diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/pdb2pqr/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch | 24 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild | 6 |
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 |