gentoo resync : 10.02.2020

38 files changed, 248 insertions, 150 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 11aff635982e..f2af858e028a 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index b727a4092ac8..68deb91152ce 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1,5 +1,6 @@
 AUX 1.1.2-gentoo.patch 2448 BLAKE2B f63add1d0fec8716672672af78fe8f34053bf060044e78fcf30ca6054e4075a5f12ac3a903812c9cd619dc34fa854603c8369c8acfcf17130d1b24b50b3d5373 SHA512 d8165d88f3e91064c74f1506a7f58473a74f6ebf993165827694d78170b29227dc378c61a7f096a3c49708b713583aca3d5714827d1fe43a5bb37f3d648d2613
 AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 BLAKE2B 70c55e95e9728221ba80177989fde0cc6c93b479779aa0dda45dcad79b97018fe934ea56b4ede4af20ce867b6ed39c3958a5529b8f286aec33ec7ea53d339ada SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7
+AUX autodock_vina-1.1.2-missing-debug-decl.patch 365 BLAKE2B 959b46facdce27850a1f9fd6c66ecc297e4ad089e79896b9fe2127e425bd1bfcfce5d676cf2e4336c47d3a72b0e8319c791fdf1a5807f244cf5b4528de8cbb25 SHA512 ddbdca76fca16b46fd042b57eb941b7ba67f59f46c35dc18428ea6873c8ed5f03051247b8c667a08af8de40fccb0caf851848bb9082536225cacf8eb3e313c98
 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9
-EBUILD autodock_vina-1.1.2.ebuild 932 BLAKE2B 57b02ce051bada78490a4c335f6b10d380ce900dad66c5f3228aea927d7e1814baecf357b080683df87e26ae15ab2c3b97cc3f3ceb7e93502f67e8a834257190 SHA512 39f8acb795d17786a5112a4e70bf67c6ab594d25ab5eb4b739e2b0c70a9e0548265bcd5f36b6d4915b82b43a0f463187f8d9dc5aaa62f925c5172950a6bc26ee
+EBUILD autodock_vina-1.1.2.ebuild 945 BLAKE2B 034a455deebf74c3f5170e5fd33eb30f4a2f8d5668af864d28dd0835c9a4a17367077c16c507ba5d798a2dbcb1b6d6b6f74f4de27a2b5869ef175100f0a732f8 SHA512 8174a0431930d8f591bf03601ea67b0bdf720a6d2fe102f4eda2e5d10f68c36166ae051abdd46dc2b4355213472c85da79d60d50f7ff1e7e2dd05683e06525a1
 MISC metadata.xml 1244 BLAKE2B 7df9f6f260c038c4f6b02a9fe35b54dbdc165975373ece6fb27856893536b3af7218ca1ff487ba908caa8c9beea43dc3f503fc83b6cf685754b8f17e53d771a9 SHA512 121a82bab7f4126fe5afe4ad39bbc9e397483c485e8a5771129d8eff883e87248acb1d689d47a57bf792ea8e1e23e82dec9bde811dae44e9b86a6736944c3484
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
index bbff27f85e2f..59f14e8086c9 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -1,40 +1,43 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils flag-o-matic versionator
+inherit flag-o-matic
 
-MY_P="${PN}_$(replace_all_version_separators _)"
+MY_P="${PN}_$(ver_rs 1- _)"
 
 DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
 HOMEPAGE="http://vina.scripps.edu/"
 SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz"
 
+LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="amd64 x86"
-LICENSE="Apache-2.0"
 IUSE="debug"
 
-RDEPEND="dev-libs/boost[threads]"
+RDEPEND="dev-libs/boost:=[threads]"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${MY_P}/build/linux/release
 
+PATCHES=(
+	"${FILESDIR}"/${PV}-gentoo.patch
+	"${FILESDIR}"/${P}-boost-filesystem.patch
+	"${FILESDIR}"/${P}-missing-debug-decl.patch
+)
+
 src_prepare() {
 	cd "${WORKDIR}"/${MY_P} || die
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${P}-boost-filesystem.patch
+	default
 }
 
-src_compile() {
-	local c_options
-
+src_configure() {
 	use debug || c_options="-DNDEBUG"
-
 	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+}
 
+src_compile() {
 	emake \
 		BASE="${EPREFIX}"/usr/ \
 		GPP="$(tc-getCXX)" \
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
new file mode 100644
index 000000000000..c68adb1bff21
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
@@ -0,0 +1,11 @@
+--- a/src/lib/quaternion.h
++++ b/src/lib/quaternion.h
+@@ -70,6 +70,8 @@
+ 	return sqr(q.R_component_1()) + sqr(q.R_component_2()) + sqr(q.R_component_3()) + sqr(q.R_component_4());

+ }

+ 

++bool quaternion_is_normalized(const qt& q);

++

+ inline void quaternion_normalize(qt& q) {

+ 	const fl s = quaternion_norm_sqr(q);

+ 	assert(eq(s, sqr(boost::math::abs(q))));

diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index 6992b72c5e83..6474026f3896 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,3 +1,3 @@
 DIST chemex-0.6.1.tar.gz 1449216 BLAKE2B 6b7f7597b09cd43b9bec89b6359d1f650fdd7d4f3a373e706da80dafaf438417458f34af6bc378442b5b4a84cb8222103ebc8026c85583e8dece3fad0dc77204 SHA512 40f538ef9c162759c7a6863886da8d46746ac362fc19154f0a5f3dd8703f7fea7397c3f34092c86dbce486c452e0d3b09a76e4c11ae119834d7ca4912e7f3fdf
-EBUILD chemex-0.6.1-r2.ebuild 1002 BLAKE2B 0122f5cd2ec6e61f8d24b6aa14b84e707e9344ee0dbef42eccf3a07354c36d5ac22d5be33eb390da4ff1cf9299fe47f6be4d77e1489e70fb1a9d6fd43ae89d67 SHA512 c7c5cd0a21032aa0f18ebffba48739f29a2511e387ca3ec53dc7495cac63dfb2527841a2454030179cfc217f87c29351d91b0ae2e8b038c6f87e4e644964fed7
+EBUILD chemex-0.6.1-r3.ebuild 1037 BLAKE2B 8d1d5ed8e4aea24247816a7db54644e421e720cc86e469abc62b3f0c61ad1b3178ecd6ab6318d0419f1e6d27796526f42c68f95574d65594c681142f64f71cd9 SHA512 5d0b85517336e7c47de49a0f5cc061c4eb46e6b6f02eff6d964e467cef78d19077635140d0150ad3cec698d5e98d1fae4abebcce834e1b31b485fe3b52efa75e
 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6
diff --git a/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild b/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild
index 0b85b22ffc3d..c6facbd71020 100644
--- a/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild
+++ b/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild
@@ -17,22 +17,22 @@ KEYWORDS="~amd64"
 IUSE=""
 
