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(Portage version: 2.2.0_alpha161/cvs/Linux x86_64, unsigned Manifest commit)

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diff --git a/sci-chemistry/ghemical/ghemical-3.0.0.ebuild b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild
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+++ b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild
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+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ghemical/ghemical-3.0.0.ebuild,v 1.1 2013/02/02 05:57:09 patrick Exp $
+
+EAPI="3"
+
+inherit autotools eutils
+
+DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
+HOMEPAGE="http://bioinformatics.org/ghemical/"
+SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="openbabel seamonkey threads"
+
+RDEPEND="
+	dev-libs/glib:2
+	gnome-base/libglade:2.0
+	sci-chemistry/mpqc
+	>=sci-libs/libghemical-3.0.0
+	>=x11-libs/liboglappth-1.0.0
+	virtual/opengl
+	x11-libs/pango
+	x11-libs/gtk+:2
+	x11-libs/gtkglext
+	openbabel? ( sci-chemistry/openbabel )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	epatch "${FILESDIR}"/2.99.2-docs.patch
+	eautoreconf
+}
+
+src_configure() {
+# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now.
+
+# Change the built-in help browser.
+	if use seamonkey ; then
+		sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!"
+	else
+		sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for firefox!"
+	fi
+
+	econf \
+		$(use_enable openbabel) \
+		$(use_enable threads)
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "install failed"
+	make_desktop_entry /usr/bin/ghemical Ghemical /usr/share/ghemical/${PV}/pixmaps/ghemical.png
+}