diff options
author | Donnie Berkholz <dberkholz@gentoo.org> | 2010-12-07 15:43:16 -0600 |
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committer | Donnie Berkholz <dberkholz@gentoo.org> | 2010-12-07 15:43:16 -0600 |
commit | d4464d8a6166f90ebd47b491d6ab4bbe2e0bd75d (patch) | |
tree | 44c7d8c3d285a0366c964460e680406ed37e2844 /sci-chemistry | |
parent | New ebuild: A shell tool for executing jobs in parallel. (diff) | |
download | dberkholz-d4464d8a6166f90ebd47b491d6ab4bbe2e0bd75d.tar.gz dberkholz-d4464d8a6166f90ebd47b491d6ab4bbe2e0bd75d.tar.bz2 dberkholz-d4464d8a6166f90ebd47b491d6ab4bbe2e0bd75d.zip |
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).
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/openbabel/ChangeLog | 152 | ||||
-rw-r--r-- | sci-chemistry/openbabel/Manifest | 10 | ||||
-rw-r--r-- | sci-chemistry/openbabel/files/allow-15-entries-in-charge-or-radical-lines.patch | 18 | ||||
-rw-r--r-- | sci-chemistry/openbabel/files/openbabel-2.3.0-test_lib_path.patch | 12 | ||||
-rw-r--r-- | sci-chemistry/openbabel/metadata.xml | 3 | ||||
-rw-r--r-- | sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild | 68 | ||||
-rw-r--r-- | sci-chemistry/openbabel/openbabel-2.3.0.ebuild | 53 |
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 +} |