openbabel: add a version that accepts 15 atoms in radical/charge lines.

This violates the molfile spec, but it happens in reality (see
emolecules SDF files).

7 files changed, 103 insertions, 213 deletions

diff --git a/sci-chemistry/openbabel/ChangeLog b/sci-chemistry/openbabel/ChangeLog
index e8444c6..827386e 100644
--- a/sci-chemistry/openbabel/ChangeLog
+++ b/sci-chemistry/openbabel/ChangeLog
@@ -1,148 +1,18 @@
 # ChangeLog for sci-chemistry/openbabel
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel/ChangeLog,v 1.24 2009/04/18 15:02:22 jer Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
 
-  18 Apr 2009; Jeroen Roovers <jer@gentoo.org> openbabel-2.2.1:
-  Marked ~hppa (bug #260777).
+  14 Nov 2010; Reinis Danne <rei4dan@gmail.com> openbabel-2.3.0.ebuild,
+  +files/openbabel-2.3.0-test_lib_path.patch:
+  Fix library path for tests.
 
-*openbabel-2.2.1 (02 Mar 2009)
+  14 Nov 2010; Reinis Danne <rei4dan@gmail.com> openbabel-2.3.0.ebuild,
+  metadata.xml:
+  Use system libinchi, add gui USE-flag and build tests only if requerd.
 
-  02 Mar 2009; Marcus D. Hanwell <cryos@gentoo.org>
-  -openbabel-2.2.1_beta3-r1.ebuild, +openbabel-2.2.1.ebuild:
-  Version bump, removed old beta.
+*openbabel-2.3.0 (13 Nov 2010)
 
-  01 Mar 2009; Marcus D. Hanwell <cryos@gentoo.org>
-  +files/openbabel-2.2.0-doxyfile.patch:
-  Added missing patch file, sorry.
-
-*openbabel-2.2.1_beta3-r1 (28 Feb 2009)
-
-  28 Feb 2009; Marcus D. Hanwell <cryos@gentoo.org>
-  -openbabel-2.2.1_beta3.ebuild, +openbabel-2.2.1_beta3-r1.ebuild:
-  Integrated some improvements from My Th <rei4dan@gmail.com> in bug 212212.
-
-*openbabel-2.2.1_beta3 (18 Feb 2009)
-
-  18 Feb 2009; Marcus D. Hanwell <cryos@gentoo.org>
-  -openbabel-2.2.0_beta5.ebuild, +openbabel-2.2.1_beta3.ebuild:
-  Removed old version, added updated version of upcoming patch release.
-
-  02 Nov 2008; Mike Frysinger <vapier@gentoo.org> openbabel-2.2.0.ebuild:
-  Add ppc64 love for KDE 4.
-
-*openbabel-2.2.0 (06 Jul 2008)
-
-  06 Jul 2008; Markus Dittrich <markusle@gentoo.org> openbabel-2.0.2.ebuild,
-  -openbabel-2.1.0.ebuild, openbabel-2.1.1.ebuild,
-  -openbabel-2.2.0_beta4-r1.ebuild, +openbabel-2.2.0.ebuild:
-  Version bump (fixes bug #230803). Removed old ebuilds.
-
-*openbabel-2.2.0_beta5 (19 May 2008)
-
-  19 May 2008; Marcus D. Hanwell <cryos@gentoo.org>
-  +openbabel-2.2.0_beta5.ebuild:
-  Version bump.
-
-  27 Apr 2008; Marcus D. Hanwell <cryos@gentoo.org>
-  -openbabel-2.2.0_beta4.ebuild:
-  Removed in favour of newer revision.
-
-*openbabel-2.2.0_beta4-r1 (21 Apr 2008)
-
-  21 Apr 2008; Marcus D. Hanwell <cryos@gentoo.org>
-  +files/openbabel-2.2.0_beta4-obconversion_api_fix.diff,
-  +openbabel-2.2.0_beta4-r1.ebuild:
-  Bug 216057 - added back in missing API element.
