Version Bump; 340867; removed old

Package-Manager: portage-2.2_rc95/cvs/Linux x86_64

10 files changed, 296 insertions, 365 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 895261d329f3..8cd3fcbcff82 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.26 2010/07/07 09:22:45 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.27 2010/10/14 17:53:56 jlec Exp $
+
+*pdb2pqr-1.7.0 (14 Oct 2010)
+
+  14 Oct 2010; Justin Lecher <jlec@gentoo.org> +files/1.7.0-install.patch,
+  -pdb2pqr-1.3.0.ebuild, -files/pdb2pqr-1.3.0-gcc4.3.patch,
+  -files/pdb2pqr-1.3.0-ldflags.patch, -pdb2pqr-1.4.0-r1.ebuild,
+  -files/pdb2pqr-1.4.0-gcc44.patch, -pdb2pqr-1.5.0.ebuild,
+  +pdb2pqr-1.7.0.ebuild:
+  Version Bump; 340867; removed old
 
   07 Jul 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org>
   pdb2pqr-1.5.0-r2.ebuild:
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 2cc1bbf8bb4f..a29eced6cdd8 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,15 +1,20 @@
-AUX pdb2pqr-1.3.0-gcc4.3.patch 349 RMD160 a7e241b288738faaee678609c61968dba990b9a3 SHA1 95e0dcb30e926f0bab2068bff550427a1a3a623e SHA256 4e65916b3370bc3c4690ca9424629a928f9753879939f0ebb881304331fab946
-AUX pdb2pqr-1.3.0-ldflags.patch 803 RMD160 ecc52d97bae89e1a961531eb5e4c87d456e87919 SHA1 ba777c53835045fd4538f3e1104a18d12df8d935 SHA256 8d2cf1f0d206e4162193877dd577ff0835f8e390d779ddfa4b73d30734dede77
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 1.7.0-install.patch 5165 RMD160 6937f62cd4035c40d3575455f1faed6114b1bfd2 SHA1 304cdd46d76745e29a8bd00f4bdbd63dbe4b135c SHA256 965c0bf8077eebc733c60d4e80d05167ce31d7188b01ca43c0fb5c0b27ede22b
 AUX pdb2pqr-1.4.0-automagic.patch 3526 RMD160 c4d662e68352d93f913fdc83b5c733a555a9bc17 SHA1 64598bff69e627a27ffa550ad5f3b38898a3a9cf SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a
-AUX pdb2pqr-1.4.0-gcc44.patch 229 RMD160 c5c1d51e6c695a3df8c04245a8d93168bef7a6b8 SHA1 5614b75a17b089624558026e51ba440479a5f658 SHA256 76a1bd592579d712bb6b22e6547edf1094d628e9d2b00b8d6ec89f8d9043c6df
 AUX pdb2pqr-1.4.0-install.patch 5372 RMD160 8d6c5f3c85ceea0562a767a3792228e6ff0eee96 SHA1 77a70693687be8d14eb3221ffc62a3daccc38f8e SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643
 AUX pdb2pqr-1.4.0-ldflags.patch 1293 RMD160 47c2e4b484cf0936176683342afa6e89bb0b0712 SHA1 6c9088bbbf87a91c28fe6fdd39b3db097143f103 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726
-DIST pdb2pqr-1.3.0.tar.gz 2641989 RMD160 469b38457a10e93ce96c7ea4e580cb4656ba3218 SHA1 e2095a7130ff6114d15466b009cc8ed335d8ffd1 SHA256 7e8a733aacdb76ec8f920b6827ebbc86712044a10c50363535978bc22b7fd413
-DIST pdb2pqr-1.4.0.tar.gz 5471743 RMD160 4d5596da5f9bdb2c657e7d0d88d91d20d00569e2 SHA1 967f3f2f2ab532e7a0abeb253bac95185bca1602 SHA256 19bfa106e7b41537594ab627c8c670c03c3445e9efb69d878528355825080fd5
 DIST pdb2pqr-1.5.tar.gz 5747178 RMD160 543545513811bae058e23cfe1f24e02eaa094b87 SHA1 5249064cf4ebfb2291a382121ecea4d457e65e6a SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
-EBUILD pdb2pqr-1.3.0.ebuild 1941 RMD160 c32fd92b8fcbaca244408901914e05fb84d5b04d SHA1 ae76775016eae67af8c0edaf3ace7f355c07bba4 SHA256 58e36b7a6ac25c0b71946fab19634c21d61b4306ce86e1fcc85466e3569c20cf
