--- /usr/portage/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild	2008-07-02 04:11:02.000000000 +0200
+++ pdb-extract-3.004-r1.ebuild	2008-12-05 17:53:51.000000000 +0100
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild,v 1.6 2008/07/02 01:39:27 dberkholz Exp $
+# $Header: $
 
 inherit eutils toolchain-funcs multilib
 
@@ -10,28 +10,36 @@
 SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
 LICENSE="PDB"
 SLOT="0"
-KEYWORDS="~amd64 ppc x86"
+KEYWORDS="~amd64 ~ppc ~x86"
 IUSE=""
 RDEPEND=""
 DEPEND="${RDEPEND}
-	sci-libs/cifparse-obj"
-PDEPEND="sci-libs/rcsb-data"
+	>=sci-libs/cifparse-obj-7.025"
+
 S="${WORKDIR}/${MY_P}"
 
 src_unpack() {
+	local libdir=$(get_libdir)
 	unpack ${A}
 	epatch "${FILESDIR}"/respect-cflags-and-fix-install.patch
 	cd "${S}"
+	epatch "${FILESDIR}"/${P}-gcc-4.3.patch
+	epatch "${FILESDIR}"/${P}-Makefile.patch
+	epatch "${FILESDIR}"/${P}-env.patch
+
+	sed -i "s:GENTOOLIBDIR:${libdir}:g" \
+		pdb-extract-v3.0/Makefile || die "fix libdir"
 
 	# Get rid of unneeded directories, to make sure we use system files
 	ebegin "Deleting redundant directories"
-	rm -rf btree-obj* ciflib-common* cifobj-common* cif-table-obj* maxit* \
-		misclib* regex* validation*
+	rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
+		misclib-v2.2 regex-v2.2 tables-v8.0
 	eend
 
 	sed -i \
 		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
-		-e "s:^\(GINCLUDE=\).*:\1-I/usr/include/rcsb:g" \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(GINCLUDES=\).*:\1-I/usr/include/cifparse-obj:g" \
 		-e "s:^\(LIBDIR=\).*:\1/usr/$(get_libdir):g" \
 		"${S}"/etc/make.*
 }
@@ -41,12 +49,18 @@
 }
 
 src_install() {
-	exeinto /usr/bin
-	doexe bin/* || die
-	dolib.a lib/* || die
+	dobin bin/* || die
+	dolib.a lib/pdb-extract.a || die
 	insinto /usr/include/rcsb
 	doins include/* || die
 	dodoc README-source README
 	insinto /usr/lib/rcsb/pdb-extract-data
 	doins pdb-extract-data/* || die
+
+	cat >> "${T}"/envd <<- EOF
+	PDB_EXTRACT="/usr/lib/rcsb/"
+	PDB_EXTRACT_ROOT="/usr/"
+	EOF
+
+	newenvd "${T}"/envd 20pdb-extract
 }