-
-*openbabel-2.2.0_beta4 (01 Mar 2008)
-
-  01 Mar 2008; Marcus D. Hanwell <cryos@gentoo.org>
-  +openbabel-2.2.0_beta4.ebuild:
+  13 Nov 2010; Reinis Danne <rei4dan@gmail.com> +openbabel-2.3.0.ebuild,
+  +metadata.xml:
   Version bump.
 
-*openbabel-2.1.1 (11 Jul 2007)
-
-  11 Jul 2007; Marcus D. Hanwell <cryos@gentoo.org> +openbabel-2.1.1.ebuild:
-  Version bump.
-
-*openbabel-2.1.0 (08 Apr 2007)
-
-  08 Apr 2007; Marcus D. Hanwell <cryos@gentoo.org> metadata.xml,
-  +openbabel-2.1.0.ebuild:
-  Version bump and added a longdescription in metadata.
-
-  07 Jan 2007; Danny van Dyk <kugelfang@gentoo.org>
-  -openbabel-1.100.2.ebuild, -openbabel-2.0.1.ebuild:
-  QA: Removed unused versions.
-
-  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  (#148281) Change herd to sci-chemistry from sci.
-
-  28 Aug 2006; Gustavo Zacarias <gustavoz@gentoo.org>
-  openbabel-2.0.2.ebuild:
-  Stable on sparc
-
-  23 Aug 2006; <blubb@gentoo.org> openbabel-2.0.2.ebuild:
-  stable on amd64
-
-  20 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
-  openbabel-2.0.2.ebuild:
-  Stable on x86/ppc.
-
-  03 Aug 2006; Gustavo Zacarias <gustavoz@gentoo.org>
-  openbabel-2.0.1.ebuild:
-  Stable on sparc
-
-*openbabel-2.0.2 (25 Jul 2006)
-
-  25 Jul 2006; Patrick Kursawe <phosphan@gentoo.org>
-  +openbabel-2.0.2.ebuild:
-  Version bump
-
-  09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>;
-  openbabel-2.0.1.ebuild:
-  x86/ppc stable.
-
-*openbabel-2.0.1 (13 May 2006)
-
-  13 May 2006; Donnie Berkholz <spyderous@gentoo.org>;
-  +openbabel-2.0.1.ebuild:
-  Bump. Many of the changes are internal, to help adding new translators etc.
-  Also adds support for Perl and Python scripting, better batch conversion,
-  support for reading gzipped files and support for InChI identifiers.
-
-*openbabel-1.100.2 (24 Dec 2004)
-
-  24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
-  +openbabel-1.100.2.ebuild:
-  Moved from app-sci/openbabel to sci-chemistry/openbabel.
-
-  06 Jun 2004; Danny van Dyk <kugelfang@gentoo.org> openbabel-1.100.2.ebuild:
-  Marked stable on amd64.
-
-  15 May 2004; Danny van Dyk <kugelfang@gentoo.org> openbabel-1.100.2.ebuild:
-  Marked ~amd64.
-
-  01 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> openbabel-1.100.1.ebuild:
-  Cleanup
-
-  01 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> openbabel-1.100.2.ebuild:
-  Stable for ppc
-
-  24 Feb 2004; Luca Barbato <lu_zero@gentoo.org> openbabel-1.100.2.ebuild:
-  Marked ~ppc
-
-*openbabel-1.100.2 (24 Feb 2004)
-
-  24 Feb 2004; Patrick Kursawe <phosphan@gentoo.org> openbabel-1.100.2.ebuild:
-  Version bump
-
-  16 Dec 2003; Jason Wever <weeve@gentoo.org> openbabel-1.100.1.ebuild:
-  Added ~sparc keyword to fix broken dependencies in app-sci/xdrawchem.
