gentoo resync : 16.09.2020

16 files changed, 657 insertions, 15 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 88efb4aabae7..01116e7b4fff 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest
index 4e49779120c9..cc1d83445357 100644
--- a/sci-chemistry/chemical-mime-data/Manifest
+++ b/sci-chemistry/chemical-mime-data/Manifest
@@ -5,4 +5,4 @@ AUX chemical-mime-data-0.1.94-rsvg-convert-r2.patch 1305 BLAKE2B 22809dbd6c769a0
 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-r4.ebuild 1091 BLAKE2B 2014dc00aed88c563263444a32fa008b440413ddacca3a8e08a9f07191a0595f5166715e12f31c5454b32fe0561476b4b4400aeee6e7a99c9d791f923bd8b4fa SHA512 6760106eb5303b951b3a245de3da8356cf73a7bc6ba788554b308fd31c004ff18729e7c223264df011ac2a3493e201525e394b4f2a63bc4e7fbade9f0056663f
-MISC metadata.xml 474 BLAKE2B c4d6ffbdf66f856fc9e404202d9a9956d8bbfaeb31eb1eb056300ca5049c02d0499ead32a2013080e397eba272bd3a290b81f343baab1fb40204364bfa5208ec SHA512 59cfe759a75bf49fb020652168434fb610c2d5ba56507945253f556b5542a119bc9c9dc4f2b71ceed93f6672b31e5713cc9d76c433e95b0a08c51e9e577bac00
+MISC metadata.xml 358 BLAKE2B 0797b69d8086372b01c949a083d0aff8099d5741a89026e0a207c955d4869a2c518bc840df6363b91f17026f02231b95b509da5cdff53044bc2220742214c918 SHA512 72f35d647b350ba988e253eb7c44b2bd9f4b2255df59126f4f8f1b6fd8829bdd078072e48423e5007a0ffff4a2de34ab2aa5d1a94c9e121d3a291598ffc617f6
diff --git a/sci-chemistry/chemical-mime-data/metadata.xml b/sci-chemistry/chemical-mime-data/metadata.xml
index fa1ab91bf749..a11dac390182 100644
--- a/sci-chemistry/chemical-mime-data/metadata.xml
+++ b/sci-chemistry/chemical-mime-data/metadata.xml
@@ -5,9 +5,6 @@
     <email>sci-chemistry@gentoo.org</email>
     <name>Gentoo Chemistry Project</name>
   </maintainer>
-  <longdescription lang="en">
-A collection of data files to add support for chemical MIME types.
-</longdescription>
   <upstream>
     <remote-id type="sourceforge">chemical-mime</remote-id>
   </upstream>
diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest
index 3d0221b4f199..728938a13a88 100644
--- a/sci-chemistry/freeon/Manifest
+++ b/sci-chemistry/freeon/Manifest
@@ -4,4 +4,4 @@ DIST freeon-1.0.10.tar.bz2 5872019 BLAKE2B c3fde00a9ed67550bb5820ac78ff32d9f6d01
 DIST freeon-1.0.8.tar.bz2 5957707 BLAKE2B b76ae0ca17cc8407b37fac243523d2f8db63382a6f39d24380d2f01356ac78fbe2fb905bb525d979c9832b820623bffa7a0930d312c36f29138defb0d8bce106 SHA512 1227f670a73b4ea39beb26e4136ad535e126ad17d66171c31b3bd403a3886eee150cda865806a2d9dad85646ccb086a6be4f645455eab24603cb064fb725efbd
 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
+MISC metadata.xml 376 BLAKE2B 04d5215096c154f2414dc0475c6510a66b6978bd85169311d4b17303bafea893f8e3c2afb83080d72492c5dc82a62b2522ca079e300c917c00e439da932fee68 SHA512 578a3221496eb1470d9fcac9e784f62bb39591448a35a24e1881b5be69473689770bbc928c5779b76bed8c657b1e44d929093e6a39812d135199e37a0e8938e2
diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml
index 8f4e98e7e5bf..2fe5325ae7fa 100644
--- a/sci-chemistry/freeon/metadata.xml
+++ b/sci-chemistry/freeon/metadata.xml
@@ -1,9 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<longdescription lang="en">
-		FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry.