-EBUILD pdb2pqr-1.4.0-r1.ebuild 2771 RMD160 43513f5a73a2a3b6b6a92a51fbe1d40995ca413a SHA1 2ac7eb4020c3a33096ce2f6dee7003a3a2c1062e SHA256 b2ca0b35b7a2c38423d2b7cb7e5e2bed9273e72a7aa65ea93702605d39acb3cd
+DIST pdb2pqr-1.7.tar.gz 6906538 RMD160 606fd8451c52e642a08d5f6c7cdcd51659ea57bc SHA1 23a0a0a5ed54b55269b60b4c4161d914cb30ecca SHA256 8d27f2df430c40b99cde7952d0e96e72e433871a289d39c970b5eefe34345757
 EBUILD pdb2pqr-1.5.0-r2.ebuild 3452 RMD160 b6b392fdbcd98e47c68c7999bcf6ba037f495d61 SHA1 1e85340c28662d2203ebc0bd3408d756415a3cae SHA256 3aca202f604ac814e1862c7bd98a25a84c4bd591542a73b5568accbffe7f3937
-EBUILD pdb2pqr-1.5.0.ebuild 3000 RMD160 49b568365038c5397b08f8431a9f64861cc1901e SHA1 4e27aea0f23dff166e3b662b3b7bcaa48563247d SHA256 e655ba586d48c3ae3e71c338872f01011370ce4b29d42a1f515713696408b6ce
-MISC ChangeLog 4199 RMD160 c1daffdaf091236f121fcd664512c4ea392749b8 SHA1 c4897b474710bdf267130922b48b26ce58c23331 SHA256 0efd3c094f99905a4ccd39d3fd4b2e565ade3d47b33539513a28a62b3e9d5302
+EBUILD pdb2pqr-1.7.0.ebuild 3439 RMD160 bb93f2c05697d80fa179df088b280d016ec3fef9 SHA1 8ba85c3a02c810f6526ab125f76a5b366573135e SHA256 0b46dc54389b243d74f657206e3ddb588432bf5de760329c4ac6d6746e0b7496
+MISC ChangeLog 4543 RMD160 654d59f14b54d2de7ecf61fd154ca5f36acad3a6 SHA1 8048a1522aac03de7542f0b1d8b38287d5327700 SHA256 9105e80eea1a376ceca8af277fee3fd89fbd7d8888ab375b161ca809d339e36c
 MISC metadata.xml 239 RMD160 50377a558ee5880950af2b01bbc1c4e091b7f1bf SHA1 e4c893842e7bae177b435aea9846f02635c9c5dc SHA256 86c2c8d5211035cbd6ee6267ba9d865107aad9298c8c52b0b03900c5c5bb169a
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+
+iEYEARECAAYFAky3Q7kACgkQgAnW8HDreRbiBQCdGHL2yrhqkTugmSc8TCNInO/4
++L8AmwW/LyUS9kD6ossOaPKxCYTR76EY
+=YgYS
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
new file mode 100644
index 000000000000..77ee077937dc
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
@@ -0,0 +1,131 @@
+diff --git a/Makefile.am b/Makefile.am
+index d5d020d..550d52a 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -113,24 +113,11 @@ install:
+ 	    mkdir $(CWD)/$$dir/tmp ; \
+ 	  fi ; \
+ 	  chmod 777 $(CWD)/$$dir/tmp ; \
+-	  echo "Adding server.html" ; \
+-	  cp $$c/html/server.html $(CWD)/$$dir/index.html ; \
+-	  echo "Adding python files" ; \
+-	  cp $$c/*.py* $(CWD)/$$dir/. ; \
++	  cp $$c/main*.py $(CWD)/$$dir/. ; \
+ 	  echo "Adding __init__.py" ; \
+ 	  cp $$c/__init__.py $(CWD)/$$dir/__init__.py ; \
+ 	  echo "Adding pdb2pqr.py" ; \
+ 	  cp $$c/pdb2pqr.py $(CWD)/$$dir/. ; \
+-	  echo "Adding pdb2pqr.cgi" ; \
+-	  cp $$c/pdb2pqr.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding pdb2pqr.css" ; \
+-	  cp $$c/apbs_cgi.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding apbs_cgi.cgi" ; \
+-	  cp $$c/visualize.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding visualize.cgi" ; \
+-	  cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding querystatus.cgi" ; \
+-	  cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \
+ 	  if ! test -d $(CWD)/$$dir/dat  ; then \
+ 	    mkdir $(CWD)/$$dir/dat ; \
+ 	  fi ; \
