gentoo resync : 02.06.2019

13 files changed, 321 insertions, 398 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 88dc6c45c203..556564f17fc7 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index 3fb7f463629c..d8afb6a89cc3 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -1,8 +1,6 @@
 DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe
 DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b
 DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
-EBUILD molmol-2k_p2-r2.ebuild 1786 BLAKE2B eda77c9e82f6b48eb38c5f47dfdd74d5916f376cc2d07fe54542fef4c1c7ecffd90ec3af82f4abd8453b15ea2044f56280dfa14274aa3d8a549136153f43c709 SHA512 cffa98ccf69382a64b4005d8971e6ecd1ed02d4199d8b494819d62439daa74b50244f6cb599c7ea73231d60f2d45d1aa49543121fc07b0e7d2ae30da044b7240
-EBUILD molmol-2k_p2-r3.ebuild 1918 BLAKE2B 134be8d8f1c11b60117c701a9b19c5f857dc554d8cd3221eae63d8f8f2d1e7d6382da8071c1d10f08294823bb1e8acabe7c3018d4817ecc9e62959f1fb204c22 SHA512 a1442eb74cc7aaa49ca81765601d1272138ed2ca3d7cebdadedd3bee4f561abf340bcfeabe4556d893df8d1be7983ac488b8773661ffc74a93a379fd503ebf0d
-EBUILD molmol-2k_p2-r4.ebuild 1935 BLAKE2B f0efe15c919180becacbd408e9974b7699276c31307773865c78ba4a2c2d122dee693af69d3aac14f3f58417410cfc0c0701207870bd474e0cda546dceab24d9 SHA512 3a59f7e5df34e0762289e6156a24bbaa7f1853c54c8db3436beae457f1c4f7e49656234f843d529099d9e2ad79ade7aff6f463f12fd5495c58265f538156c180
-EBUILD molmol-2k_p2-r5.ebuild 1947 BLAKE2B 85d1f2c7dde895f466fa334f5163be3b21eca7cc06cadb1fa15598351ea5f4bc0400680f92ed69e42031e3bfbe6a7ffcb85d9460e55055d3760eed5429360038 SHA512 6c0b9db7453acb3a14d762317548ace5a88143d9d3add2104acab0c7c2a7c6901b2086edf5bd5c48caa5fa1059664cf2c24304a88ba28e26ff77f895c1f03084
+DIST molmol.png 509 BLAKE2B 981217602d128da2eb3765ca07580ed58164a4aa8c2d3e016cd54d9f5133418a7c87bbf0f8a83bcbd5d60ad568bf4938ce680eea315716166592e37f815b5aab SHA512 233d3be0c2e2759a8b064b4cf3708f96817f34eb2a397d5122b26a902864a0f1dca1762f8bcc6981cd030e2644cbedef9eb20c7756016fcf27565e3ed586c271
+EBUILD molmol-2k_p2-r5.ebuild 2222 BLAKE2B 701c748446929618b42916e94b2742969d7b66acb055dab37834463bd5420f22e2d0119440dd58685236054a61745a36d8cd385dfd1593217595a48f9978111b SHA512 49dafa2d8a771ec2f8e3ff76f16790d61de84419037f7132581ef5de3f7c2ba12aedaf2ec778139420996d610788aef4c23ee8ac4339a8fe81cba4d36f99ebf8
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
deleted file mode 100644
index 888c738d4f15..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils multilib prefix toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	|| (
-		(	media-libs/mesa
-			x11-libs/libGLw )
-		media-libs/mesa[motif] )
-	media-libs/libpng:0
-	media-libs/tiff:0
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	epatch "${WORKDIR}"/patches/prefix.patch
-	eprefixify molmol
-
-	epatch "${WORKDIR}"/patches/ldflags.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
-		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-i "${S}"/makedef || die
-
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	newexe src/main/molmol molmol.lnx
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	dodoc HISTORY README
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
deleted file mode 100644
index 22f3e6a03bdf..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils multilib prefix toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	|| (
-		(	media-libs/mesa
-			x11-libs/libGLw )
-		media-libs/mesa[motif] )
-	media-libs/libpng:0
-	media-libs/tiff:0
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	epatch "${WORKDIR}"/patches/prefix.patch
-	eprefixify molmol
-
-	epatch "${WORKDIR}"/patches/ldflags.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
-		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-i "${S}"/makedef || die
-
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
-
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${WORKDIR}"/patches/${P}-fink.patch
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	newexe src/main/molmol molmol.lnx
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	dodoc HISTORY README
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
deleted file mode 100644
index 26a294922182..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib prefix toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	|| (
-		(	media-libs/mesa
-			x11-libs/libGLw )
-		media-libs/mesa[motif] )
-	media-libs/libpng:0
-	media-libs/tiff:0
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg:0
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	epatch "${WORKDIR}"/patches/prefix.patch
-	eprefixify molmol
-
-	epatch "${WORKDIR}"/patches/ldflags.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
-		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-i "${S}"/makedef || die
-
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
-
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${WORKDIR}"/patches/${P}-fink.patch
-
-	tc-export AR
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	newexe src/main/molmol molmol.lnx
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	dodoc HISTORY README
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
index 41b041609f2f..a09bfe07847b 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
@@ -1,39 +1,48 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils multilib prefix toolchain-funcs
+EAPI=7
+inherit desktop prefix toolchain-funcs
 
