From 2eb0c82949440e08b96879491fc06e9a9d02c956 Mon Sep 17 00:00:00 2001 From: Donnie Berkholz Date: Tue, 29 Mar 2011 08:26:52 -0500 Subject: openbabel: 2.3 is in the tree now. --- sci-chemistry/openbabel/ChangeLog | 18 ---- sci-chemistry/openbabel/Manifest | 10 -- ...w-more-entries-in-charge-or-radical-lines.patch | 18 ---- .../openbabel/files/openbabel-2.2.0-doxyfile.patch | 27 ----- ...openbabel-2.2.0_beta4-obconversion_api_fix.diff | 110 --------------------- .../files/openbabel-2.2.1-fix-gzmat-reading.patch | 20 ---- ...-2.2.1-handle-negative-torsions-correctly.patch | 34 ------- .../files/openbabel-2.3.0-test_lib_path.patch | 12 --- sci-chemistry/openbabel/metadata.xml | 14 --- sci-chemistry/openbabel/openbabel-2.3.0.ebuild | 53 ---------- 10 files changed, 316 deletions(-) delete mode 100644 sci-chemistry/openbabel/ChangeLog delete mode 100644 sci-chemistry/openbabel/Manifest delete mode 100644 sci-chemistry/openbabel/files/allow-more-entries-in-charge-or-radical-lines.patch delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.2.0_beta4-obconversion_api_fix.diff delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.2.1-fix-gzmat-reading.patch delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.2.1-handle-negative-torsions-correctly.patch delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.3.0-test_lib_path.patch delete mode 100644 sci-chemistry/openbabel/metadata.xml delete mode 100644 sci-chemistry/openbabel/openbabel-2.3.0.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/openbabel/ChangeLog b/sci-chemistry/openbabel/ChangeLog deleted file mode 100644 index 827386e..0000000 --- a/sci-chemistry/openbabel/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-chemistry/openbabel -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 14 Nov 2010; Reinis Danne openbabel-2.3.0.ebuild, - +files/openbabel-2.3.0-test_lib_path.patch: - Fix library path for tests. - - 14 Nov 2010; Reinis Danne openbabel-2.3.0.ebuild, - metadata.xml: - Use system libinchi, add gui USE-flag and build tests only if requerd. - -*openbabel-2.3.0 (13 Nov 2010) - - 13 Nov 2010; Reinis Danne +openbabel-2.3.0.ebuild, - +metadata.xml: - Version bump. - diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest deleted file mode 100644 index aade817..0000000 --- a/sci-chemistry/openbabel/Manifest +++ /dev/null @@ -1,10 +0,0 @@ -AUX allow-more-entries-in-charge-or-radical-lines.patch 1247 RMD160 4ac96ac295ea2a11de00d3f8706a6d3c3984ea2c SHA1 ca5a4ee4e09f99d62f3cf507e4612228e88a19c6 SHA256 2de4ed1872e3cabbdc9ee7ff459992b84e261b19f30fc8977f4959ba3adcbeef -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 -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 1345 RMD160 293c1c0dd0d06f5556b6242d43eabe1c9a934010 SHA1 fdf0798869251337af4d803e1c419631648fbf40 SHA256 9b42438ab368dd1fb6ab98d5580cf446dd95afee1e9c433e90472d58487bc88e -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-more-entries-in-charge-or-radical-lines.patch b/sci-chemistry/openbabel/files/allow-more-entries-in-charge-or-radical-lines.patch deleted file mode 100644 index bcb95e6..0000000 --- a/sci-chemistry/openbabel/files/allow-more-entries-in-charge-or-radical-lines.patch +++ /dev/null @@ -1,18 +0,0 @@ -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 100)\n" + line, obError); - return false; - } -- if (n > 8) { -- obErrorLog.ThrowError(__FUNCTION__, "Invalid line: too many items, only 8 items are allowed:\n" + line, obWarning); -+ if (n > 100) { -+ obErrorLog.ThrowError(__FUNCTION__, "Invalid line: too many items, only 100 items are allowed:\n" + line, obWarning); - } - int pos = 10; - for (; n > 0; n--, pos += 8) { diff --git a/sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch b/sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch deleted file mode 100644 index e54a530..0000000 --- a/sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- 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 deleted file mode 100644 index 14aa4a0..0000000 --- a/sci-chemistry/openbabel/files/openbabel-2.2.0_beta4-obconversion_api_fix.diff +++ /dev/null @@ -1,110 +0,0 @@ ---- 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 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();/// 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 deleted file mode 100644 index 5baf7db..0000000 --- a/sci-chemistry/openbabel/files/openbabel-2.2.1-fix-gzmat-reading.patch +++ /dev/null @@ -1,20 +0,0 @@ -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 - ---- ./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/files/openbabel-2.2.1-handle-negative-torsions-correctly.patch b/sci-chemistry/openbabel/files/openbabel-2.2.1-handle-negative-torsions-correctly.patch deleted file mode 100644 index 82967a3..0000000 --- a/sci-chemistry/openbabel/files/openbabel-2.2.1-handle-negative-torsions-correctly.patch +++ /dev/null @@ -1,34 +0,0 @@ -r3036 - -Author: mbanck -Date: Fri May 29 19:01:19 2009 UTC (3 hours, 32 minutes ago) -Log Message: - -2009-05-29 Michael Banck - - * src/formats/gausszmatformat.cpp (ReadMolecule): Account for negative - variable reference in dihedral angles, patch by Hugh Chaffey-Millar. - Fixes PR#2798297. - ---- openbabel/branches/openbabel-2-2-x/src/formats/gausszmatformat.cpp 2009/05/28 20:13:53 3035 -+++ openbabel/branches/openbabel-2-2-x/src/formats/gausszmatformat.cpp 2009/05/29 19:01:19 3036 -@@ -350,10 +350,15 @@ - vic[j]->_c = mol.GetAtom(atoi(vs[5].c_str())); - - temp = strtod((char*)vs[6].c_str(), &endptr); -- if (endptr != (char*)vs[6].c_str()) -- vic[j]->_tor = temp; -- else -- vic[j]->_tor = variables[vs[6].c_str()]; -+ if (endptr != (char*)vs[6].c_str()) { -+ vic[j]->_tor = temp; -+ } else { -+ const char* tor_str = vs[6].c_str(); -+ if (tor_str[0] == '-') -+ vic[j]->_tor = -1 * variables[tor_str+1]; -+ else -+ vic[j]->_tor = variables[tor_str]; -+ } - } - } - } 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 deleted file mode 100644 index 014da6b..0000000 --- a/sci-chemistry/openbabel/files/openbabel-2.3.0-test_lib_path.patch +++ /dev/null @@ -1,12 +0,0 @@ -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 deleted file mode 100644 index 9216990..0000000 --- a/sci-chemistry/openbabel/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ - - - - sci-chemistry - - 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. - - - Build wxWidgets GUI. - - diff --git a/sci-chemistry/openbabel/openbabel-2.3.0.ebuild b/sci-chemistry/openbabel/openbabel-2.3.0.ebuild deleted file mode 100644 index a9f3bb2..0000000 --- a/sci-chemistry/openbabel/openbabel-2.3.0.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# 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 "${FILESDIR}"/allow-more-entries-in-charge-or-radical-lines.patch || die - - epatch "${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 -} -- cgit v1.2.3-65-gdbad