+@@ -138,49 +125,12 @@ install:
+ 	  cp $$c/dat/*.xml $(CWD)/$$dir/dat/. ; \
+ 	  cp $$c/dat/*.DAT $(CWD)/$$dir/dat/. ; \
+ 	  cp $$c/dat/*.names $(CWD)/$$dir/dat/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc  ; then \
+-	    mkdir $(CWD)/$$dir/doc ; \
+-	  fi ; \
+-	  echo "Adding doc/" ; \
+-	  cp $$c/doc/*.html $(CWD)/$$dir/doc/. ; \
+-	  cp $$c/doc/*.sh $(CWD)/$$dir/doc/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc/images  ; then \
+-	    mkdir $(CWD)/$$dir/doc/images ; \
+-	  fi ; \
+-	  cp $$c/doc/images/*.png $(CWD)/$$dir/doc/images/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc/pydoc ; then \
+-	    mkdir $(CWD)/$$dir/doc/pydoc ; \
+-	  fi ; \
+-	  cp $$c/doc/pydoc/*.html $(CWD)/$$dir/doc/pydoc/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples ; then \
+-	    mkdir $(CWD)/$$dir/examples ; \
+-	  fi ; \
+-	  echo "Adding examples/" ; \
+-	  cp $$c/examples/*.html $(CWD)/$$dir/examples/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples/1a1p ; then \
+-	    mkdir $(CWD)/$$dir/examples/1a1p ; \
+-	  fi ; \
+-	  cp $$c/examples/1a1p/*.pdb $(CWD)/$$dir/examples/1a1p/. ; \
+-	  cp $$c/examples/1a1p/README $(CWD)/$$dir/examples/1a1p/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples/ligands ; then \
+-	    mkdir $(CWD)/$$dir/examples/ligands ; \
+-	  fi ; \
+-	  cp $$c/examples/ligands/*.mol* $(CWD)/$$dir/examples/ligands/. ; \
++	  echo "Adding extensions" ; \
+ 	  if ! test -d $(CWD)/$$dir/extensions ; then \
+ 	    mkdir $(CWD)/$$dir/extensions ; \
+ 	  fi ; \
+ 	  echo "Adding extensions" ; \
+ 	  cp $$c/extensions/*.py $(CWD)/$$dir/extensions/. ; \
+-	  if ! test -d $(CWD)/$$dir/html  ; then \
+-	    mkdir $(CWD)/$$dir/html ; \
+-	  fi ; \
+-	  cp $$c/html/master-index.html $(CWD)/$$dir/html/. ; \
+-	  cp $$c/html/server.html $(CWD)/$$dir/html/server.html ; \
+-	  if ! test -d $(CWD)/$$dir/jmol ; then \
+-	    mkdir $(CWD)/$$dir/jmol ; \
+-	  fi ; \
+-	  echo "Adding jmol/" ; \
+-	  cp -rf $$c/jmol/*.* $(CWD)/$$dir/jmol/. ; \
+ 	  if ! test -d $(CWD)/$$dir/src ; then \
+ 	    mkdir $(CWD)/$$dir/src ; \
+ 	  fi ; \
+@@ -229,49 +179,6 @@ install:
+ 	  echo PDB2PQR has been installed in $(CWD)/$$dir ; \
+ 	  echo ; \
+ 	  cd $(CWD)/$$dir ; \
+-	  cd $$c; \
+-	  rm lastfieldfile prefixfile dir1file fieldfile ; \
+-	  echo $(URL) > url_file ; \
+-	  awk -F"/" '{print $$(NF-1)}' url_file > url_file_2 ; \
+-	  last_url=`cat url_file_2` ; \
+-	  echo $(PREFIX) > p_file ; \
+-	  awk -F"/" '{print $$(NF-1)}' p_file > p_file_2 ; \
+-	  last_p=`cat p_file_2` ; \
+-	  rm -f url_file* p_file* ; \
+-	  if test `whoami` = "root" ; then \
+-            webviewable="true" ; \
+-	    echo ${prefix} > prefix_file_tmp ; \
+-            first=`awk -F"/" '{ print $$2 }' prefix_file_tmp` ; \
+-	    second=`awk -F"/" '{ print $$3 }' prefix_file_tmp` ; \
+-	    third=`awk -F"/" '{ print $$4 }' prefix_file_tmp` ; \
+-	    rm -f prefix_file_tmp ; \
+-	    if test $$first != var || test $$second != www || test $$third != html ; then  \
+-	      webviewable=false ; \
+-	    fi ; \
+-	    if test "$$last_url" != "$$last_p" || test "$$webviewable" = "false" ; then \