 RDEPEND="
-	|| (
-		>=dev-python/matplotlib-python2-1.1[${PYTHON_USEDEP}]
-		>=dev-python/matplotlib-1.1[${PYTHON_USEDEP}]
-	)
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	|| (
-		>=sci-libs/scipy-python2-0.11[${PYTHON_USEDEP}]
-		>=sci-libs/scipy-0.11[${PYTHON_USEDEP}]
-	)
-"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
+	$(python_gen_cond_dep '
+		|| (
+			>=dev-python/matplotlib-python2-1.1[${PYTHON_MULTI_USEDEP}]
+			>=dev-python/matplotlib-1.1[${PYTHON_MULTI_USEDEP}]
+		)
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+		|| (
+			>=sci-libs/scipy-python2-0.11[${PYTHON_MULTI_USEDEP}]
+			>=sci-libs/scipy-0.11[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 "
+DEPEND="${RDEPEND}"
 
 src_prepare() {
 	# Fix quotes to detect the version properly
diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest
index f0d861fd3d5a..1ea5baf98461 100644
--- a/sci-chemistry/chemical-mime-data/Manifest
+++ b/sci-chemistry/chemical-mime-data/Manifest
@@ -1,7 +1,9 @@
+AUX chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch 934 BLAKE2B 8c35adddc5dbed044a68c1f0f485faf01ae4d6fb4724e82956e9e73292e2b7e37f527a8225fce3fa4b3c6629038086f30912b8bce21d704244dc18ba52673f8a SHA512 f1ca2c08b33f77ccc1355edbbba53971e4c09ed004ec35554617d57cb6dd90c9a8a712ebfe1c7e0b01d9a97790004a048029a9e96323e7a105e9b15408a0d4cd
 AUX chemical-mime-data-0.1.94-namespace-svg.patch 798 BLAKE2B 4ab826dd3c76234c903a740b2e59dd4403d01aff856327d31c6707ab4563931d9fe4d9d57bdc19d6102d63d860eb2d88220844b934aa63cc3be984621ac52d28 SHA512 64addfac817a7f056f381515561b4311936410dc46385a3ded8c65f8fbc3d5dda731c4ec02e9369299c8122e7c43a6dc53005a4957e4165bbf958f683708513d
 AUX chemical-mime-data-0.1.94-pigz.patch 481 BLAKE2B dee47e41645b5d196326fb7439e1a96b3d46983fa9c9ec4295b17676d51f966f48ff51668203e59f18580939337d83d5ae904ef33fe2044dcc62fedd90fcb82e SHA512 a16839c1b88486ed26b4987a22594d0c3d45254d31157560135bdba008e5caa0a372d11e7db858564f1eca75452d2e43509899a91c2a8872465ea06277a1fb6c
 AUX chemical-mime-data-0.1.94-rsvg-convert.patch 1039 BLAKE2B 2eff2aa39206181f56bc802c30b4b043a0aeccef55c5d4e34755dcca69cc3afadd6cac364307729d8d83c88b7ba1d91d7200a80c7bd577e22c6ec5aec3b1921d SHA512 9c12f96f16e7982a5ba11fc546293a2e74f8918ef6eb274e3b1a618fc28aff244402c9b28ffebc2e01c8f6eb0e9e2516da82852bd0f9142c10e97f027670e60d
 AUX chemical-mime-data-0.1.94-turbomole.patch 2451 BLAKE2B 86b4b08b2af4503e0f8a525ebaa4231a3d0d3727c951b9e957c9fdac790bc41b7f01092350099a64cce66dbb61bc4cbd3654ef91834310c6c7cd1dc156ca87e8 SHA512 1bfa8818d159f0f917a24a06b0bfe926f0854f4242d8c2dbbedcd4210ffd38a459298862dc1d1aedbbe648a933db99c5d647c5409af74f88b03dd3033946df54
 DIST chemical-mime-data-0.1.94.tar.bz2 146077 BLAKE2B 9996c240446dc9571b6b4afbcdc6cf16a08e11314da9f785490b1b20933b6d18a333132492e30315c08f4441c048ec593a111815253050cfb5ab562aadb784f1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00
 EBUILD chemical-mime-data-0.1.94-r3.ebuild 1007 BLAKE2B 20203fada235e55c4614a8f5f80271adb91ecb8e21e553aeaf3ef2d0bb9f94b78ae7f4905db9698f2d4a0971cc309eb863277261dae0cb4fc19d60cc6a8037c4 SHA512 421ee83448926cc336065c22f270d2c8d4f7fdd0517b684ecd4faa002b16bad0113d9de3fb88a548a7e35e028d3572932a7fc8907d516d3878cc4cafb1474131
+EBUILD chemical-mime-data-0.1.94-r4.ebuild 1132 BLAKE2B aade2545fbe6e9c255ed7d1f3da543bb05456355d56acbded2f599e10f24117daba19cb9d51090e8dbb79090a722d39a0c8c2573672beea1c8373557c715e781 SHA512 8b5e5fcd3a83b046341b2afeabc397c8416f97f7bb47edd6b4b5270540377dd46c01ac1cc342d6ed2f6994bb063bccbb29c0fcda7cb82212a188cd135ad72dba
 MISC metadata.xml 474 BLAKE2B c4d6ffbdf66f856fc9e404202d9a9956d8bbfaeb31eb1eb056300ca5049c02d0499ead32a2013080e397eba272bd3a290b81f343baab1fb40204364bfa5208ec SHA512 59cfe759a75bf49fb020652168434fb610c2d5ba56507945253f556b5542a119bc9c9dc4f2b71ceed93f6672b31e5713cc9d76c433e95b0a08c51e9e577bac00
diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild
new file mode 100644
index 000000000000..ad703d678720
--- /dev/null
+++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit autotools xdg
+
+DESCRIPTION="A collection of data files to add support for chemical MIME types"
+HOMEPAGE="https://github.com/dleidert/chemical-mime"
+SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE=""
+
+RDEPEND="
+	x11-misc/shared-mime-info
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-util/intltool
+	dev-util/desktop-file-utils
+	dev-libs/libxslt
+	|| (
+		gnome-base/librsvg
