openbabel: 2.3 is in the tree now.

10 files changed, 0 insertions, 316 deletions

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 <rei4dan@gmail.com> openbabel-2.3.0.ebuild,
-  +files/openbabel-2.3.0-test_lib_path.patch:
-  Fix library path for tests.
-
-  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.
-
-*openbabel-2.3.0 (13 Nov 2010)
-
-  13 Nov 2010; Reinis Danne <rei4dan@gmail.com> +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<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
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 <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/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  <mbanck@gmx.net>
-
-        * 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 @@
-<?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>
-  <use>
-    <flag name="gui">Build wxWidgets GUI.</flag>
-  </use>
-</pkgmetadata>
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
-}