-	</longdescription>
 	<maintainer type="person">
 		<email>nicolasbock@gentoo.org</email>
 		<name>Nicolas Bock</name>
diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest
index 9b7a014b2025..05e55b4e65bc 100644
--- a/sci-chemistry/molequeue/Manifest
+++ b/sci-chemistry/molequeue/Manifest
@@ -1,4 +1,5 @@
 AUX molequeue-0.9.0-qt-5.11b3.patch 6380 BLAKE2B 8d4a66dab1b233880269559cff9b566593ec271fc2b0982a92eec1d60a7c2c42e7186c0007be2afc956200d28c250822b36d3146d1a9ff1fb33b574f97969c60 SHA512 09429566422a1490c2621fd895238d4aeba3c324563cab411290a60942c749e9fa967dd6399f4f4efdc635fa77c339d08824def3e6a175aadc1061893df7df9c
 DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335
+EBUILD molequeue-0.9.0-r1.ebuild 1959 BLAKE2B e395842e8456fb5a9d8d1ac8bf560105d3a04a93041ce478cd3b59890fcee337a1892bda3e07802102a2ea62608b86157f990527c464f386a77119669fde9c99 SHA512 b95e16f135d040508952a46c6064a21c64d0bddb6e472c305f372cda582395088fd6622fb3b96da50d93b58aebe9e197550e5fe867cdbd2d6e9d1a998ed3c92e
 EBUILD molequeue-0.9.0.ebuild 1506 BLAKE2B e1e8a1a55cbe1da01199049ff97ca9e1950c5eb258a07e65e3d8e9eb3f5260e809c96a0abc96d1986f1fd822abc94a8a561538d8560195b8237284556e888edd SHA512 9fc628c00e53d86a4a0c9fc94bc4fc9f30375adb1ab9b89b64369770fb464544b2d49c2a8b62029f1319794d1dffcde0fdff4b6b99a3788ac5bb6d5f7792be12
 MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058
diff --git a/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild
new file mode 100644
index 000000000000..f9c43a6463b2
--- /dev/null
+++ b/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild
@@ -0,0 +1,91 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit cmake python-r1 virtualx
+
+DESCRIPTION="Abstract, manage and coordinate execution of tasks"
+HOMEPAGE="https://www.openchemistry.org/projects/molequeue/"
+SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+IUSE="+client doc server test +zeromq"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="
+	server? ( client )
+	test? ( server )
+	zeromq? ( ${PYTHON_REQUIRED_USE} )
+"
+
+BDEPEND="
+	doc? ( app-doc/doxygen )
+"
+RDEPEND="
+	dev-qt/qtcore:5
+	dev-qt/qtgui:5
+	dev-qt/qtnetwork:5
+	dev-qt/qtwidgets:5
+	zeromq? (
+		${PYTHON_DEPS}
+		net-libs/cppzmq:0=
+	)
+"
+DEPEND="${RDEPEND}"
+
+# Some tests still fail
+RESTRICT="test"
+
+src_configure() {
+	configuration() {
+		local mycmakeargs=(
+			-DMoleQueue_USE_EZHPC_UIT=OFF
+			-DBUILD_DOCUMENTATION=$(usex doc)
+			-DMoleQueue_BUILD_CLIENT=$(usex client)
+			-DMoleQueue_BUILD_APPLICATION=$(usex server)
+			-DENABLE_TESTING=$(usex test)
+			-DUSE_ZERO_MQ=$(usex zeromq)
+			-DINSTALL_LIBRARY_DIR=$(get_libdir)
+			)
+		use zeromq && \
+			mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" )
+
+		cmake_src_configure
+	}
+	if use zeromq; then
+		python_foreach_impl run_in_build_dir configuration
+	else
+		configuration
+	fi
+}
+
+src_compile() {
+	if use zeromq; then
+		python_foreach_impl run_in_build_dir cmake_src_compile all $(usex doc documentation "")
+	else
+		cmake_src_compile all $(usex doc documentation "")
+	fi
+}
+
+src_test() {
+	if use zeromq; then
+		python_foreach_impl run_in_build_dir virtx cmake_src_test
+	else
+		virtx cmake_src_test
+	fi
+}
+
+src_install() {
+	use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
+	if use zeromq; then
+		python_foreach_impl run_in_build_dir cmake_src_install
+		python_foreach_impl run_in_build_dir python_optimize
+	else
+		cmake_src_install
+	fi
+}
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 8abc86141e85..ea30c1bac1ac 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -2,6 +2,6 @@ AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02f