+		media-gfx/imagemagick[xml,png,svg]
+	)
+	media-gfx/imagemagick[png]
+	virtual/pkgconfig
+"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-turbomole.patch
+	"${FILESDIR}"/${P}-pigz.patch
+	"${FILESDIR}"/${P}-namespace-svg.patch
+	"${FILESDIR}"/${P}-rsvg-convert.patch
+	# https://github.com/dleidert/chemical-mime/issues/1
+	"${FILESDIR}"/${P}-drop-turbomole-vibrational.patch
+)
+
+src_prepare() {
+	xdg_src_prepare
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--disable-update-database \
+		--without-gnome-mime \
+		--without-pixmaps \
+		--without-kde-mime \
+		--htmldir=/usr/share/doc/${PF}/html
+}
diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch
new file mode 100644
index 000000000000..4c25b1a18343
--- /dev/null
+++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch
@@ -0,0 +1,20 @@
+diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole_vibration chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in
+--- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole_vibration	2020-01-29 17:32:45.000000000 +0100
++++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in	2020-01-29 17:32:45.000000000 +0100
+@@ -1401,16 +1401,6 @@
+ 		<specification url="http://www.cosmologic.de/data/DOK_HTML/"/>
+ 	</mime-type>
+ 
+-	<mime-type type="chemical/x-turbomole-vibrational" support="yes">
+-		<_comment>Turbomole Vibrational Data File</_comment>
+-		<glob pattern="???"/>
+-		<sub-class-of type="text/plain"/>
+-		<icon kde="qc"/>
+-		<supported-by>
+-			<application name="viewmol"/>
+-		</supported-by>
+-		<specification url="http://www.cosmologic.de/data/DOK_HTML/"/>
+-	</mime-type>
+
+	<mime-type type="chemical/x-vamas-iso14976" cm:support="no">
+		<_comment>VAMAS document</_comment>
diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest
index 4f6aba7fa386..3d0221b4f199 100644
--- a/sci-chemistry/freeon/Manifest
+++ b/sci-chemistry/freeon/Manifest
@@ -2,6 +2,6 @@ AUX freeon-1.0.10-stop.patch 970 BLAKE2B 6c1e5dfe5ad881fbbceb071c53cf3fcaa187ae1
 AUX freeon-1.0.8-blas.patch 5076 BLAKE2B 198f65079462b8c7af860b98894526bdc98172035c3d0b5ccd0cfd8bca14e36790c9e20771b7ec8ce5ca4d47f2d5dc7f768c7cf1a4b4868bb48285ef518851fd SHA512 89012c6f8583a8736344a7bfa74a64bbe1af793443b7255ccb1fd73366d44527ed40c6dc3124caff1af02f4e662227c66aeced8d8526dbd26bb7a50e294b5da3
 DIST freeon-1.0.10.tar.bz2 5872019 BLAKE2B c3fde00a9ed67550bb5820ac78ff32d9f6d011db9291c45c0b7e62cacb62b48e7506d7bf1aa86e176577d18e679e859435f0d3b63289bc08e502a35f86c036d3 SHA512 5bae89d6421600792bf986f6fb7504d321d5d51782587237ecba35191e54c1ec6c5ea1fdc50ed2d339551c527e4efcc5421048ccce0404c4b06875cbd0800862
 DIST freeon-1.0.8.tar.bz2 5957707 BLAKE2B b76ae0ca17cc8407b37fac243523d2f8db63382a6f39d24380d2f01356ac78fbe2fb905bb525d979c9832b820623bffa7a0930d312c36f29138defb0d8bce106 SHA512 1227f670a73b4ea39beb26e4136ad535e126ad17d66171c31b3bd403a3886eee150cda865806a2d9dad85646ccb086a6be4f645455eab24603cb064fb725efbd
-EBUILD freeon-1.0.10.ebuild 642 BLAKE2B c25d6ac3201a4f607022e2d887101f8cd8be2f76054a93f7fd6ef95ab640e6500989393e5ef8dd8b61447fa2ff40894b46cc07bede6480060c76fa061f3078c0 SHA512 56d4d8b356f2e7b55deb3ecdd632b7e00b2a0c907d9e5dc1941ef3695e0da14ded7e025b990df46d9c3a19705123e4a5acde4a838e66a61052c9dd698def6d63
+EBUILD freeon-1.0.10.ebuild 636 BLAKE2B 79e5034c4ba6fe4e5a862d4c18566504b73cea81e16b75f2b871ec44b0e0c0f95fc4f44a53bf0d016a872efdc276359583e66947e6cce2d33daecf6986e9dd1e SHA512 d6ab2836564776cbe004f1fd4121188e625810e1a37aae24af30becb056b4e66a9d5a53923505533d9d7fd3191595d5b013413896ba9bd00d5b6a0d68f935376
 EBUILD freeon-1.0.8-r1.ebuild 626 BLAKE2B 5d5a53bd58c81ff88775f1370d0daf71e94d043b5c3fc825cb2e040cbdb4b3129c1b97b88b5eaaed1a21aaa592c0fa27fb4c7d403cacfdb5d2cfef724c8c72f9 SHA512 8474400965e790a50285e2d5687952535e5d2ee4797086dd64b7f62a990d993937f13d28f92f01057185378944f6baa939427b2a9253749cadb992afd9a72940
 MISC metadata.xml 528 BLAKE2B aa64697b42ac5f829fc893ae2c05f0bae6bb9bb16f067539ca9a11b9469a9a9f4b203eb2f0242f9fde744ea6905223da2249e50622a479975548ef552e7286dc SHA512 4eea3876d046b423706f565571cbe20dbe2ff724ecd8de7f92ba0103c83f78d9e1d28789d6c35e62a8f0527f13bdadf6303695c529b7b6622bc2e14cf57044da
diff --git a/sci-chemistry/freeon/freeon-1.0.10.ebuild b/sci-chemistry/freeon/freeon-1.0.10.ebuild
index 8dd980d33176..f17708da523a 100644
--- a/sci-chemistry/freeon/freeon-1.0.10.ebuild
+++ b/sci-chemistry/freeon/freeon-1.0.10.ebuild
@@ -4,7 +4,7 @@
 EAPI=6
 
