--- /usr/portage/local/layman/science/sci-chemistry/modeller/modeller-9.3.ebuild	2008-04-11 08:04:35.000000000 +0200
+++ modeller-bin-9.4.ebuild	2008-05-16 12:42:26.000000000 +0200
@@ -2,25 +2,43 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-inherit eutils python
+NEED_PYTHON=2.3
+
+inherit eutils python distutils
 
 MY_PV="${PV/./v}"
-LICENSE="modeller"
+MY_PN="${PN%-bin}"
+LICENSE="MODELLER"
 KEYWORDS="~amd64 ~x86"
-DESCRIPTION="MODELLER is used for homology or comparative modeling of protein three-dimensional structures"
-SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz"
-HOMEPAGE="http://salilab.org/${PN}/"
-IUSE=""
+DESCRIPTION="Protein structure modeling by satisfaction of spatial restraints"
+SRC_URI="http://salilab.org/${MY_PN}/${MY_PV}/${MY_PN}-${MY_PV}.tar.gz"
+HOMEPAGE="http://salilab.org/${MY_PN}/"
+IUSE="doc examples python"
 RESTRICT="mirror"
 SLOT="0"
 
-RDEPEND=">=dev-lang/python-2.4"
+RDEPEND=">=dev-lang/swig-1.3
+		  python? ( dev-lang/python:2.3 )"
 DEPEND=""
 
+S="${WORKDIR}/${MY_PN}-${MY_PV}"
+
+src_unpack(){
+	unpack ${A}
+	epatch "${FILESDIR}"/${MY_PV}-setup.patch
+}
+
+src_compile(){
+	cd src/swig
+	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i
+	distutils_src_compile
+}
+
 src_install(){
 	python_version
 
-	VER=9v3
+	IN_PATH=/opt/${MY_PN}
+
 	case ${ARCH} in
 		x86)	EXECUTABLE_TYPE="i386-intel8";;
 		amd64)	EXECUTABLE_TYPE="x86_64-intel8";;
@@ -28,75 +46,90 @@
 				die "Unsupported Arch";;
 	esac
 
-	IN_PATH=/opt/modeller${VER}
-
-	sed -e "s:EXECUTABLE_TYPE${VER}=xxx:EXECUTABLE_TYPE${VER}=${EXECUTABLE_TYPE}:g" \
-	-e "s:MODINSTALL${VER}=xxx:MODINSTALL${VER}=\"${IN_PATH}\":g" \
-	modeller-${VER}/bin/modscript > "${T}/mod${VER}"
+	sed -e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECUTABLE_TYPE}:g" \
+		-e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${IN_PATH}\":g" \
+		bin/modscript > "${T}/mod${MY_PV}"
 	exeinto ${IN_PATH}/bin/
-	doexe "${T}/mod${VER}"
-	dosym ${IN_PATH}/bin/mod${VER} /opt/bin/mod${VER}
+	doexe "${T}/mod${MY_PV}"
+	dosym ${IN_PATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV}
 
 	sed -e "s;@TOPDIR\@;\"${IN_PATH}\";" \
-	-e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \
-	modeller-${VER}/bin/modpy.sh.in > "${T}/modpy.sh"
+		-e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \
+		bin/modpy.sh.in > "${T}/modpy.sh"
 	doexe "${T}/modpy.sh"
 
-	insinto ${IN_PATH}/bin/
-	doins -r modeller-${VER}/bin/{*top,lib}
-	exeinto ${IN_PATH}/bin/
-	doexe modeller-${VER}/bin/{modslave.py,mod${VER}_${EXECUTABLE_TYPE}}
+	insinto ${IN_PATH}
+	doins -r modlib
 
-	exeinto /usr/lib/python${PYVER}/site-packages/
-	doexe modeller-${VER}/lib/${EXECUTABLE_TYPE}/_modeller.so
-	dosym ${IN_PATH}/modlib/modeller /usr/lib/python${PYVER}/site-packages/modeller
-	dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/_modeller.so\
-		  /usr/lib/python${PYVER}/site-packages/_modeller.so
+	insinto ${IN_PATH}/bin
+	doins -r bin/{lib,*top}
+	exeinto ${IN_PATH}/bin
+	doexe bin/{modslave.py,mod${MY_PV}_${EXECUTABLE_TYPE}}
 