 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 2224 BLAKE2B 2a6c2caa6c766fc69b24b7a2d106e810bf1f8e976ab206d0269a4bef13737295ca11f83243ebfac66abc0235d1660829600d63a4f641955d79391c77d499a574 SHA512 e53c23736048745fbfeaff91fc4727e6156fdf12729529bf8f847944cd427e7a818bb35bb20d001badcbd2c5294a19bf009e696186fe0cf816eac90dfa980829
-EBUILD openbabel-2.4.1.ebuild 2053 BLAKE2B 23899cd9331281a54f1c0850dda49ff1d132d832841e15ac59d5473009cc882b1ea3ef2ff727da6d86a66d3cba2a9041596c8e9ba8e15125a0933ae4ba4d5a65 SHA512 e19d68d5e96c98a73a25e834d56c9573cc0f10b5fee1f8b3b87efc28eb4f89d64770bde90f35389554433ce9a843dadf7979e30ca59da2ac81215ccdca4dc836
+EBUILD openbabel-2.4.1-r1.ebuild 2228 BLAKE2B 7a96aeaf595bb4f948d572537611d4be2b2785637388dcb83e1ec004e9ef5b5f9641d285c52e1fe93e7c6ef176d7c8e3185f57d93c5521e6ec59192a868d496e SHA512 9b4c4c0c8439f8bb0619a22a40fd5bf17de262649c3af22874fb25d104451edfc90eed60dc41fb21cb06a779cc274c53ac8f7ce42534b1e29ed5bfbf7ba0314e
+EBUILD openbabel-2.4.1.ebuild 2057 BLAKE2B 265cc20a061747321c4a15b25cb98dbaed80fcca5be79af17fc7a5e391082f4c9df665d0aba15083d70f2511359e88bf119f960bed39d720f3f8d23df0130545 SHA512 f2a276d04439bc9b195c32e528f9ced7d4be7127f8088c45963e91d6220020dfc918b14dc76238e1e10a9fdfeec043dd45460af6766514d3fc5e954f5f85ff05
 MISC metadata.xml 665 BLAKE2B 4657b85c826c006b6d69e06240dd908a72397a32cb0c0512810e22d1b02478eaa3ab460535b300eba653a334a79c81a102007da1a901d6d1dbd04fc5e795df73 SHA512 0555e7c7401dfd5fbeee339302f8eb7a104ad6538db2839d8e89c20ac5ad2184070335677671a58eb91be2780ae485467d33302f3a14d0caab4ae8c0148f03bb
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
index febff8ef60cf..02f4b074850b 100644
--- a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
@@ -4,7 +4,7 @@
 EAPI=7
 WX_GTK_VER="3.0"
 
-inherit cmake-utils desktop eutils toolchain-funcs wxwidgets
+inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets
 
 DESCRIPTION="Interconverts file formats used in molecular modeling"
 HOMEPAGE="http://openbabel.org/wiki/Main_Page"
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
index 410d0c89fe0f..6f60a5ab1354 100644
--- a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
@@ -5,7 +5,7 @@ EAPI=6
 
 WX_GTK_VER="3.0"
 
-inherit cmake-utils eutils toolchain-funcs wxwidgets
+inherit cmake-utils optfeature toolchain-funcs wxwidgets
 
 DESCRIPTION="Interconverts file formats used in molecular modeling"
 HOMEPAGE="http://openbabel.sourceforge.net/"
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 69bc84fa32a7..80203d4cea2a 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-r3.ebuild 3005 BLAKE2B 697c52ef412f18a8088c82c6f71ef7b10ffb28201aaaf5b651cfad512ce1f3340f74292dc54e9005e5c153d50bf8d3c9de1df1a71516c5258b4a6256fc9b9429 SHA512 9f248137b6cd1c4a0233c83738597e42b43b65f1331c6a19a841a36719328996fc9902f599848d791963f41e65dc9f7c76f967dae26286488a49b5cfd13572d1
+EBUILD pymol-2.3.0-r3.ebuild 3016 BLAKE2B c048aadae470e41d56109d82d61bc9250667a6b40641ac60d8ca0d672087a7e998ef9c9089a76dc1da5ad6864da5bd0114e348c4f6cb45bf2b195977222116ad SHA512 9bd12710a79f331f1da261e7233650f262942de73d574cbec85f1d91bcd1931dc46f18e04b5b0a0fbea645484de0ab46862f4510c63d40fd9bd0e02e6a00225e
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index 58c0d6707c41..e469b6431e82 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{6,7,8} )
 
-inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
+inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="https://www.pymol.org/"
@@ -81,7 +81,7 @@ python_install_all() {
 
 	# These environment variables should not go in the wrapper script, or else