 FORTRAN_STANDARD=90
-PYTHON_COMPAT=( python{2_7,3_6} )
+PYTHON_COMPAT=( python3_6 )
 
 inherit autotools fortran-2 python-any-r1
 
diff --git a/sci-chemistry/gmxapi/Manifest b/sci-chemistry/gmxapi/Manifest
index 8e7fbb119013..70f42f526c0f 100644
--- a/sci-chemistry/gmxapi/Manifest
+++ b/sci-chemistry/gmxapi/Manifest
@@ -1,3 +1,3 @@
 DIST gmxapi-0.0.7.1.tar.gz 671400 BLAKE2B 5db024bceaed262fc1bd2ef35c0c24a31eff12abde7766ba0eea9d5aabe04c435cdf3c79c04d7932f2110de837a0d06e1f66239f22ba6f313410ed8c9d899788 SHA512 4103d67be3c869907613ec74fc46f14b15242ad93a973fc984dbb25e79bb0bb697d9d2ad9b67a8da2500e5a89b8f78ea1ef1632455af29830e11c2bf1f11bc44
-EBUILD gmxapi-0.0.7.1.ebuild 1232 BLAKE2B ce5e1d18626a71dc760181efa246d9ca422c2710545d0096faac5f0a5f03237011cf27eae74a4d7102427355893beb5e1f830327c66d8e76dfabf788fac4ed9e SHA512 d01b515af311217f0e27c037c93188f1381937b69b9cd2c51ced1bb73a8b6d03c773faf80932d510da2d33c4fdae4267b7156f52a855b994cbcf5bfb9fb10b9c
+EBUILD gmxapi-0.0.7.1.ebuild 1230 BLAKE2B 411e89543b4ad4c0c55664c77d0e538e3031339869cc043d30570f2fde2eab168c6fe73e9f37e864328c6d64dbb3cce5f6b3c5d05823c3b0745b637688685bb1 SHA512 e35365d42f3f81f7bf404dfbb64130d5b2b30346b2b80a05e2ba35850d98932b3ce2f942160d0d28319a149f6a6a38e98230504bd8c13676b1f5e8095387897f
 MISC metadata.xml 374 BLAKE2B d93e2ad2f09971909382ad65fc5f5033487979b0694f9dc656439573973f55ce1865e5a30584e55e1c48fdd93898601ac2b11e269fb2b1c5adc3ff8dde66f35d SHA512 1c61c58e1cfbbb42342f7a87625e0044e51523f7a2f7270ecfea537c622965e64195fc88eb8f70fac648a0154a19f4a852b88383de1dcd6e17ff0ac0dc6e22d8
diff --git a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
index 5bb47665f026..d7ad455c4f27 100644
--- a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
+++ b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
@@ -34,7 +34,7 @@ src_configure() {
 	my_impl_src_configure() {
 		local mycmakeargs=(
 			-DCMAKE_STRIP="${EPREFIX}/bin/true"
-			-DCMAKE_INSTALL_PREFIX="${ED%/}/usr"
+			-DCMAKE_INSTALL_PREFIX="${ED}/usr"
 			-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
 			-DGMXAPI_INSTALL_PATH="${EPREFIX}/usr/$(get_libdir)/${EPYTHON}/site-packages/gmx"
 		)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 9fb8c517a917..b3569e237fad 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -7,9 +7,9 @@ DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f
 DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821
 EBUILD gromacs-2018.8.ebuild 8784 BLAKE2B 8c08b6c4f4278ed6455a0489b765c97c748835e49973bb83b7fe8e15d9453c8c9b6c6e26cd27a2d5a927aa87a36bfdef3874020f6658c9b2dcb774043e4547e3 SHA512 b66644847daa453b9a764faaa7f3145e16f3819d0d7ffdad12c1209a398cd03dbf7c2d60e0510f514b18f6ed8c09dfadb77bca6ff2f1eb044c65632842a7499a
 EBUILD gromacs-2018.9999.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
-EBUILD gromacs-2019.5.ebuild 9232 BLAKE2B d6983b3c0cc508e278fd5fe358d1f5351f6fb6cc028cb1ee68ffaac484b11c8d88de43ac6d2b51f64ed08c4cb73f3d17ee7bc8af3947683bd3765d6b1038212d SHA512 1ff5231b3e3e6921f65295f7baa3371dd481cb004fd045005a8f9646f54b0053645bd9eb05f2cf260482e05689d668a02e7fbb851afc4d06ff2eb139f25483a7
-EBUILD gromacs-2019.9999.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256
-EBUILD gromacs-2020.9999.ebuild 9793 BLAKE2B 0a689e24c71085d134e51a091d647e64a3bdfdbc9678f27cc0fb86b7caa8b4e1e4bdda4e8a379bfe593408fc0ea236141db9e8fd89e58987aadb2003054227d6 SHA512 0efe1abfcd815248f6a77d47e33867b88aae79d71c3be146da3264ae91036fd5305129515b3ae12cad757ad802c18ba79e588581c910fe06606883cacb2c9a19
-EBUILD gromacs-2020.ebuild 9793 BLAKE2B 0a689e24c71085d134e51a091d647e64a3bdfdbc9678f27cc0fb86b7caa8b4e1e4bdda4e8a379bfe593408fc0ea236141db9e8fd89e58987aadb2003054227d6 SHA512 0efe1abfcd815248f6a77d47e33867b88aae79d71c3be146da3264ae91036fd5305129515b3ae12cad757ad802c18ba79e588581c910fe06606883cacb2c9a19
-EBUILD gromacs-9999.ebuild 9789 BLAKE2B 661122ba2791c7af9e6db3439ee166d4a29278d06b43f4281e7e467638bb4babdb554af35148d51732cc4686ffd5460943d5b74b96d169e8eb98fdb6c8cd1324 SHA512 487f42c089de666e832d5ce25c5d1c63de977557362b0018be09a69a261ad5096908443295b609b3c8a1d059dab603d340a481ebe2c46ef63677b265b97db8c3
+EBUILD gromacs-2019.5-r1.ebuild 9270 BLAKE2B 7bc19e1950bb824a0d30b6340ea181f0089f44237e324ec926698aaacfddfc33cc6a59644bf63ce56498f6fed80c3720e143f65fbd27f3b1e4fbbd021d08573d SHA512 651a096ed78b067b5d27591d64d552c2b31b759237375a278865afcb9123986a3e5c3785d46d54b71facf54b5d62ec76610eda0f7df6aed583c3b1e6b0a940e7
