:21:39 UTC (rev 11414)
@@ -6,12 +6,13 @@
UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//')
# Compile with -fPIC on all platforms (fix for #636204, #654240)
-CFLAGS = $(shell dpkg-buildflags --get CFLAGS) -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
-CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS) -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
-FFLAGS = $(shell dpkg-buildflags --get FFLAGS) -fPIC
+CFLAGS += -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+CPPFLAGS += -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+CXXFLAGS += -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+FFLAGS += -fPIC
%:
- dh $@
+ dh $@ --with python2
override_dh_auto_clean:
( cd pdb2pka && \
@@ -20,7 +21,7 @@
dh_auto_clean
override_dh_auto_configure:
- dh_auto_configure -- CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" FFLAGS="$(FFLAGS)"
+ dh_auto_configure -- CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" CXXFLAGS="$(CXXFLAGS)" FFLAGS="$(FFLAGS)" LDFLAGS="$(LDFLAGS)"
( cd pdb2pka && \
cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \
cp -a pMC_mult.py pMC_mult.py.saved && \
@@ -30,8 +31,6 @@
override_dh_auto_test:
override_dh_auto_install:
-### Fix !#/bin/env shebang: substitute with #!/usr/bin/python
-## sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py
# Install Debian-provided stuff
# Install wrappers
for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \
@@ -39,15 +38,15 @@
>debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \
chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \
done
- for app in /usr/share/propka/propka.py; do \
+ for app in /usr/share/pdb2pqr/propka30/propka.py; do \
sed -e "s, at SCRIPT@,$${app}," debian/wrapper.sh \
- >debian/propka/usr/bin/$$(basename $${app} .py) && \
- chmod 0755 debian/propka/usr/bin/$$(basename $${app} .py); \
+ >debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \
+ chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \
done
# Install man pages
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
- xmlto -o debian/propka/usr/share/man/man1/ man debian/propka.1.xml
+ xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml
# dh_auto_install
override_dh_fixperms:
@@ -58,7 +57,7 @@
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
- chmod 0755 debian/propka/usr/share/propka/propka.py
+ chmod 0755 debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
.PHONY: get-orig-source
get-orig-source:
More information about the debian-med-commit
mailing list