Fixed automagic patch to honor --without-opal (fixes bug #278199).

(Portage version: 2.1.6.13/cvs/Linux x86_64)

3 files changed, 24 insertions, 13 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 7bc7aa0be186..fb5b45682d24 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.17 2009/05/24 07:50:41 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.18 2009/09/24 23:43:11 markusle Exp $
+
+  24 Sep 2009; Markus Dittrich <markusle@gentoo.org>
+  pdb2pqr-1.4.0-r1.ebuild, files/pdb2pqr-1.4.0-automagic.patch:
+  Fixed automagic patch to honor --without-opal (fixes bug #278199).
+  Thanks much to Kacper Kowalik for his patch.
 
 *pdb2pqr-1.4.0-r1 (24 May 2009)
 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
index f837e90390e3..addb76b9b4e6 100644
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
@@ -1,5 +1,6 @@
---- configure.ac	2009-04-02 16:53:56.000000000 +0200
-+++ configure.ac.new	2009-04-22 11:41:28.000000000 +0200
+diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
+--- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
++++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
 @@ -255,38 +255,6 @@
  
    # Test for Numeric install
@@ -39,7 +40,14 @@
  
    # If failed, test for numpy
    AC_MSG_CHECKING([whether you defined numpy])
-@@ -463,23 +431,8 @@
+@@ -457,29 +425,14 @@
+   HAVE_PDB2PQR_OPAL=1
+ fi
+ 
+-if test "$PDB2PQR_OPAL_URL" != ""; then 
++if test "$PDB2PQR_OPAL_URL" != "no"; then 
+   HAVE_PDB2PQR_OPAL=1
+   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
      echo ZSI is installed
    else
      #  need to install ZSI
@@ -65,8 +73,9 @@
    fi
  fi  
  
---- pdb2pka/NEWligand_topology.py	2007-10-12 21:52:40.000000000 +0200
-+++ pdb2pka/NEWligand_topology.py.new	2009-04-22 17:01:11.000000000 +0200
+diff -Naur pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py
+--- pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py	2007-10-12 15:52:40.000000000 -0400
++++ pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py	2009-09-24 19:36:07.000000000 -0400
 @@ -3,10 +3,7 @@
  # PC 2005/09/23
  # Get ligand topologies
@@ -79,8 +88,9 @@
      
  from sets import Set
  from ligandclean.trial_templates import *
---- pdb2pka/ligand_topology.py	2008-06-13 16:15:38.000000000 +0200
-+++ pdb2pka/ligand_topology.py.new	2009-04-22 17:02:59.000000000 +0200
+diff -Naur pdb2pqr-1.4.0/pdb2pka/ligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py
+--- pdb2pqr-1.4.0/pdb2pka/ligand_topology.py	2008-06-13 10:15:38.000000000 -0400
++++ pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py	2009-09-24 19:36:07.000000000 -0400
 @@ -3,10 +3,7 @@
  # PC 2005/09/23
  # Get ligand topologies
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
index 4dce16038bc2..0121e9bcee04 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2009 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 1.2 2009/05/24 16:17:18 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild,v 1.3 2009/09/24 23:43:11 markusle Exp $
 
 inherit eutils fortran multilib flag-o-matic distutils python
 
@@ -43,8 +43,6 @@ src_compile() {
 		econf \
 		$(use_with opal) || \
 		die "econf failed"
-#die
-#		$(use_with opal)="http://ws.nbcr.net/opal/services/pdb2pqr_1.4.0" || \
 	emake || die "emake failed"
 }
 
@@ -55,9 +53,7 @@ src_test() {
 }
 
 src_install() {
-#	emake -j1 PREFIX="${D}"/$(python_get_sitedir)/${PN} install || die
 	dodir $(python_get_sitedir)/${PN}
-#	emake -j1 DESTDIR="${D}"/$(python_get_sitedir)/${PN}  install || die
 	emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" PREFIX=""  install || die
 
 	if use doc; then