+EBUILD gromacs-2019.9999.ebuild 9272 BLAKE2B 6d6484a75d2f6ec9d97a33766ff42f0a3b364f8d71f9d8c0af8265e1dffd9eee93dce6a4e7edf93fe316abef0dd8ec1ee0beb9b7cfa04f0ffbe8aa15cefb6c04 SHA512 c0e81e4312accad7377e9e221b636c1870fdf85928ca221c8272b7af6d2d422c2c44b4e6e3cca9818b922e7f194f1e45208e545d5a65e77d57aa29df1d0474dc
+EBUILD gromacs-2020-r1.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
+EBUILD gromacs-2020.9999.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
+EBUILD gromacs-9999.ebuild 9827 BLAKE2B 20a6e2e5b0d70a1c0ada0cafcb12eb170b99ebb37778f467dda1800cabb05d6a34d0dfef9bfaa04b5e6f3b781ed2e5eb97a1f61044e54e526559a9f9093be648 SHA512 19c73f34eda0ed83e58b67c7feb87e6540fb441806c27ae3b6b7d0e59c33cd220d87873fa3b3b9b5c72e8f9f73b778d41d69f21a3fded51a030d1ac6854bc2a2
 MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77
diff --git a/sci-chemistry/gromacs/gromacs-2019.5.ebuild b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
index 793ffa7a363f..dab1a95179dd 100644
--- a/sci-chemistry/gromacs/gromacs-2019.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
@@ -55,7 +55,9 @@ BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
-		dev-python/sphinx[${PYTHON_USEDEP}]
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
 		media-gfx/mscgen
 		media-gfx/graphviz
 		dev-texlive/texlive-latex
diff --git a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
index a08d3ecc9027..b3fc105b550a 100644
--- a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -55,7 +55,9 @@ BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
-		dev-python/sphinx[${PYTHON_USEDEP}]
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
 		media-gfx/mscgen
 		media-gfx/graphviz
 		dev-texlive/texlive-latex
diff --git a/sci-chemistry/gromacs/gromacs-2020.ebuild b/sci-chemistry/gromacs/gromacs-2020-r1.ebuild
index f40242167fd7..a2dcda755c8b 100644
--- a/sci-chemistry/gromacs/gromacs-2020.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020-r1.ebuild
@@ -58,7 +58,9 @@ BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
-		dev-python/sphinx[${PYTHON_USEDEP}]
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
 		media-gfx/mscgen
 		media-gfx/graphviz
 		dev-texlive/texlive-latex
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index f40242167fd7..a2dcda755c8b 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -58,7 +58,9 @@ BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
-		dev-python/sphinx[${PYTHON_USEDEP}]
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
 		media-gfx/mscgen
 		media-gfx/graphviz
 		dev-texlive/texlive-latex
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index aa6382b595a9..11c545362c66 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -58,7 +58,9 @@ BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
-		dev-python/sphinx[${PYTHON_USEDEP}]
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
 		media-gfx/mscgen
 		media-gfx/graphviz
 		dev-texlive/texlive-latex
diff --git a/sci-chemistry/nmrdepaker/Manifest b/sci-chemistry/nmrdepaker/Manifest
index a3f94f72a9a2..0348215f3e6d 100644
--- a/sci-chemistry/nmrdepaker/Manifest
+++ b/sci-chemistry/nmrdepaker/Manifest
@@ -1,3 +1,3 @@
 DIST nmrdepaker-1.0.tar.gz 2233765 BLAKE2B 9b638a36fc50d7c020d56833b6ca78d7079ad357f42431088c4c0735b7e9ce63a0e6318915ec751b42e6628c0da76b93ca16ffea1ffe6b311480e8d278ce1a1a SHA512 9d1a9048a85f85eacaeeb582c5550345efa673b1f517dad121e2b2e19125f93e71a26f2f8240ea9b8a06489814eb833e7b3653f882a46bad699b01fd1aa4299f
-EBUILD nmrdepaker-1.0-r2.ebuild 920 BLAKE2B 684f7f2a3475a04abf4592da1b70033a2c7c9f29ef99be234a927555e39f3d4a3241968e4ac7ed1c23cfb37d99c97c407251e933a7bec61c0ebd7d0a38a84dd1 SHA512 f1bf2fa3827f1f161447b439d82599ee2fd7628e96aea35fba9019dd350efa6816b1a351d3e80d4182462b0e5b3ff0629edebee38f24011d9cdfe792cbec1ca4
+EBUILD nmrdepaker-1.0-r3.ebuild 988 BLAKE2B 37878502c166f163c8d0288635cfe01b9b05e2752424203f4cc327bf3309a62d054f44acaebdd5f5a6c2b8baf2216635e5bc5e72ac6af3e8f2b89105f388db50 SHA512 60ce7c8c486d15fd717705b007629d311ce7520e422806f347a14b6bb546c657fb0241f79371a7ec8e4ff37d24aa1fc5bea54a1a7d1ea8f416a06d2077cdeb0a
 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6
diff --git a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r3.ebuild
index 043fd37324eb..66a98a99cef1 100644
--- a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild
+++ b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r3.ebuild
@@ -17,15 +17,17 @@ KEYWORDS="~amd64"
 IUSE=""
 