+-	      echo Need to make symbolic link between $(PREFIX) and /var/www/html/"$$last_url" ; \
+-	      if test -d "/var/www/html/$$last_url" ; then \
+-	        echo "***" Warning! Directory /var/www/html/"$$last_url" already exists. ; \
+-		echo Do you want to overwrite this? \(Y/N\); \
+-		read choice ; \
+-	        while (test $$choice != "Y" && test $$choice != "y" && test $$choice != "N" && test $$choice != "n")  \
+-	          do  \
+-	          echo You have entered $$choice. Please enter Y or N: ; \
+-	          read choice ; \
+-	        done ; \
+-	        if test $$choice = "N" || test $$choice = "n" ; then  \
+-	          echo Please run configure again and specify a different --prefix ; \
+-	          exit 0 ; \
+-	        fi ; \
+-	  	rm -rf /var/www/html/"$$last_url" ; \
+-	      fi ; \
+-	      ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
+-	      echo "Symbolic link created." ; \
+-	    fi ; \
+-	  else  \
+-	    echo Ask your system administrator to make a symbolic link in /var/www/html by executing the following command; \
+-	    echo ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
+-	  fi ; \
+ 	fi
+ 
+ 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch
deleted file mode 100644
index 2ccd01785213..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.3.0/pdb2pka/pMC_mult.cpp pdb2pqr-1.3.0.new/pdb2pka/pMC_mult.cpp
---- pdb2pqr-1.3.0/pdb2pka/pMC_mult.cpp	2006-12-05 20:35:43.000000000 -0500
-+++ pdb2pqr-1.3.0.new/pdb2pka/pMC_mult.cpp	2008-06-19 08:53:22.000000000 -0400
-@@ -8,6 +8,8 @@
- //
- //
- 
-+#include <cstdlib>
-+
- void MC::reformat_arrays() {
-   //
-   // Reformat the matrix
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-ldflags.patch
deleted file mode 100644
index 57f02f264ba8..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-ldflags.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.3.0/propka/Makefile.in pdb2pqr-1.3.0.new/propka/Makefile.in
---- pdb2pqr-1.3.0/propka/Makefile.in	2007-10-11 18:26:48.000000000 -0400
-+++ pdb2pqr-1.3.0.new/propka/Makefile.in	2008-10-11 07:10:51.000000000 -0400
-@@ -169,7 +169,7 @@
- 	-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
- _propkalib.so$(EXEEXT): $(_propkalib_so_OBJECTS) $(_propkalib_so_DEPENDENCIES) 
- 	@rm -f _propkalib.so$(EXEEXT)
--	$(_propkalib_so_LINK) $(_propkalib_so_LDFLAGS) $(_propkalib_so_OBJECTS) $(_propkalib_so_LDADD) $(LIBS)
-+	$(_propkalib_so_LINK) $(_propkalib_so_LDFLAGS) $(LDFLAGS) $(_propkalib_so_OBJECTS) $(_propkalib_so_LDADD) $(LIBS)
- propka$(EXEEXT): $(propka_OBJECTS) $(propka_DEPENDENCIES) 
- 	@rm -f propka$(EXEEXT)
- 	$(F77LINK) $(propka_LDFLAGS) $(propka_OBJECTS) $(propka_LDADD) $(LIBS)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch
deleted file mode 100644
index 09405ec7c3f3..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- pdb2pka/pMC_mult.cpp.orig	2009-05-19 23:35:45.000000000 +0400
-+++ pdb2pka/pMC_mult.cpp	2009-05-19 23:36:27.000000000 +0400
-@@ -7,7 +7,7 @@
- //
- //
- //
--
-+#include <stdio.h>
- #include <cstdlib>
- 
- void MC::reformat_arrays() {
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
