From d42200bec37eef2a7478d88988ff00addd0a9202 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Sat, 25 Jan 2020 11:50:47 +0000
Subject: gentoo resync : 25.01.2020

---
 sci-chemistry/vmd/Manifest            |   2 +-
 sci-chemistry/vmd/vmd-1.9.3-r2.ebuild | 269 ----------------------------------
 sci-chemistry/vmd/vmd-1.9.3-r3.ebuild | 269 ++++++++++++++++++++++++++++++++++
 3 files changed, 270 insertions(+), 270 deletions(-)
 delete mode 100644 sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
 create mode 100644 sci-chemistry/vmd/vmd-1.9.3-r3.ebuild

(limited to 'sci-chemistry/vmd')

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index b97cc2703b74..d9ce76a3bb96 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -8,6 +8,6 @@ DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f
 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba
 EBUILD vmd-1.9.2.ebuild 7210 BLAKE2B 939b500dd5a0b9d8c0d3c5aaa55a7fe82a5b3c5b92da1d8a422a0c9dbfce8141d121884c5028df44f74f3c5f0c4ef7d6b85fa47cc7adbbf58db4a449d224c74a SHA512 1c8ae6a79494116d5e07cd98921c35ade1bdf7b209b673c9360d0a4edb4b881b8a000eb4c8c0b64d51616011c2e8a7858ba7ce348877eb897882a459b9688cad
 EBUILD vmd-1.9.3-r1.ebuild 7567 BLAKE2B b6a6fd153b890881be02c2a5cdc085802cb356658939401b7958e65f375f763d84872fc31b12fb21b195a810247e1624ae7a123bbf417fdd05ad4288a23c7d8c SHA512 48ef4d47d68211f7443be546566f20e4bbebdf6948027c6649d1730fb0b77e98d540a26a0ab18000a6937ae3a536b9cdefe2bc0d4c7c0724dd63f0eacd63c1ed
-EBUILD vmd-1.9.3-r2.ebuild 7748 BLAKE2B 2f0d785b37f195b6b87dd3d16902a11b899aef466134604d985f7d55380c75b471ea9540a19799cdf0b8316c709fb9453b3c041aa73c4ae623719ef1cd118fa1 SHA512 0321b3fb46edb1224ba133dbd6798ccefe5376a8a2d8fb71d416b1c1401f2676f25003f73260a70cf695c25e2b3ed32cfcea79f1c0721b193d4584db0ad1d8d1
+EBUILD vmd-1.9.3-r3.ebuild 7748 BLAKE2B 2f0d785b37f195b6b87dd3d16902a11b899aef466134604d985f7d55380c75b471ea9540a19799cdf0b8316c709fb9453b3c041aa73c4ae623719ef1cd118fa1 SHA512 0321b3fb46edb1224ba133dbd6798ccefe5376a8a2d8fb71d416b1c1401f2676f25003f73260a70cf695c25e2b3ed32cfcea79f1c0721b193d4584db0ad1d8d1
 EBUILD vmd-1.9.3.ebuild 7165 BLAKE2B fed03484e69abef1d82f52985becb144642141b18d01993f58073a4063f91e7d89cc45a506573cec2a523131eb0d75033cdd4cc3595d14bd491fca60f46540ab SHA512 83356c309cd1332a13677ca086394de9adb741e167c40f80b8585545c4c7931ad7108a80ddab6cd25aa71fb843afb11b2e12264098dd9a4933e76fac79005684
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
deleted file mode 100644
index 8d8897a57f8a..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
+++ /dev/null
@@ -1,269 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1:0=
-	dev-lang/perl
-	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )
-"
-DEPEND="${CDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-	dev-lang/swig
-"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/chemical-mime-data
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-	elog
-	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
-	elog "file may get downloaded as a compressed tarball or not. In that case"
-	elog "you will need to ensure you uncompress the file and rename it"
-	elog "as ${P}.src.tar"
-}
-
-src_prepare() {
-	xdg_src_prepare
-
-	use cuda && cuda_sanitize
-
-	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
-
-	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
-	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
-	eapply "${FILESDIR}"/${P}-tmpdir.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
-		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	# Open PDB files with VMD
-	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild
new file mode 100644
index 000000000000..8d8897a57f8a
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild
@@ -0,0 +1,269 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python2_7 )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
+	${P}.src.tar
+"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	>=dev-lang/tk-8.6.1:0=
+	dev-lang/perl
+	dev-libs/expat
+	|| (
+		dev-python/numpy-python2[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+	)
+	sci-libs/netcdf:0=
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	${PYTHON_DEPS}
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
+	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
+	sqlite? ( dev-db/sqlite:3= )
+	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
+	xinerama? ( x11-libs/libXinerama )
+"
+DEPEND="${CDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	dev-lang/swig
+"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/chemical-mime-data
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
+	elog "Place both into your DISTDIR directory"
+	elog
+	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
+	elog "file may get downloaded as a compressed tarball or not. In that case"
+	elog "you will need to ensure you uncompress the file and rename it"
+	elog "as ${P}.src.tar"
+}
+
+src_prepare() {
+	xdg_src_prepare
+
+	use cuda && cuda_sanitize
+
+	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
+
+	cd "${WORKDIR}"/plugins || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${S}" || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
+	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
+	eapply "${FILESDIR}"/${P}-tmpdir.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags::g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
+		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+	if use cuda; then
+		sed \
+			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+		sed \
+			-e '/compute_/d' \
+			-i configure || die
+		sed \
+			-e 's:-gencode .*code=sm_..::' \
+			-i src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
+		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
+		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+
+	EMAKEOPTS=(
+		TCLINC="-I${EPREFIX}/usr/include"
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
+		TCLLDFLAGS="-shared"
+		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
+		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
+		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
+		NETCDFDYNAMIC=1
+		EXPATINC="-I${EPREFIX}/usr/include"
+		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
+		EXPATLDFLAGS="-shared"
+		EXPATDYNAMIC=1
+	)
+	if use gromacs; then
+		EMAKEOPTS+=(
+			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+			TNGINC="-I${EPREFIX}/usr/include"
+			TNGLDFLAGS="-shared"
+			TNGDYNAMIC=1
+		)
+	fi
+	if use sqlite; then
+		EMAKEOPTS+=(
+			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+			SQLITEINC="-I${EPREFIX}/usr/include"
+			SQLITELDFLAGS="-shared"
+			SQLITEDYNAMIC=1
+		)
+	fi
+}
+
+src_configure() {
+	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+	use tachyon && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
+		PYTHON_LIBRARY="$(python_get_LIBS)" \
+		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
+
+	perl ./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins || die
+
+	emake \
+		${EMAKEOPTS[@]} \
+		LINUX
+
+	# build vmd
+	cd "${S}"/src || die
+	emake
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins || die
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib
+
+	# install vmd
+	cd "${S}"/src || die
+	emake install
+
+	# install docs
+	cd "${S}" || die
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd || die
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}"/vmd.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	# Open PDB files with VMD
+	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}
-- 
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