 RDEPEND="
-	|| (
-		>=dev-python/matplotlib-python2-0.98.5[gtk2,${PYTHON_USEDEP}]
-		>=dev-python/matplotlib-0.98.5[gtk2,${PYTHON_USEDEP}]
-	)
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		>=dev-python/numpy-1.2[${PYTHON_USEDEP}]
-	)
-	>=dev-python/pygtk-2.12:2[${PYTHON_USEDEP}]
+	$(python_gen_cond_dep '
+		|| (
+			>=dev-python/matplotlib-python2-0.98.5[gtk2,${PYTHON_MULTI_USEDEP}]
+			>=dev-python/matplotlib-0.98.5[gtk2,${PYTHON_MULTI_USEDEP}]
+		)
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			>=dev-python/numpy-1.2[${PYTHON_MULTI_USEDEP}]
+		)
+		>=dev-python/pygtk-2.12:2[${PYTHON_MULTI_USEDEP}]
+	')
 "
 DEPEND="${RDEPEND}"
 
diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest
index ed04c0eac855..5ded7d1cda4a 100644
--- a/sci-chemistry/openbabel-python/Manifest
+++ b/sci-chemistry/openbabel-python/Manifest
@@ -1,4 +1,4 @@
-AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
+AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 637 BLAKE2B e913c1d1bc93fd8443faa20fc9d7b28b89b276f7561d4208a42abd379111d19ff26179b2fbdca946a9df38e42d31f32b68423be073611e79615dcd6ae20d8f0d SHA512 0108f7bc83e046e29b2ae0b822787f58c6930de775dc94df89ba741f41cb3873a3bd2b677c11ccad4c32172e486b8331c25492127c83e4ab8d066bd129aa5538
 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
 EBUILD openbabel-python-2.4.1-r1.ebuild 2166 BLAKE2B 45ed425ebe47014c04d8f71661d0e29259d7b3d598695de0c7f0c7027b1488e70855ab4acb74b3d901f706bd58a8cb43ef7f4b1d5f927f8a16220f0cf7ffba41 SHA512 03bfaad27c45362252ebd719d7b526e977b1330e02251e8c82e0568c9f8a8759a5796dd2a22f22419d0f3465fe325d45c4f41a40b9a85edb14cd0a8ad4bed1b7
 MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch
index e23dc6020ee5..1624262e6982 100644
--- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch
+++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch
@@ -7,7 +7,7 @@ index 0ee545cf..7f4b944e 100755
  if(CMAKE_COMPILER_IS_GNUCXX)
    exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
 -  string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-+  string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
++  string(REGEX MATCH "[3456789]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
    # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
    # patch level, handle this here:
    if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 2681ad9f8d71..1e0262b0ccb0 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,5 +1,5 @@
 AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
-AUX openbabel-2.4.1-gcc-8.patch 706 BLAKE2B 085b2f5a1678c02a6a8efc5f760dc43ef311774a47d80c87efb75111ac750ec6bf520286fa74325eca71138eecff4b2772ab087d4de1b9b9a5f1c81806d6be87 SHA512 04884d47a9549d2c107bbeb9c36edbe18ee68a7edd447fce405f39a4297bdacf3f81ddf4c5c19e9728355f07960b836e684087573b3a2b7892225de8b7beaea1
+AUX openbabel-2.4.1-gcc-8.patch 707 BLAKE2B 2b40d3e573664d036ef961e0298d34e093370485a07790ec2bb9628b02928f3977c70381ba1337e1394601300c2b7b1f05306476302ef0b894ebfadcd01322d9 SHA512 c23fc09ea9cc72c84782a95cfcc59cba5270bbeb24bc50e8aa5349bb22d691c59684c9ca8fdc870733432429e3d9e0a5c660317ee19fa7e8f3fb62c9ebc2dbbd
 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
 EBUILD openbabel-2.4.1-r1.ebuild 2208 BLAKE2B 388a26c0e190f24a10081eaa0fb901fab153b05fe67cd82734a75265cdb9f18877f58ae5db0f9d0cf8b8ee0158ef967ee5eb2079245ea3b9becf41d5118439dd SHA512 e6dbdbaea505c769e6e639b8135c6da460a2918f02f72c817263425ff9618583642324a9aef3226713e20a3c500a6963b56602a289620581519c41f023822dac
diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
index 632ffa867613..a4aa3947f2ee 100644
--- a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
+++ b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
@@ -9,7 +9,7 @@ index dc38d1b..801207e 100644
  if(CMAKE_COMPILER_IS_GNUCXX)
    exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
 -  string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-+  string(REGEX MATCH "[345678]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
++  string(REGEX MATCH "[3456789]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
    # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
    # patch level, handle this here:
    if (NOT _gcc_version)
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 911dbff7ccca..d057f25d651e 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -3,5 +3,5 @@ AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b
 AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b
 AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2
 DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f
-EBUILD pdb2pqr-1.9.0-r2.ebuild 2961 BLAKE2B b8aa0bba7cb9d94f8a8fcc3246ae63d6c8a92f8148fbf28b73b683425b00bedb58069250b06e6e08e21ca483343723738c70c8c7e19309559d05c032c5bb4d62 SHA512 5e613fe7a2e927634fde7f685a8ab9429f171d469280a21c8004dd718a22e4ed5bcfb30e0d5ea6426744e0a75f4ffd366ae93d7c458d6bd72e0269e7dcb006a4
+EBUILD pdb2pqr-1.9.0-r3.ebuild 2679 BLAKE2B 882e244c9764c317df96195e4c9049a8a23872c458487ed4e897263cc99b5e1fa8bb7a3a70bf34fda447d71767ee4eb59fa49c4beecbd04fd2577438bb8aaf8e SHA512 f5037488f9ecdc9be44fb1dcc15ec55db932fc4268b61db7d95375e0e22d9f54f0315a5c0eb4398919f8620c167adbdd5e632bcdb241724ebc77efb7e7442802
 MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
index ad95f8f410fa..179e6448d605 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
@@ -5,7 +5,7 @@ EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
+inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
 
 DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
 HOMEPAGE="https://www.poissonboltzmann.org/"
@@ -19,13 +19,15 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="${PYTHON_DEPS}
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
-	opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+		sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}]
+		opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] )
+	')
+	pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )"
 DEPEND="${RDEPEND}
 	dev-lang/swig:0"
 
@@ -43,6 +45,7 @@ pkg_setup() {
 		einfo "Allow usage of ${MAXATOMS} during calculations"
 	fi
 	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
 }
 
 src_prepare() {
@@ -54,15 +57,10 @@ src_prepare() {
 	epatch "${PATCHES[@]}"
 	tc-export CXX
 	rm -rf scons || die
-
-	python_copy_sources
 }
 
 src_configure() {
-	python_configure() {
-		cd "${BUILD_DIR}" || die
-
-		cat > build_config.py <<- EOF
+	cat > build_config.py <<- EOF
 		PREFIX="${D}/$(python_get_sitedir)/${PN}"
 		#URL="http://<COMPUTER NAME>/pdb2pqr/"
 		APBS="${EPREFIX}/usr/bin/apbs"
@@ -71,51 +69,35 @@ src_configure() {
 		MAX_ATOMS=${MAXATOMS}
 		BUILD_PDB2PKA=$(usex pdb2pka True False)
 		REBUILD_SWIG=True
-		EOF
-	}
-
-	python_foreach_impl python_configure
+	EOF
 }
 
 src_compile() {
-	python_compile() {
-		cd "${BUILD_DIR}" || die
-		escons
-	}
-	python_foreach_impl python_compile
+	escons
 }
 
 src_test() {
-	python_test() {
-		local myesconsargs=( -j1 )
-		cd "${BUILD_DIR}" || die
-		escons test
-		escons advtest
-		escons complete-test
-	}
-	python_foreach_impl python_test
+	local myesconsargs=( -j1 )
+	escons test
+	escons advtest
+	escons complete-test
 }
 
 src_install() {
 	dodir /usr/share/doc/${PF}/html
-	python_install() {
-		local lib
-
-		cd "${BUILD_DIR}" || die
+	local lib
 