 MY_PV="${PV/_p/.}.0"
 MY_P="${PN}-${MY_PV}"
 
 DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
+
+# Original page dead
+#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
+HOMEPAGE="
+	http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html
+	http://pjf.net/science/molmol.html
+"
 SRC_URI="
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2
+	https://dev.gentoo.org/~pacho/${PN}/${PN}.png
+"
 
 LICENSE="molmol"
 SLOT="0"
 KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-DEPEND="
+RDEPEND="
 	|| (
 		(	media-libs/mesa
 			x11-libs/libGLw )
 		media-libs/mesa[motif] )
-	media-libs/libpng:0
+	media-libs/libpng:0=
 	media-libs/tiff:0
 	sys-libs/zlib
 	virtual/glu
 	virtual/jpeg:0
 	x11-libs/libXpm
 	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
+	x11-apps/xdpyinfo
+"
+DEPEND="${RDEPEND}"
+BDEPEND=""
 
 S="${WORKDIR}"
 
@@ -44,12 +53,14 @@ pkg_setup() {
 }
 
 src_prepare() {
+	default
+
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
+	eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
 
-	epatch "${WORKDIR}"/patches/ldflags.patch
-	epatch "${WORKDIR}"/patches/opengl.patch
+	eapply "${WORKDIR}"/patches/ldflags.patch
+	eapply "${WORKDIR}"/patches/opengl.patch
 
 	ln -s makedef.lnx "${S}"/makedef || die
 
@@ -62,14 +73,14 @@ src_prepare() {
 		-e "s:^CC.*:CC = $(tc-getCC):" \
 		-i "${S}"/makedef || die
 
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
+	eapply "${WORKDIR}"/patches/cast.patch
+	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
 
 	# patch from fink
 	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${WORKDIR}"/patches/${P}-fink.patch
+	eapply "${WORKDIR}"/patches/${P}-fink.patch
 
-	epatch "${WORKDIR}"/patches/wild.patch
+	eapply "${WORKDIR}"/patches/wild.patch
 	tc-export AR
 }
 
@@ -81,5 +92,9 @@ src_install() {
 	insinto ${MMDIR}
 	doins -r auxil help macros man setup tips
 