deleted file mode 100644
index ec3de87292b1..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild,v 1.7 2010/06/15 12:46:05 arfrever Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils
-
-DESCRIPTION="pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="dev-lang/python
-		dev-python/numpy"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-gcc4.3.patch
-	epatch "${FILESDIR}"/${P}-ldflags.patch
-}
-
-src_compile() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-	F77="${FORTRANC}" econf || die "econf failed"
-	emake || die "emake failed"
-}
-
-src_install() {
-	INPATH="$(python_get_sitedir)/${PN}"
-
-	insinto "${INPATH}"
-	doins __init__.py || \
-		die "Setting up the pdb2pqr site-package failed."
-
-	exeinto "${INPATH}"
-	doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-	exeinto "${INPATH}"/propka
-	doexe propka/_propkalib.so || \
-		die "Failed to install propka."
-
-	exeinto "${INPATH}"/extensions
-	doexe extensions/* || \
-		die "Failed to install extensions."
-
-	insinto "${INPATH}"/propka
-	doins propka/propkalib.py propka/__init__.py || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/src
-	doins src/* || die "Installing of python scripts failed."
-
-	insinto "${INPATH}"/dat
-	doins dat/* || die "Installing data failed."
-
-	# generate pdb2pqr wrapper
-	cat >> "${T}"/${PN} <<-EOF
-		#!/bin/sh
-		$(PYTHON) ${INPATH}/${PN}.py \$*
-	EOF
-
-	exeinto /usr/bin
-	doexe "${T}"/${PN} || die "Failed to install pdb2pqr wrapper."
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-	dohtml -r doc/* || die "Failed to install html docs."
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
deleted file mode 100644
index 266708692675..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild,v 1.4 2010/06/15 12:46:05 arfrever Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils python
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-lang/python
-	dev-python/numpy
-	opal? ( dev-python/zsi )"
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-ldflags.patch
-	epatch "${FILESDIR}"/${P}-automagic.patch
-	epatch "${FILESDIR}"/${P}-install.patch
-	epatch "${FILESDIR}"/${P}-gcc44.patch
-
-	sed '50,200s:CWD:DESTDIR:g' -i Makefile.am
-
-	eautoreconf
-}
-
-src_compile() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-	# Avoid automagic to numeric
-	NUMPY="$(python_get_sitedir)" \
-		F77="${FORTRANC}" \
-		econf \
-		$(use_with opal) || \
-		die "econf failed"
-	emake || die "emake failed"
-}
-
-src_test() {
-	emake -j1 test && \
-		F77="${FORTRANC}" emake -j1 adv-test || \
-		die "test failed"
-}
-
-src_install() {
-	dodir $(python_get_sitedir)/${PN}
-	emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" PREFIX=""  install || die
-
-	if use doc; then
-		cd doc
-		sh genpydoc.sh || die
-		dohtml -r *.html images pydoc || die
-		cd -
-	fi
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples || die
-	fi
-
-	INPATH="$(python_get_sitedir)/${PN}"
-
-	# generate pdb2pqr wrapper
-	cat >> "${T}"/${PN} <<-EOF
-		#!/bin/sh
-		$(PYTHON) ${INPATH}/${PN}.py \$*
-	EOF
-
-	exeinto /usr/bin
-	doexe "${T}"/${PN} || die "Failed to install pdb2pqr wrapper."
