diff options
author | Donnie Berkholz <dberkholz@gentoo.org> | 2009-05-28 15:50:11 -0700 |
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committer | Donnie Berkholz <dberkholz@gentoo.org> | 2009-05-28 15:50:11 -0700 |
commit | 92eee9c7ee2b4905b2d93d75274c8e9982d13584 (patch) | |
tree | a32bc33bc242e502191d1b1a8ba008661707d7b4 /sci-chemistry | |
parent | Unmask git-9999 since it's not here anymore. (diff) | |
download | dberkholz-92eee9c7ee2b4905b2d93d75274c8e9982d13584.tar.gz dberkholz-92eee9c7ee2b4905b2d93d75274c8e9982d13584.tar.bz2 dberkholz-92eee9c7ee2b4905b2d93d75274c8e9982d13584.zip |
openbabel: add patch that fixes Gaussian Z-Matrix reading.
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/openbabel/ChangeLog | 148 | ||||
-rw-r--r-- | sci-chemistry/openbabel/Manifest | 7 | ||||
-rw-r--r-- | sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch | 27 | ||||
-rw-r--r-- | sci-chemistry/openbabel/files/openbabel-2.2.0_beta4-obconversion_api_fix.diff | 110 | ||||
-rw-r--r-- | sci-chemistry/openbabel/files/openbabel-2.2.1-fix-gzmat-reading.patch | 20 | ||||
-rw-r--r-- | sci-chemistry/openbabel/metadata.xml | 11 | ||||
-rw-r--r-- | sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild | 67 |
7 files changed, 390 insertions, 0 deletions
diff --git a/sci-chemistry/openbabel/ChangeLog b/sci-chemistry/openbabel/ChangeLog new file mode 100644 index 0000000..e8444c6 --- /dev/null +++ b/sci-chemistry/openbabel/ChangeLog @@ -0,0 +1,148 @@ +# 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 $ + + 18 Apr 2009; Jeroen Roovers <jer@gentoo.org> openbabel-2.2.1: + Marked ~hppa (bug #260777). + +*openbabel-2.2.1 (02 Mar 2009) + + 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. + + 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: + 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 new file mode 100644 index 0000000..9701386 --- /dev/null +++ b/sci-chemistry/openbabel/Manifest @@ -0,0 +1,7 @@ +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 +DIST openbabel-2.2.1.tar.gz 6507473 RMD160 47c6afecc1a7c847052dcb8570eee89a52416586 SHA1 736fc5b69851d72b58545c5ba8c2bbd361d64e46 SHA256 822345d70778de1d2d9afe65a659f1719b8ca300066fb1fa2f473bc97c457e80 +EBUILD openbabel-2.2.1-r1.ebuild 1571 RMD160 378a37d4caeea70f7e91031454429e0fb7f1c8ee SHA1 a632629a439901402112ed80629b810e08a7da0b SHA256 45817827f9b4d91a72c15be52a853b39b7d9424cf489a4723a1876e72b0c313e +MISC ChangeLog 4739 RMD160 fbf10363941f75945060ce5497e7f0a76b5f6d25 SHA1 6016cc327caeeab4ce95ff887115f5c1e075d830 SHA256 d5ea4e955a4647a6a9618739e264ee2a04c56866cd576d5abc8f1b16e28418b6 +MISC metadata.xml 490 RMD160 443b08385246148cc37ad53df59658eabcb07cf3 SHA1 4a031d5b463dbcc4fea187c155f4771ee57683fc SHA256 dba1cb37e8e79e9816a15bcad3ceeffd991572ddad57ad58607ebb110a79b5a5 diff --git a/sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch b/sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch new file mode 100644 index 0000000..e54a530 --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch @@ -0,0 +1,27 @@ +--- Doxyfile.orig 2008-07-01 20:55:40.000000000 +0300 ++++ Doxyfile 2009-02-10 01:30:56.000000000 +0200 +@@ -752,13 +752,13 @@ + # each generated HTML page. If it is left blank doxygen will generate a + # standard header. + +-HTML_HEADER = doc/api-header.html ++HTML_HEADER = + + # The HTML_FOOTER tag can be used to specify a personal HTML footer for + # each generated HTML page. If it is left blank doxygen will generate a + # standard footer. + +-HTML_FOOTER = doc/api-footer.html ++HTML_FOOTER = + + # The HTML_STYLESHEET tag can be used to specify a user-defined cascading + # style sheet that is used by each HTML page. It can be used to +@@ -767,7 +767,7 @@ + # the style sheet file to the HTML output directory, so don't put your own + # stylesheet in the HTML output directory as well, or it will be erased! + +-HTML_STYLESHEET = doc/api-style.css ++HTML_STYLESHEET = + + # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, + # files or namespaces will be aligned in HTML using tables. If set to diff --git a/sci-chemistry/openbabel/files/openbabel-2.2.0_beta4-obconversion_api_fix.diff b/sci-chemistry/openbabel/files/openbabel-2.2.0_beta4-obconversion_api_fix.diff new file mode 100644 index 0000000..14aa4a0 --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.2.0_beta4-obconversion_api_fix.diff @@ -0,0 +1,110 @@ +--- include/openbabel/obconversion.h 2008-02-29 14:06:19.000000000 -0500 ++++ include/openbabel/obconversion.h 2008-04-20 20:17:14.000000000 -0400 +@@ -49,6 +49,9 @@ + + OBERROR extern OBMessageHandler obErrorLog; + ++ typedef std::map<const char*,OBFormat*,CharPtrLess > FMapType; ++ typedef FMapType::iterator Formatpos; ++ + //************************************************* + /// @brief Class to convert from one format to another. + // Class introduction in obconversion.cpp +@@ -75,7 +78,7 @@ + static OBFormat* FormatFromMIME(const char* MIME); + + ///Repeatedly called to recover available Formats +-// static bool GetNextFormat(Formatpos& itr, const char*& str,OBFormat*& pFormat); ++ static bool GetNextFormat(Formatpos& itr, const char*& str,OBFormat*& pFormat); + //@} + + /// @name Information +@@ -142,7 +145,7 @@ + { return &OptionsArray[opttyp];}; + + ///@brief Set an option of specified type, with optional text +- void AddOption(const char* opt, Option_type opttyp, const char* txt=NULL); ++ void AddOption(const char* opt, Option_type opttyp=OUTOPTIONS, const char* txt=NULL); + + bool RemoveOption(const char* opt, Option_type optype); + +@@ -279,7 +282,7 @@ + + protected: + bool SetStartAndEnd(); +-// static FMapType& FormatsMap();///<contains ID and pointer to all OBFormat classes ++ static FMapType& FormatsMap();///<contains ID and pointer to all OBFormat classes + // static FMapType& FormatsMIMEMap();///<contains MIME and pointer to all OBFormat classes + typedef std::map<std::string,int> OPAMapType; + static OPAMapType& OptionParamArray(Option_type typ); + +--- src/obconversion.cpp 2008-02-29 14:06:05.000000000 -0500 ++++ src/obconversion.cpp 2008-04-20 20:18:28.000000000 -0400 +@@ -324,6 +324,42 @@ + return count; + } + ++ FMapType& OBConversion::FormatsMap() ++ { ++ static FMapType* fm = new FMapType; ++ return *fm; ++ } ++ ++ bool OBConversion::GetNextFormat(Formatpos& itr, const char*& str,OBFormat*& pFormat) ++ { ++ pFormat = NULL; ++ if(str==NULL) ++ itr = FormatsMap().begin(); ++ else ++ itr++; ++ if(itr == FormatsMap().end()) ++ { ++ str=NULL; ++ pFormat=NULL; ++ return false; ++ } ++ static string s; ++ s =itr->first; ++ pFormat = itr->second; ++ if(pFormat) ++ { ++ string description(pFormat->Description()); ++ s += " -- "; ++ s += description.substr(0,description.find('\n')); ++ } ++ ++ if(pFormat->Flags() & NOTWRITABLE) s+=" [Read-only]"; ++ if(pFormat->Flags() & NOTREADABLE) s+=" [Write-only]"; ++ ++ str = s.c_str(); ++ return true; ++ } ++ + ////////////////////////////////////////////////////// + /// Sets the formats from their ids, e g CML. + /// If inID is NULL, the input format is left unchanged. Similarly for outID +@@ -486,7 +522,7 @@ + if(!ret) + { + //error or termination request: terminate unless +- // -e option requested and sucessfully can skip past current object ++ // -e option requested and successfully can skip past current object + if(!IsOption("e", GENOPTIONS) || pInFormat->SkipObjects(0,this)!=1) + break; + } +@@ -1093,7 +1129,14 @@ + + //INPUT + if(FileList.empty()) +- pIs = NULL; ++ { ++ pIs = NULL; ++ if(HasMultipleOutputFiles) ++ { ++ obErrorLog.ThrowError(__FUNCTION__,"Cannot use multiple output files without an input file", obError); ++ return 0; ++ } ++ } + else + { + if(FileList.size()>1 || OutputFileName.substr(0,2)=="*.") diff --git a/sci-chemistry/openbabel/files/openbabel-2.2.1-fix-gzmat-reading.patch b/sci-chemistry/openbabel/files/openbabel-2.2.1-fix-gzmat-reading.patch new file mode 100644 index 0000000..5baf7db --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.2.1-fix-gzmat-reading.patch @@ -0,0 +1,20 @@ +Because of a likely copy-and-paste error, the Gaussian Z-matrix format +was reading dihedral angles into the bond-angle parameter. This resulted +in a squashed molecule because no dihedrals were set. Fix that. + +- Donnie Berkholz <dberkholz@gentoo.org> + +--- ./src/formats/gausszmatformat.cpp.orig 2009-05-28 11:58:03.000000000 -0700 ++++ ./src/formats/gausszmatformat.cpp 2009-05-28 12:08:43.000000000 -0700 +@@ -351,9 +351,9 @@ + + temp = strtod((char*)vs[6].c_str(), &endptr); + if (endptr != (char*)vs[6].c_str()) +- vic[j]->_ang = temp; ++ vic[j]->_tor = temp; + else +- vic[j]->_ang = variables[vs[6].c_str()]; ++ vic[j]->_tor = variables[vs[6].c_str()]; + } + } + } diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml new file mode 100644 index 0000000..d0238dd --- /dev/null +++ b/sci-chemistry/openbabel/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + Open Babel is a chemical toolbox designed to speak the many languages of + chemical data. It's an open, collaborative project allowing anyone to + search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas. + </longdescription> +</pkgmetadata> diff --git a/sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild new file mode 100644 index 0000000..26e2354 --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-2.2.1-r1.ebuild @@ -0,0 +1,67 @@ +# 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" +} + +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." +} |