-
-*openbabel-1.100.1 (24 Sep 2003)
-
-  24 Sep 2003; Patrick Kursawe <phosphan@gentoo.org> metadata.xml,
-  openbabel-1.100.1.ebuild:
-  Initial import, modified from bug 28536
-
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index ef4e6d2..93ec8fa 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,8 +1,10 @@
+AUX allow-15-entries-in-charge-or-radical-lines.patch 1262 RMD160 804704ec43d408584d22b81b6a8dd8c2cfc44415 SHA1 3639ecf911908314aee5d1435e5a39f2646b74f4 SHA256 2c3ed60bfc3d76c7e9055637d8d67722b5714e860a095b4592974ae5edebae11
 AUX openbabel-2.2.0-doxyfile.patch 1074 RMD160 26a22e205fde6c778ed19e961e676d99f0ffa2a7 SHA1 89c68eab7c2f144bf664f1c8abb7322430893658 SHA256 28d8b3e4730bdd347ddb1a0bff238bf52b2eb591d23d693812d99bb02c7190ec
 AUX openbabel-2.2.0_beta4-obconversion_api_fix.diff 3729 RMD160 56b58a8eeabad1f24f35056f339533ba22372941 SHA1 6a3741bbe8517687c9da6017a427868ac5cbc4aa SHA256 790ff6821debb8958bbb89fcd2ff5015207c91a5568ac4a19aba37a39ada64c7
 AUX openbabel-2.2.1-fix-gzmat-reading.patch 749 RMD160 e77d90fc9713ddee84eedb0c75f67c109278a2b9 SHA1 77202576f24bdabe0e1ef0ba6dcf9b6eb7010bdf SHA256 38ec6d0f47aa1dc5eb2378deb1990bf3ef6a73bf51881700b0b70566cdd248d5
 AUX openbabel-2.2.1-handle-negative-torsions-correctly.patch 1100 RMD160 d79903ab76d18033e326fe05ea429f692d187d0c SHA1 25f256fd2db17c3283379331a689781e8a80120f SHA256 726fee92cbe229ad7536ae7c99f30f2649ddf4195ac6effa36360fc8bd4fe96c
-DIST openbabel-2.2.1.tar.gz 6507473 RMD160 47c6afecc1a7c847052dcb8570eee89a52416586 SHA1 736fc5b69851d72b58545c5ba8c2bbd361d64e46 SHA256 822345d70778de1d2d9afe65a659f1719b8ca300066fb1fa2f473bc97c457e80
-EBUILD openbabel-2.2.1-r1.ebuild 1639 RMD160 38c207db67d35567abc376dfb5fb5e10572852a2 SHA1 6ffe9345bddd7ef65db39b038ba20fbf738d551b SHA256 78b89f50da854e7d611919fe930448bb7cb7bcec71a527e287a6f5bf8d81a489
-MISC ChangeLog 4739 RMD160 fbf10363941f75945060ce5497e7f0a76b5f6d25 SHA1 6016cc327caeeab4ce95ff887115f5c1e075d830 SHA256 d5ea4e955a4647a6a9618739e264ee2a04c56866cd576d5abc8f1b16e28418b6
-MISC metadata.xml 490 RMD160 443b08385246148cc37ad53df59658eabcb07cf3 SHA1 4a031d5b463dbcc4fea187c155f4771ee57683fc SHA256 dba1cb37e8e79e9816a15bcad3ceeffd991572ddad57ad58607ebb110a79b5a5
+AUX openbabel-2.3.0-test_lib_path.patch 637 RMD160 08d27b2de2aa7c323808373d5874dd4fd08528c9 SHA1 f5539ee8e213444f05965b3636f0bf1edd7212a7 SHA256 3f6e2f4ba94a85cb901f37142097fd74a484c948c17123af3bd646ad48ea8517
+DIST openbabel-2.3.0.tar.gz 14321281 RMD160 96dafa3c2aca544f79e08b5617ab0da845c28a16 SHA1 408a4bddb7f052fd89c57ea51b4204b721856b16 SHA256 6dadcb256d83b1f2e616fa1853dd1afadb23550a20d1c118b406231a09f861fb
+EBUILD openbabel-2.3.0.ebuild 1343 RMD160 d5dae6868949296df6a900aee545ceb51daf26b3 SHA1 f4e3fd5591b1729597f78dc58d0d9060d8e2ca32 SHA256 a3515d2ced2286041f3dddd5eed39f262909a0aae00c7a844ab40e7ed8b07fdc
+MISC ChangeLog 574 RMD160 a2c7ca5e8edac9a0733b9a6118733a8fdc7f7f82 SHA1 d751ba59632a0303fa3d9d3f940c8b479725597d SHA256 da45d5ce40c9e07adeea2fb449e78972ff129ad2c73b873914c5d411beae37e9