-		escons install
+	escons install
 
-		find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
+	find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
 
-		python_doscript "${FILESDIR}"/{${PN},pdb2pka}
+	python_doscript "${FILESDIR}"/{${PN},pdb2pka}
 
-		for lib in apbslib.py{,c,o}; do
-			dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-		done
-		dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
-		python_optimize
-	}
-	python_foreach_impl python_install
+	for lib in apbslib.py{,c,o}; do
+		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
+	done
+	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
+	python_optimize
 
 	if use doc; then
 		pushd doc > /dev/null
diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest
index fe180d2bdaba..6a19b100ad23 100644
--- a/sci-chemistry/prodecomp/Manifest
+++ b/sci-chemistry/prodecomp/Manifest
@@ -1,3 +1,3 @@
 DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d
-EBUILD prodecomp-3.0-r2.ebuild 1146 BLAKE2B fd477a14bd9e47bc8857446fc072633301f6114f30dfcc27997fc7b3d58c52a384ae8b7391bcb58f6bc23db1bbc24e0be0c7b010c971fb4d4e27c34355a38abb SHA512 b914399f357dfd514f55a82c1fb65b752725f62f0025ecdbe6524c6f0191ede74c629852d80e3c4998928649168702aa91361258c22473f499f76c3a3c4ebfc7
+EBUILD prodecomp-3.0-r3.ebuild 1191 BLAKE2B 25903c84628554ea37a9d20ee8fc0b0315d30526ed2c7e41bc6697235c04e3f9682ebb64aed7358009fd45502fcfe1fb66355c3f7209e39aeee6a1064cb34a5d SHA512 692a231b2e180d4a4114ce2441eb178adafb9ab725fcc2b1a0bdbeb675134ee823fb694546d033832393d4562c948073f47715ee29daaad9a938ce5112dd5f1e
 MISC metadata.xml 825 BLAKE2B 6874942c301b7d68f9184de8eb7482b790d2bd51c3a853132da3ed7bb0eacf54f608f816965bbfb27b81b90fecc3eee77596d73a78f5ec67703c53ad2bc2556d SHA512 94e41d5648ac93257f11f305bf2aaf926cc103240beec884142cda42c3d4e4fae5629e26b43cd945c945af706d5b5172fcd2c30ec6cb9067b152a22cd09bddcf
diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild
index e66cac2b0b4f..65683c21b0fa 100644
--- a/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild
+++ b/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild
@@ -20,10 +20,12 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 DEPEND="${PYTHON_DEPS}"
 RDEPEND="${DEPEND}
-	|| (
-		sci-libs/scipy-python2[${PYTHON_USEDEP}]
-		sci-libs/scipy[${PYTHON_USEDEP}]
-	)"
+	$(python_gen_cond_dep '
+		|| (
+			sci-libs/scipy-python2[${PYTHON_MULTI_USEDEP}]
+			sci-libs/scipy[${PYTHON_MULTI_USEDEP}]
+		)
+	')"
 
 S="${WORKDIR}"/NMRProjAnalys
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 7948415a7bf8..2b6e1d1125bd 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,4 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
-EBUILD pymol-2.3.0-r2.ebuild 3190 BLAKE2B a72434867a8589dda7a334f71e1aaa58f16d3caea1eb1615c44c2b813b1d0b84ed308369eb89c45251daf7bfbabed470e7d5abe42334b3fe28b484217fa29653 SHA512 5c2d08baa9407a2abe733d1753e622ea450b7c939b4f57d8e47adb5f57ac5a5e2b95264b6876698c70a5af926d378d75b6ba4ae02c85affbcfda7327d718ea14
+EBUILD pymol-2.3.0-r2.ebuild 3225 BLAKE2B bd378cf0a461ce741ee375bc9e4a2db7153a060125292905e4e050244de22c9ac4df2d32e3c8c049c04cdf256a6240beba9955878419fd574ce2b7965200924b SHA512 6c4ead16743147b4e983e2e626f19e489cd4676ea8610db33104e987e52759d6edd0f355675f723053eb234399b8cf7d7f8235ae479ad38ac48fe980e6cfa292
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
index 6e8433b403ec..36cc913f7b09 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
@@ -38,7 +38,9 @@ DEPEND="
 	sys-libs/zlib
 	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
 	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+	sci-chemistry/chemical-mime-data
+"
 
