openbabel: add patch that fixes Gaussian Z-Matrix reading.

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."
+}