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-
-	insinto "${INPATH}"
-	doins __init__.py || \
-		die "Setting up the pdb2pqr site-package failed."
-
-	exeinto "${INPATH}"
-	doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-	insinto "${INPATH}"/dat
-	doins dat/* || die "Installing data failed."
-
-	exeinto "${INPATH}"/extensions
-	doexe extensions/* || \
-		die "Failed to install extensions."
-
-	insinto "${INPATH}"/src
-	doins src/*.py || die "Installing of python scripts failed."
-
-	exeinto "${INPATH}"/propka
-	doexe propka/_propkalib.so || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/propka
-	doins propka/propkalib.py propka/__init__.py || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/pdb2pka
-	doins pdb2pka/*.{py,so,DAT,h} || \
-		die "Failed to install pdb2pka."
-
-	insinto "${INPATH}"/pdb2pka/
-	doins pdb2pka/*.{py,so,DAT,h} || \
-		die "Failed to install pdb2pka."
-
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild
deleted file mode 100644
index 72ee264d493e..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild,v 1.2 2010/06/15 12:46:05 arfrever Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils python versionator
-
-MY_PV=$(get_version_component_range 1-2)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-lang/python
-	dev-python/numpy
-	opal? ( dev-python/zsi )"
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
-	epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
-	epatch "${FILESDIR}"/${PN}-1.4.0-install.patch
-	sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
-		|| die "Failed to fix Makefile.am"
-	eautoreconf
-}
-
-src_compile() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-
-	# Avoid automagic to numeric
-	NUMPY="$(python_get_sitedir)" \
-		F77="${FORTRANC}" \
-		econf \
-		$(use_with opal) || \
-		die "econf failed"
-	emake || die "emake failed"
-}
-
-src_test() {
-	emake -j1 test && \
-		F77="${FORTRANC}" emake -j1 adv-test \
-		|| die "tests failed"
-}
-
-src_install() {
-	dodir $(python_get_sitedir)/${PN}
-	emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" \
-		PREFIX=""  install || die "install failed"
-
-	if use doc; then
-		cd doc
-		sh genpydoc.sh \
-			|| die "genpydoc failed"
-		dohtml -r *.html images pydoc \
-			|| die "failed to install html docs"
-		cd -
-	fi
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples || die "Failed to install examples."
-	fi
-
-	INPATH="$(python_get_sitedir)/${PN}"
-
-	# generate pdb2pqr wrapper
-	cat >> "${T}"/${PN} <<-EOF
-		#!/bin/sh
-		$(PYTHON) ${INPATH}/${PN}.py \$*
-	EOF
-
-	exeinto /usr/bin
-	doexe "${T}"/${PN} || die "Failed to install pdb2pqr wrapper."
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-
-	insinto "${INPATH}"
-	doins __init__.py || \
-		die "Setting up the pdb2pqr site-package failed."
-
-	exeinto "${INPATH}"
-	doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-	insinto "${INPATH}"/dat
-	doins dat/* || die "Installing data failed."
-
-	exeinto "${INPATH}"/extensions
-	doexe extensions/* || \
-		die "Failed to install extensions."
-
-	insinto "${INPATH}"/src
-	doins src/*.py || die "Installing of python scripts failed."
-
-	exeinto "${INPATH}"/propka
-	doexe propka/_propkalib.so || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/propka
-	doins propka/propkalib.py propka/__init__.py || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/pdb2pka
-	doins pdb2pka/*.{py,so,DAT,h} || \
-		die "Failed to install pdb2pka."