 	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
+	cat >> "${T}"/20pymol <<- EOF || die
 		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
 		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
 		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 7185dba46aa6..d305a69e14e2 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,7 +1,11 @@
 AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00
 AUX vmd-1.9.3-cuda.patch 15569 BLAKE2B a26ce893fd2808b7ce1ad36f6d2d690be482d24805f44030434fd3aadaa9f9a834ae8b73d7f1c759161e20041c2372181b90ae17f71eab50c94e6b38e3b133a3 SHA512 ba6f435601a53d5ed26ceab9ab86a9734e6a3b60f9cb61be5c9f59676a5145a4c64a538ddadf446e82608ade5a3d86ec6b8cb7257d9c402e245f845371feb571
 AUX vmd-1.9.3-tmpdir.patch 673 BLAKE2B 074456a8a68a36f16a804aeb8caee9abf14505cb76a2661b03ad97119bf4afb13a994c9cf22eeb952a79a980fcf03bd3dee5c93cf63bf82a19831f71bcbd83c2 SHA512 f7f570c729259f9133fb6411047266312c3d5f802d4cffe316cfdc4094f0fd0830c3eaae6408f56ea17dadba283e1a1fdf86fec858a5211b1c00ed927f160ea4
+AUX vmd-1.9.4-gentoo-paths.patch 11523 BLAKE2B 3e02c73b49a3686ce00deb44f4bca0809c527a53d7fb13315c5799c5e9fe1d8ada9664452e41f49ad084abed96d2e5a6d01b000e49393e97eeb5fb2378af888f SHA512 da8e723d12ca7728d67dffcd0bf2e9c856764917d3f3ef07756febbc981bae20b061e0ead3fa617de18b94918d855c09f68c24a979c6f9f0cdea12b343a22756
+AUX vmd-1.9.4-tmpdir.patch 398 BLAKE2B cf61240688f111d4763f458f0e10319a8154c5427172ba99d4bcfc7a9d8fd559fe7777c1ff703f81b68b2f10ec2a8c4af5cf61fd91d147aec2f4fafcf6753c82 SHA512 c5f96b3ef880ccdcf86d3927308c85aeaf3260ed0e54d60cbf186a0d63f6a88da16e49b14d6815d97bfd1ff4500bf9ce99d183d26ee78b67fed388e2217a7f10
 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
+DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
 EBUILD vmd-1.9.3-r5.ebuild 7822 BLAKE2B 2a3933c1008dcde65b37846ae5cfc993036d387a9a62a4cb207865187a22e8cf41401000171d083e059abc17c43adf773490aafcfbc576480b241fd359f6fb88 SHA512 9abc8facc673387ee0fcc77b27e4f421f2c7cb590b451b5d8ce4165a66be27ad1b69a45d9c939718a4359f1c76591855219bdb5956947aa2408d61f338eb78ca
+EBUILD vmd-1.9.4_alpha43.ebuild 7539 BLAKE2B ea95aabc508d753de691e2986b1c36b03d9edf56d9b3843e564977fceb9974519219710c311efc677bcfb941c0aed49247980146678911e7a7a5c52202aff59e SHA512 4fa5a8681a76272f524901fe8a1e1b9b222227d48e86def3edd112b543f5c1f9feb0c046f050715ef7a4d66a7d31096a6d62609691944e778e71204a15b61819
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
new file mode 100644
index 000000000000..ca74b868d8f4
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
@@ -0,0 +1,276 @@
+--- a/bin/vmd.sh.old	2020-09-09 18:02:09.135798193 +0200
++++ b/bin/vmd.sh	2020-09-09 18:37:22.355511675 +0200
+@@ -436,6 +436,7 @@
+ 
+ # set the path to a few external programs
+ # Stride -- used to generate cartoon representations etc.
++export STRIDE_BIN="gentoo-stride"
+ if [ -z "$STRIDE_BIN" ]
+ then
+   if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
+@@ -446,6 +447,7 @@
+ fi
+ 
+ # Surf -- used to generate molecular surfaces
++export SURF_BIN="gentoo-surf"
+ if [ -z "$SURF_BIN" ]
+ then
+   if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
+@@ -456,6 +458,7 @@
+ fi
+ 
+ # Tachyon -- used to generate ray traced graphics
++export TACHYON_BIN="gentoo-tachyon"
+ if [ -z "$TACHYON_BIN" ]
+ then
+   if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
+--- a/configure.old	2020-09-09 18:05:55.778655084 +0200
++++ b/configure	2020-09-09 18:38:01.607083112 +0200
+@@ -13,11 +13,10 @@
+ $install_name = "vmd";
+ 
+ # Directory where VMD startup script is installed, should be in users' paths.