 	exeinto ${IN_PATH}/lib/${EXECUTABLE_TYPE}/
-	doexe modeller-${VER}/lib/${EXECUTABLE_TYPE}/{lib*,_modeller.so}
-	exeinto ${IN_PATH}/lib/${EXECUTABLE_TYPE}/python${PYVER}/
-	doexe modeller-${VER}/lib/${EXECUTABLE_TYPE}/python2.5/_modeller.so
-	dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so.1 \
-		  ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so
-
-	insinto ${IN_PATH}/modlib/
-	doins -r modeller-${VER}/modlib/{*mat,*lib,*prob,*mdt,*bin,*de,*inp,*ini,modeller}
-
-	insinto ${IN_PATH}/
-	doins -r modeller-${VER}/src
-
-	insinto /usr/share/${PN}/
-	doins -r modeller-${VER}/examples
-	dohtml modeller-${VER}/doc/*
-	dodoc modeller-${VER}/{README,ChangeLog}
-
-	cat >> "${T}/config.py" <<- EOF
-	install_dir = "${IN_PATH}/"
-	license = "YOURLICENSEKEY"
-	EOF
-
-	insinto ${IN_PATH}/modlib/modeller/
-	doins "${T}/config.py"
-}
-
-pkg_postinst(){
-	#Adapted from BUG #127628
-	einfo ""
-	einfo " If you need to define your own residues"
-	einfo " read the FAQ and edit the following files:"
-	einfo ""
-	einfo "    ${MY_D}/modlib/top_heav.lib"
-	einfo "    ${MY_D}/modlib/radii.lib"
-	einfo "    ${MY_D}/modlib/radii14.lib"
-	einfo "    ${MY_D}/modlib/restyp.lib"
-	einfo ""
-	einfo "    Good Luck and Happy Modeling :D"
-	einfo ""
-	echo
-	echo
-	ewarn "Obtain a license Key from"
-	ewarn "http://salilab.org/modeller/registration.html"
-	ewarn "and change the appropriate line in"
-	ewarn "${IN_PATH}/modlib/modeller/config.py"
+	doexe lib/${EXECUTABLE_TYPE}/lib*
+	dosym libmodeller.so.3 ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so
+	doexe src/swig/build/lib.linux-$(uname -m)-${PYVER}/_modeller.so
+
+	dodoc README INSTALLATION
+	if use doc; then
+		dohtml doc/*
+	fi
+	if use examples; then
+		insinto /usr/share/${PN}/
+		doins -r examples
+	fi
+
+	dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/_modeller.so \
+		  /usr/$(get_libdir)/python${PYVER}/site-packages/_modeller.so
+}
+
+pkg_postinst() {
+	python_mod_optimize "${ROOT%/}/${IN_PATH}/"
+	
+	if [[ ! -e "${IN_PATH}/modlib/modeller/config.py" ]]; then
+		echo install_dir = '"'"${IN_PATH}/"'"'> ${IN_PATH}/modlib/modeller/config.py
+	fi
+
+	if grep -q license ${IN_PATH}/modlib/modeller/config.py; then
+		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
+	else
+		ewarn "Obtain a license Key from"
+		ewarn "http://salilab.org/modeller/registration.html"
+		ewarn "And run this before using modeller:"
+		ewarn "emerge --config =${CATEGORY}/${PF}"
+		ewarn "That way you can [re]enter your license key."
+	fi
+}
+
+pkg_postrm() {
+	python_mod_cleanup "${ROOT%/}/${IN_PATH}/"
+	ewarn "This package leaves a license Key file in ${IN_PATH}/modlib/modeller/config.py"
+	ewarn "that you need to remove to completely get rid of modeller."
+}
+
+pkg_config() {
+	ewarn "Your license key is NOT checked for validity here."
+	ewarn "  Make sure you type it in correctly."
+	eerror "If you CTRL+C out of this, modeller will not run!"
+	while true
+	do
+		einfo "Please enter your license key:"
+		read license_key1
+		einfo "Please re-enter your license key:"
+		read license_key2
+		if [[ "$license_key1" == "" ]]
+		then
+			echo "You entered a blank license key.  Try again."
+		else
+			if [[ "$license_key1" == "$license_key2" ]]
+			then
+				echo license = '"'$license_key1'"' >> "${IN_PATH}/modlib/modeller/config.py"
+				einfo "Thank you!"
+				break
+			else
+				eerror "Your license key entries do not match.  Try again."
+			fi
+		fi
+	done
 }