-	dodoc HISTORY README
+	make_desktop_entry "${PN}"
+	doicon "${DISTDIR}/${PN}.png"
+
+	einstalldocs
+	dodoc HISTORY
 }
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 1bbeb6cfbd8e..53adcde9c072 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,8 +1,6 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.2.0.tar.gz 10514753 BLAKE2B 54bf7c639ec1af0c318438f6dcbe5878aded5cc360dee3a5f1dee4b6eea588f4242865ae8adf1e044628ad5f71aa8f6d58d0cc71baf7c1f20eed3045ed3a1cb1 SHA512 56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 EBUILD pymol-1.8.4.0-r1.ebuild 3009 BLAKE2B a076dd994e90f886e65cbb5b3f976e75eacd0a6f153c1b9417c476b53d2169495b08b6d3361ab5fcb55102a2e93a86b7f0ac6d0f25bca947f6b13f52dadde6bd SHA512 c696905b2e28c28249bf458e37dfe05237b307e3af1727fe17ebfd6a818322e6f9dc947d720df7ee29d694fe6501791f3a2f6fdc554a8e7dd43adf9727c8ece8
-EBUILD pymol-2.2.0.ebuild 3123 BLAKE2B d5d39aca27089614f5f095eaef2d89bc783f1b3144a944b5e03fa80c2eb3a15402a6041dbe7e59af8c04e9b5e4668d93073cc6173495079f803537485390830c SHA512 4c6a01df6417ea2e28f1a90a2e690b078b853e7bfc4d42f418a095ae605b7fcd316b57e201e1b0debcd15fb8102f9c6e20e7a0a7067af3e1f4372eef76faa635
-EBUILD pymol-2.3.0.ebuild 3142 BLAKE2B d03631d7794b9557c6dcac84895bb0a10766a97a5b81a93ce2a54f8b6d89c0f27f2249109e51c8a8f315948786ba6f49f716f23810d438c36de9fd1237c11de4 SHA512 c90b2798a36403c316f36a483fbc2887d84e55afea4667704543c388a5803ed678830276c4621b7499fb759ea67a29545c399acdea4d88a1c22feb9b31ca2aeb
+EBUILD pymol-2.3.0-r1.ebuild 3134 BLAKE2B 5dac0f4ca3041d02d27d9484bd3a6fe9ac037ffd367e36308ace5c6e5b3389c42cdcde5939c3a5af03f782ebb2fee994547e3251747e02f1c2df610dda17f9f1 SHA512 2fdffad45d70aa2117f295027701ebb2c6d6b523c939caf2c4d128f40e557d118377a5e93612ce1db247341509740274c8520af9f11d121cf66bb502565229d5
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.2.0.ebuild b/sci-chemistry/pymol/pymol-2.2.0.ebuild
deleted file mode 100644
index 1e53d9ab3397..000000000000
--- a/sci-chemistry/pymol/pymol-2.2.0.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils xdg-utils flag-o-matic
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	"
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-	dev-libs/msgpack[cxx]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freeglut
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/glm
-	media-libs/libpng:0=
-	media-video/mpeg-tools
-	sys-libs/zlib
-	virtual/python-pmw[${PYTHON_USEDEP}]
-	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-	sed \
-		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
-		-i setup.py || die
-
-	append-cxxflags -std=c++0x
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install \
-		--pymol-path="${EPREFIX}/usr/share/pymol"
-
-	sed \
-		-e '1d' \
-		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
-		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
-		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
-		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed \
-		-e '1i#!/usr/bin/env python' \
-		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
-
-	python_foreach_impl python_doscript "${T}"/${PN}
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
-	xdg_desktop_database_update
-	xdg_mimeinfo_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	xdg_desktop_database_update
-	xdg_mimeinfo_database_update
-}
diff --git a/sci-chemistry/pymol/pymol-2.3.0.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
index 0f1975780234..89aef82c8e96 100644
--- a/sci-chemistry/pymol/pymol-2.3.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
@@ -4,9 +4,8 @@
 EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 eutils xdg-utils flag-o-matic
+inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://www.pymol.org/"
@@ -14,7 +13,6 @@ SRC_URI="
 	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
 	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
 	"
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
@@ -26,7 +24,8 @@ DEPEND="
 	dev-libs/mmtf-cpp
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freeglut
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
 	media-libs/freetype:2
 	media-libs/glew:0=
 	media-libs/glm
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 72040c83b5ce..e170171ba4f4 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,9 +1,11 @@
-AUX vmd-1.9.1-cuda-device_ptr.patch 934 BLAKE2B c0a6f938df4f9ac8d85bc147d83904deb5c3e93d7912a11a75e31a91029d7319228b0cffc09b9e154957e9d8d148089628de262e8d30d7acab5637951d5d25b0 SHA512 274756fe17fdcc39ce471c3187f3076407d34b64e49b0006ee30525a952277b2b5c713fffa8786162dc542eef2b021f2bf7339736cf9e81b673d5146114829ed
+AUX vmd-1.9.1-cuda-device_ptr.patch 894 BLAKE2B 96aeab7c2b9d29e5cd3558e69d1365d6b7dc2d78284bb1185d63a57300a83a4c7c0b8f1c1718027ff33333d34bba116d6898fbee74ab23dfd1a77c560160d659 SHA512 9a561773562873dad077f0f2903299952cb935c69ae4bd1463a5f79d6f27ae3845ac5a24ee295ff3569d9c65ae00a9fe3974f4ead003109246f97d130c2c48bf
 AUX vmd-1.9.2-format-security.patch 550 BLAKE2B d50d05d8697c345f5888b1344c827be1282c5b2e06cfddac022d562688550a728a91a943f9b31c4247f683dcd062ab8fe8ed360aa97a202f20af0467a3148cd3 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d
+AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00
 DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51
 DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba
 EBUILD vmd-1.9.2.ebuild 7155 BLAKE2B 734137c1a02d76da109d35faf11f29138a8e48dda6d84b7151f93f2095481127f136a5f8954a80912c85ae7031a01c3374783a042bf5461fd9d1049b577a082b SHA512 3f9fc1f4cc8f6f5031de74a8211db2a9e11d07de110689832d408c343a307ba25efa354f5862d4e6d8d06d3d18b567820401fc9fcdc8818f65a33ea24a3c657b
+EBUILD vmd-1.9.3-r1.ebuild 7512 BLAKE2B cfd3259efcf3457e520f8f9ebf809373a99b6d6d5d3ab36192bf7ddd694835d7dd5c113957591d9041b583e58ac419f6cb8649f24ded0e62c89cabf056d45020 SHA512 cb0fc6cbc37c39351d51a3535569adaa69f4aee81942c0eeb83fbd7f1ca5aa3005bc8c87a74002869cc4fd81fb917601ae1bfd0a3dfd474fcf345f696cfd7d21
 EBUILD vmd-1.9.3.ebuild 7110 BLAKE2B d8ad6f495aaacdc4727e2c0e5d950a9670478aba7b55e62ed7074f06ad26151468f0f55a0786ce9dba80a181e7c36e912eaeaaa9ad7ae660739c65f482337c97 SHA512 c0eba398b6a815a59c9d8708dc796273ad3211ddc8e02aee8333f00f42f095c4d8999aaa246665ceb9282d2053c0631dc3c8ed7b60981d88ff9f8a2badf6b89a
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
index ce842448decf..67eb11bbd36b 100644
--- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
@@ -4,8 +4,8 @@
 
 diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu
 index 5bfe7bf..36faaf0 100755
---- a/vmd-1.9.1/src/CUDAMarchingCubes.cu
-+++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu
+--- a/src/CUDAMarchingCubes.cu
++++ b/src/CUDAMarchingCubes.cu
 @@ -45,6 +45,7 @@
  #include "CUDAMarchingCubes.h"
  #include <thrust/scan.h>
@@ -16,8 +16,8 @@ index 5bfe7bf..36faaf0 100755
  // (limited by shared memory size)
 diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu
 index a21ebde..56a42c8 100755
---- a/vmd-1.9.1/src/CUDAQuickSurf.cu
-+++ b/vmd-1.9.1/src/CUDAQuickSurf.cu
+--- a/src/CUDAQuickSurf.cu
++++ b/src/CUDAQuickSurf.cu
 @@ -22,6 +22,7 @@
  #include <stdlib.h>
  #include <string.h>
diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch
new file mode 100644
index 000000000000..b71cd97210a8
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch
@@ -0,0 +1,13 @@
+--- a/configure.old	2019-05-16 17:26:05.347560700 +0200
++++ b/configure	2019-05-16 17:30:25.478455770 +0200
+@@ -1105,8 +1105,8 @@
+ # This may be commented out if not required.
+ $libtachyon_defines     = "-DVMDLIBTACHYON";
+ $libtachyon_dir         = "$vmd_library_dir/tachyon";
+-$libtachyon_include     = "-I$libtachyon_dir/include";
+-$libtachyon_library     = "-L$libtachyon_dir/lib_$config_arch";
++$libtachyon_include     = "-Igentoo-libtachyon-include";
++$libtachyon_library     = "-Lgentoo-libtachyon-libs";
+ $libtachyon_libs        = "-ltachyon";
+ @libtachyon_cc          = ();
+ @libtachyon_cu          = ();
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
new file mode 100644
index 000000000000..3f24f85d6273
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
@@ -0,0 +1,262 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python2_7 )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${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[${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/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 ${P}.src.tar"
+}
+
+src_prepare() {
+	default
+
+	use cuda && cuda_sanitize
+
+	eapply "${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
+
+	# 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
+	domenu "${WORKDIR}"/vmd.desktop
+}