 S="${WORKDIR}"/${PN}-open-source-${PV}
 
diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest
index f3b0b62ccafa..56c32abe4254 100644
--- a/sci-chemistry/relax/Manifest
+++ b/sci-chemistry/relax/Manifest
@@ -1,3 +1,3 @@
 DIST relax-4.0.0.src.tar.bz2 105659752 BLAKE2B ce5fc9b7f31787f2189e75a543f8ba6fe3cd59ce7382c6c0f79c419b9f71b2d09bd16685e7fed3c9e3205be531efa2a8dc1cce707e77e2386d2a9f7a71b4b0c1 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e
-EBUILD relax-4.0.0-r3.ebuild 1760 BLAKE2B 6ea79be4c348069a5cd54ce3f9614d145febcb47a76709b5c45c9400347d9ff035cf6138005a455e2b14c1a6a498cb8ee1fdc76d8c65aa99d82bbba966bd7d16 SHA512 c3a59cbba651f752650d840b60dfda46ceb7f6f2673607e8e1b8f1265ff3595116f64830b3e00ee42a017ecd54cf27d008c841048f302a09a2c2abb87326a204
+EBUILD relax-4.0.0-r4.ebuild 1883 BLAKE2B 83dbe09ddc6feb3b7ec4af472eeac4e49c2cda90c84d2f19f19bdcf9414b97f0e7221a9e048c68535e6d5239511013738f4d969b01233034212efcefd7dca3c8 SHA512 5f657c2798e1a83626056ff7849339d3bb05f014ea579a1697e022a7b9628256c7c14a37fa71869be9d66fb1a935bc4907329c45d9cb9af7c6270ba1690046ef
 MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e
diff --git a/sci-chemistry/relax/relax-4.0.0-r3.ebuild b/sci-chemistry/relax/relax-4.0.0-r4.ebuild
index 28b0f5d9da67..ba03dbad8454 100644
--- a/sci-chemistry/relax/relax-4.0.0-r3.ebuild
+++ b/sci-chemistry/relax/relax-4.0.0-r4.ebuild
@@ -23,25 +23,27 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
 	${PYTHON_DEPS}
-	dev-python/Numdifftools[${PYTHON_USEDEP}]
-	|| (
-		dev-python/matplotlib-python2[${PYTHON_USEDEP}]
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-	)
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}]
+	$(python_gen_cond_dep "
+		dev-python/Numdifftools[\${PYTHON_MULTI_USEDEP}]
+		|| (
+			dev-python/matplotlib-python2[\${PYTHON_MULTI_USEDEP}]
+			dev-python/matplotlib[\${PYTHON_MULTI_USEDEP}]
+		)
+		|| (
+			dev-python/numpy-python2[\${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[\${PYTHON_MULTI_USEDEP}]
+		)
+		dev-python/wxpython:${WX_GTK_VER}[\${PYTHON_MULTI_USEDEP}]
+		sci-chemistry/pymol[\${PYTHON_MULTI_USEDEP}]
+		>=sci-libs/bmrblib-1.0.3[\${PYTHON_MULTI_USEDEP}]
+		>=sci-libs/minfx-1.0.11[\${PYTHON_MULTI_USEDEP}]
+		|| (
+			sci-libs/scipy-python2[\${PYTHON_MULTI_USEDEP}]
+			sci-libs/scipy[\${PYTHON_MULTI_USEDEP}]
+		)
+	")
 	sci-chemistry/molmol
-	sci-chemistry/pymol[${PYTHON_USEDEP}]
 	sci-chemistry/vmd
-	>=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}]
-	>=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}]
-	|| (
-		sci-libs/scipy-python2[${PYTHON_USEDEP}]
-		sci-libs/scipy[${PYTHON_USEDEP}]
-	)
 	sci-visualization/grace
 	sci-visualization/opendx
 	x11-libs/wxGTK:${WX_GTK_VER}[X]"
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index d9ce76a3bb96..92abd3614dc7 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -6,8 +6,8 @@ DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a
 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 7210 BLAKE2B 939b500dd5a0b9d8c0d3c5aaa55a7fe82a5b3c5b92da1d8a422a0c9dbfce8141d121884c5028df44f74f3c5f0c4ef7d6b85fa47cc7adbbf58db4a449d224c74a SHA512 1c8ae6a79494116d5e07cd98921c35ade1bdf7b209b673c9360d0a4edb4b881b8a000eb4c8c0b64d51616011c2e8a7858ba7ce348877eb897882a459b9688cad
-EBUILD vmd-1.9.3-r1.ebuild 7567 BLAKE2B b6a6fd153b890881be02c2a5cdc085802cb356658939401b7958e65f375f763d84872fc31b12fb21b195a810247e1624ae7a123bbf417fdd05ad4288a23c7d8c SHA512 48ef4d47d68211f7443be546566f20e4bbebdf6948027c6649d1730fb0b77e98d540a26a0ab18000a6937ae3a536b9cdefe2bc0d4c7c0724dd63f0eacd63c1ed
-EBUILD vmd-1.9.3-r3.ebuild 7748 BLAKE2B 2f0d785b37f195b6b87dd3d16902a11b899aef466134604d985f7d55380c75b471ea9540a19799cdf0b8316c709fb9453b3c041aa73c4ae623719ef1cd118fa1 SHA512 0321b3fb46edb1224ba133dbd6798ccefe5376a8a2d8fb71d416b1c1401f2676f25003f73260a70cf695c25e2b3ed32cfcea79f1c0721b193d4584db0ad1d8d1
-EBUILD vmd-1.9.3.ebuild 7165 BLAKE2B fed03484e69abef1d82f52985becb144642141b18d01993f58073a4063f91e7d89cc45a506573cec2a523131eb0d75033cdd4cc3595d14bd491fca60f46540ab SHA512 83356c309cd1332a13677ca086394de9adb741e167c40f80b8585545c4c7931ad7108a80ddab6cd25aa71fb843afb11b2e12264098dd9a4933e76fac79005684
+EBUILD vmd-1.9.2.ebuild 7255 BLAKE2B d59ea537a43555104edd2effc973274abae483d739bf5051efce7c1ad15e131ff0156ce2129cf882c88194f359c69eb163571e23f47025ae26cc6f85ab4999a2 SHA512 bafeb7c0448920feaa77855d29cffd2e3d9df1994c528bb738ac01551d6eb5fea4d3e681f5d4c189366e8dff973c9f8c5633f18648c31026ce749041eb5358ee
+EBUILD vmd-1.9.3-r1.ebuild 7612 BLAKE2B 62e0208cbe8fac390d942885f1e12713a88dc29eac68aa708dacfa9a2c0c0eff94982795ddc3bce47c459e8153692978744efdf520518705db0892208761dd9d SHA512 4529071928c4b63ebc35d92ff9ef7713a38d49d5579cf4351a979806ae81eb9ce3e02c438a9ce127eba217039341ae2c53e74710aa0151d4e9b0db865458facb
+EBUILD vmd-1.9.3-r4.ebuild 7793 BLAKE2B 9f023e8efb5a095d2d6b46198a4137298d7e61c697e7f1eeb57ecfa5f1df7102840b9c42f4ceeb8c5052c59031d572a50eda0a2799a11432487b15a21e97eb5c SHA512 22326601bd6908b3495ebef7e9b45f3482dbd73c8b6bd54582d02e4721bcc483ef02ea67d8e582b59777cbfc923e4464a707281a06b6459de64a7f1e301d9268
+EBUILD vmd-1.9.3.ebuild 7210 BLAKE2B a4c7a26b5c137c67adb5ea4b49acf0b8866a5b5a30840816a7c5a62c12355dfbb3bf17b2dfff39501c9d63e5bf3b479624c9186f7eaef65db455a9f29fe543a3 SHA512 fea1bf7019ae20f796be0c9fb9a5f912a491de16ecabeb6327b366120621c65401f8b4d32a575cf8d231b2c40d54f7c38537f3ce6a217856e1ec44fe49420e38
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
index 2cee984cdd47..92daf0304775 100644
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
index abf5d03202fc..f42cb4d104fe 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1:0=
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
index 8d8897a57f8a..39e7a9751cee 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1:0=
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1
diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
index 01098a723def..88394af1970d 100644
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1