-
-	insinto "${INPATH}"/pdb2pka/
-	doins pdb2pka/*.{py,so,DAT,h} || \
-		die "Failed to install pdb2pka."
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild
new file mode 100644
index 000000000000..ec9873a2834e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild
@@ -0,0 +1,141 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild,v 1.1 2010/10/14 17:53:56 jlec Exp $
+
+EAPI="3"
+
+SUPPORT_PYTHON_ABIS="1"
+PYTHON_EXPORT_PHASE_FUNCTIONS="1"
+
+inherit eutils fortran multilib flag-o-matic distutils python versionator
+
+MY_PV=$(get_version_component_range 1-2)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+LICENSE="BSD"
+HOMEPAGE="http://pdb2pqr.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="doc examples opal"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+DEPEND="
+	dev-python/numpy
+	sci-chemistry/openbabel
+	opal? ( dev-python/zsi )"
+RDEPEND="${DEPEND}"
+RESTRICT_PYTHON_ABIS="2.4 3.*"
+
+FORTRAN="g77 gfortran"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
+	epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
+	epatch "${FILESDIR}"/${PV}-install.patch
+	sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
+		|| die "Failed to fix Makefile.am"
+	python_src_prepare
+	preparation() {
+		eautoreconf
+	}
+	python_execute_function -s preparation
+}
+
+src_configure() {
+	# we need to compile the *.so as pic
+	append-flags -fPIC
+	FFLAGS="${FFLAGS} -fPIC"
+
+	configuration() {
+		# Avoid automagic to numeric
+		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
+			F77="${FORTRANC}" \
+			econf \
+			$(use_with opal) || \
+			die "econf failed"
+	}
+	python_execute_function -s configuration
+}
+
+src_test() {
+	testing() {
+		emake -j1 test \
+			|| die "tests failed"
+	}
+	python_execute_function -s testing
+}
+
+src_install() {
+	installation() {
+		dodir $(python_get_sitedir)/${PN}
+		emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
+			PREFIX=""  install || die "install failed"
+
+		INPATH="$(python_get_sitedir)/${PN}"
+
+		# generate pdb2pqr wrapper
+		cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
+			#!/bin/sh
+			$(PYTHON) ${EPREFIX}/${INPATH}/${PN}.py \$*
+		EOF
+
+		dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper."
+
+		insinto "${INPATH}"
+		doins __init__.py || \
+			die "Setting up the pdb2pqr site-package failed."
+
+		exeinto "${INPATH}"
+		doexe ${PN}.py || die "Installing pdb2pqr failed."
+
+		insinto "${INPATH}"/dat
+		doins dat/* || die "Installing data failed."
+
+		exeinto "${INPATH}"/extensions
+		doexe extensions/* || \
+			die "Failed to install extensions."
+
+		insinto "${INPATH}"/src
+		doins src/*.py || die "Installing of python scripts failed."
+
+		exeinto "${INPATH}"/propka
+		doexe propka/_propkalib.so || \
+			die "Failed to install propka."
+
+		insinto "${INPATH}"/propka
+		doins propka/propkalib.py propka/__init__.py || \
+			die "Failed to install propka."
+
+		insinto "${INPATH}"/pdb2pka
+		doins pdb2pka/*.{py,so,DAT,h} || \
+			die "Failed to install pdb2pka."
+
+		insinto "${INPATH}"/pdb2pka/
+		doins pdb2pka/*.{py,so,DAT,h} || \
+			die "Failed to install pdb2pka."
+	}
+	python_execute_function -s installation
+
+	dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
+
+	if use doc; then
+		cd doc
+		sh genpydoc.sh \
+			|| die "genpydoc failed"
+		dohtml -r *.html images pydoc \
+			|| die "failed to install html docs"
+		cd -
+	fi
+
+	if use examples; then
+		insinto /usr/share/${PN}/
+		doins -r examples || die "Failed to install examples."
+	fi
+
+	dodoc ChangeLog NEWS README AUTHORS || \
+		die "Failed to install docs"
+}