+-$install_bin_dir="/usr/local/bin";
++$install_bin_dir="gentoo-bindir";
+ 
+ # Directory where VMD files and executables are installed
+-$install_library_dir="/usr/local/lib/$install_name";
+-
++$install_library_dir="gentoo-libdir/$install_name";
+ 
+ # optionally override hard-coded defaults above with environment variables
+ if ($ENV{VMDINSTALLNAME}) {
+@@ -143,29 +142,6 @@
+ # Configure script code begins here
+ ############################################################################
+ 
+-## Test for existence of a properly compiled plugin tree
+-if (!(-e "plugins")) {
+-  print "\n";
+-  print "VMD plugin directory not found.\n";
+-  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+-  print "into a 'plugins' directory linked or located in this directory.\n";
+-  print "Be sure your PLUGINDIR environment variable is set before running\n";
+-  print "'make distrib' in the plugin build area.\n";
+-  print "\n";
+-  die "Halting configuration until VMD plugins are built.\n";
+-} else {
+-  if (!(-e "plugins/include/vmdplugin.h")) {
+-    print "\n";
+-    print "VMD plugin include files or directory not found.\n";
+-    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+-    print "into a 'plugins' directory linked or located in this directory.\n";
+-    print "Be sure your PLUGINDIR environment variable is set before running\n";
+-    print "'make distrib' in the plugin build area.\n";
+-    print "\n";
+-    die "Halting configuration until VMD plugins are built.\n";
+-  }
+-} 
+-
+ #################### Parse command line options   ###########
+ # list of allowed architectures
+ @archlist=('AIX6_64', 'ANDROIDARMV7A', 'BLUEGENEQ', 'BLUEWATERS', 'CRAY_XC', 'CRAY_XK', 'FREEBSD', 'FREEBSDAMD64', 'LINUX', 'LINUXAMD64', 'LINUXARM64', 'LINUXCARMA', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'OPENPOWER', 'SUMMIT', 'SUMMITDEV', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
+@@ -493,7 +469,7 @@
+ 
+ $arch_cc          = "cc";
+ $arch_ccpp        = "CC";
+-$arch_nvcc        = "/usr/local/cuda-10.2/bin/nvcc";
++$arch_nvcc        = "gentoo-nvcc";
+ $arch_nvccflags   = "-lineinfo --ptxas-options=-v " . 
+                     "-gencode arch=compute_30,code=compute_30 " .
+                     "-gencode arch=compute_30,code=sm_35 " .
+@@ -537,7 +513,7 @@
+ 
+ ################ Plugin options
+ #
+-$plugin_dir	= "../plugins";
++$plugin_dir    = "gentoo-plugindir";
+ $plugin_include = "-I$plugin_dir/include";
+ $plugin_library = "";
+ $plugin_libs    = "";
+@@ -550,7 +526,7 @@
+ @plugin_extra   = ();
+ 
+ if ($config_staticplugin) {
+-  $molfile_dir = "$plugin_dir/$config_arch/molfile";
++  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
+   $plugin_include .= " -I$molfile_dir";
+   $plugin_library .= " -L$molfile_dir";
+   $plugin_libs    .= " -lmolfile_plugin";
+@@ -715,8 +691,8 @@
+ ################ FLTK GUI
+ $fltk_defines     = "-DVMDGUI -DVMDFLTK";
+ $fltk_dir         = "$vmd_library_dir/fltk";
+-$fltk_include     = "-I$fltk_dir/include";
+-$fltk_library     = "-L$fltk_dir/$config_arch";
++$fltk_include     = "-Igentoo-fltk-include";
++$fltk_library     = "-Lgentoo-fltk-libs";
+ $fltk_libs        = "-lfltk -lX11";
+ #@fltk_cc          = ('forms_ui.c');
+ @fltk_cu          = ();
+@@ -777,8 +753,8 @@
+ if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
+ $tcl_library      = "-L$stock_tcl_library_dir";
+ if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
+-$tcl_libs         = "-ltcl8.5";  
+-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
++$tcl_libs         = "-ltcl";  
++if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
+ 
+ @tcl_cc           = ();
+ @tcl_cu           = ();
+@@ -1289,8 +1265,8 @@
+ # 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          = ();
+@@ -1541,8 +1517,8 @@
+ #######################
+ $netcdf_defines     = "";
+ $netcdf_dir         = "$vmd_library_dir/netcdf";
+-$netcdf_include     = "-I$netcdf_dir/include";
+-$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
++$netcdf_include     = "-Igentoo-netcdf-include";