+MISC metadata.xml 556 RMD160 cbdac54d6194392cc84af051fcc383b92efaa442 SHA1 1688c92a6f78653de1e6d20454d8ed86fa66c372 SHA256 2c77ec519a361d0e37fc17413bb67c78fe6890c2f07626c642041c8868678739
diff --git a/sci-chemistry/openbabel/files/allow-15-entries-in-charge-or-radical-lines.patch b/sci-chemistry/openbabel/files/allow-15-entries-in-charge-or-radical-lines.patch
new file mode 100644
index 0000000..1e3017a
--- /dev/null
+++ b/sci-chemistry/openbabel/files/allow-15-entries-in-charge-or-radical-lines.patch
@@ -0,0 +1,18 @@
+diff -ur openbabel-2.3.0.orig//src/formats/mdlformat.cpp openbabel-2.3.0//src/formats/mdlformat.cpp
+--- openbabel-2.3.0.orig//src/formats/mdlformat.cpp	2010-12-07 13:05:58.612098309 -0600
++++ openbabel-2.3.0//src/formats/mdlformat.cpp	2010-12-07 15:22:15.462098309 -0600
+@@ -518,11 +518,11 @@
+         if (line.size() >= 9)
+           n = ReadUIntField((line.substr(6, 3)).c_str()); //entries on this line
+         if (n <= 0 || n > 99 || 6+n*8 > line.size()) { //catch ill-formed line
+-          obErrorLog.ThrowError(__FUNCTION__, "Error in line: Invalid number following 'M  CHG', 'M  ISO' or 'M  RAD' specification (must be an integer in range 1 to 8)\n" + line, obError);
++          obErrorLog.ThrowError(__FUNCTION__, "Error in line: Invalid number following 'M  CHG', 'M  ISO' or 'M  RAD' specification (must be an integer in range 1 to 15)\n" + line + n + line.size(), obError);
+           return false;
+         }
+-	if (n > 8) {
+-	  obErrorLog.ThrowError(__FUNCTION__, "Invalid line: too many items, only 8 items are allowed:\n" + line, obWarning);
++	if (n > 15) {
++	  obErrorLog.ThrowError(__FUNCTION__, "Invalid line: too many items, only 15 items are allowed:\n" + line, obWarning);
+ 	}
+         int pos = 10;
+         for (; n > 0; n--, pos += 8) {
diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.0-test_lib_path.patch b/sci-chemistry/openbabel/files/openbabel-2.3.0-test_lib_path.patch
new file mode 100644
index 0000000..014da6b
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-2.3.0-test_lib_path.patch
@@ -0,0 +1,12 @@
+diff -ru old/openbabel-2.3.0/test/CMakeLists.txt new/openbabel-2.3.0/test/CMakeLists.txt
+--- old/openbabel-2.3.0/test/CMakeLists.txt	2010-10-26 17:39:01.000000000 +0300
++++ new/openbabel-2.3.0/test/CMakeLists.txt	2010-11-14 18:13:32.000000000 +0200
+@@ -2,7 +2,7 @@
+ add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"")
+ 
+ # define FORMATDIR for location of format plugin binaries
+-add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"")
++add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/\\"")
+ 
+ ###########################################################
+ #  new tests using obtest.h
diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml
index d0238dd..9216990 100644
--- a/sci-chemistry/openbabel/metadata.xml
+++ b/sci-chemistry/openbabel/metadata.xml
@@ -8,4 +8,7 @@
 	search, convert, analyze, or store data from molecular modeling, chemistry,
 	solid-state materials, biochemistry, or related areas.
   </longdescription>
+  <use>
+    <flag name="gui">Build wxWidgets GUI.</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild
deleted file mode 100644
index 558d64c..0000000
--- a/sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel/openbabel-2.2.1.ebuild,v 1.2 2009/04/18 15:02:22 jer Exp $
-
-EAPI=1
-
-inherit eutils
-
-DESCRIPTION="interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
-
-KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86"
-SLOT="0"
-LICENSE="GPL-2"
-IUSE="doc"
-
-RDEPEND="!sci-chemistry/babel
-	>=dev-libs/libxml2-2.6.5
-	sys-libs/zlib"
-
-DEPEND="${RDEPEND}
-	>=dev-libs/boost-1.33.1
-	dev-lang/perl
-	doc? ( app-doc/doxygen )"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}/${PN}-2.2.0-doxyfile.patch"
-	epatch "${FILESDIR}/${P}-fix-gzmat-reading.patch"
-	epatch "${FILESDIR}/${P}-handle-negative-torsions-correctly.patch"
-}
-
-src_compile() {
-	econf \
-		--enable-static \
-		|| die "econf failed"
-	emake || die "emake failed"
-	if use doc ; then
-		emake docs || "make docs failed"
-	fi
-}
-
-src_test() {
-	emake check || die "make check failed"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "make install failed"
-	dodoc AUTHORS ChangeLog NEWS README THANKS
-	cd doc
-	dohtml *.html *.png
-	dodoc *.inc README* *.inc *.mol2
-	if use doc ; then
-		dodir /usr/share/doc/${PF}/API/html
-		insinto /usr/share/doc/${PF}/API/html
-		cd API/html
-		doins *
-	fi
-}
-
-pkg_postinst() {
-	echo
-	elog "This version of OpenBabel includes InChI version 1 (software version"
-	elog "1.02_beta). It does not produce Standard InChI/InChIKey."
-	elog "To get Standard InChI/InChIKey software version 1.02 must be used."
-}
diff --git a/sci-chemistry/openbabel/openbabel-2.3.0.ebuild b/sci-chemistry/openbabel/openbabel-2.3.0.ebuild
new file mode 100644
index 0000000..912e148
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-2.3.0.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel/openbabel-2.2.3.ebuild,v 1.11 2010/07/18 14:53:22 armin76 Exp $
+
+EAPI="3"
+
+inherit cmake-utils eutils
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="http://openbabel.sourceforge.net/"
+SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
+
+KEYWORDS="~amd64"
+SLOT="0"
+LICENSE="GPL-2"
+IUSE="doc gui"
+
+RDEPEND="
+	>=dev-libs/libxml2-2.6.5
+	>=sci-chemistry/inchi-1.03
+	gui? ( x11-libs/wxGTK )
+	!sci-chemistry/babel
+	dev-cpp/eigen:2
+	sys-libs/zlib"
+
+DEPEND="${RDEPEND}
+	>=dev-util/cmake-2.4.8"
+
+src_configure() {
+	epatch "${FILESDIR}"/allow-15-entries-in-charge-or-radical-lines.patch || die
+
+	epatch "${FILESDIR}/${P}-test_lib_path.patch" \
+		|| die "Failed to apply ${P}-test_lib_path.patch"
+	local mycmakeargs=""
+	mycmakeargs="${mycmakearg}
+		-DOPENBABEL_USE_SYSTEM_INCHI=ON
+		$(cmake-utils_use gui BUILD_GUI)
+		$(cmake-utils_use_enable test TESTS)"
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	dodoc AUTHORS ChangeLog NEWS README THANKS || die
+	dodoc doc/{*.inc,README*,*.inc,*.mol2} || die
+	dohtml doc/{*.html,*.png} || die
+	if use doc ; then
+		insinto /usr/share/doc/${PF}/API/html
+		doins doc/API/html/* || die
+	fi
+
+	cmake-utils_src_install
+}