++$netcdf_library     = "-Lgentoo-netcdf-libs";
+ $netcdf_libs        = "-lnetcdf";
+ @netcdf_cc          = ();
+ @netcdf_cu          = ();
+@@ -1595,6 +1571,7 @@
+ #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
+ $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
+ $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
++$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
+ 
+ #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
+ #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
+@@ -1604,7 +1581,7 @@
+ $python_defines     = "-DVMDPYTHON";
+ $python_include     = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
+ $python_library     = "-L$stock_python_library_dir";
+-$python_libs        = "-lpython2.5 -lpthread";
++$python_libs        = "$stock_python_library -lpthread";
+ @python_h           = ('PythonTextInterp.h',
+                        'VMDTkinterMenu.h',
+ 		       'py_commands.h',
+@@ -2350,8 +2327,8 @@
+ 
+     # XFree 4.0 Direct Rendering Interface and GLX 
+     $opengl_dep_dir         = "/usr/X11R6";
+-    $opengl_dep_include     = "-I$opengl_dep_dir/include";
+-    $opengl_dep_library     = "-L$opengl_dep_dir/lib";
++    $opengl_dep_include     = "-Igentoo-opengl-include";
++    $opengl_dep_library     = "-Lgentoo-opengl-libs";
+     $opengl_dep_libs        = "-lGL"; 
+     # $opengl_dep_libs      = "-L/usr/X11R6/lib -lGL -lXext -lX11";
+ 
+@@ -2381,15 +2358,15 @@
+       $arch_lopts       .= "-i-static ";
+     } else {
+       # compling with GCC
+-      $arch_cc          = "gcc";
+-      $arch_ccpp        = "g++";
++      $arch_cc          = "gentoo-gcc";
++      $arch_ccpp        = "gentoo-g++";
+       $arch_depend_flag = "-MM";
+-      $arch_shld        = "g++ -shared";
++      $arch_shld        = "gentoo-g++ -shared";
+       $arch_shlibname   = "so";
+       $arch_shcppopts   = "-fPIC";
+-      $arch_shldopts    = "";
+-      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
+-      $arch_copts       = "-m32 -Wall -Wno-unknown-pragmas -O3";
++      $arch_shldopts    = "gentoo-ldflags";
++      $arch_opt_flag    = "gentoo-cflags";
++      $arch_copts       = "gentoo-cflags";
+ 
+       if ($config_static) {
+         $arch_lopts       = "-static";
+@@ -2407,14 +2384,13 @@
+ 
+     $arch_cppopts     = "";
+     if ($config_cuda) {
+-      $arch_nvcc     = "/usr/local/cuda-4.0/bin/nvcc";
+       $arch_nvccflags  = "--ptxas-options=-v " . 
+                     "-gencode arch=compute_13,code=sm_13 " .
+                     "-gencode arch=compute_20,code=sm_20 " .
+                     "-gencode arch=compute_20,code=compute_20 " .
+                     "--ftz=true ";
+-      $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
+-      $cuda_library     = "-L/usr/local/cuda-4.0/lib";
++      $arch_nvccflags .= "gentoo-nvflags $cuda_include";
++      $cuda_library     = "-Lgentoo-cuda-lib";
+       $cuda_libs       = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
+     }
+     # this is to make tcl happy
+@@ -2513,7 +2489,7 @@
+ 
+     if ($config_cuda) {
+       $arch_nvccflags   .= " --machine 64 -O3 $cuda_include";
+-      $cuda_library     = "-L/usr/local/cuda-10.2/lib64";
++      $cuda_library     = "-Lgentoo-cuda-lib";
+     }
+ 
+     $arch_lex		= "flex"; # has problems with vendor lex
+@@ -3502,11 +3478,11 @@
+ DEFINES     = $DEFINES
+ 
+ # compiler and compiler directives 
+-CC          = $arch_cc
+-CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CC          = gentoo-gcc
++CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ 
+-CCPP	    = $arch_ccpp
+-CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CCPP        = gentoo-g++
++CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ 
+ NVCC        = $arch_nvcc
+ NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+@@ -3555,7 +3531,7 @@
+ $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX)
+ 	\$(ECHO) "Linking " \$\@ "..."; \\
+ 	\$(CD) $vmd_arch_dir ; \\
+-	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
++	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
+ 	\$(COMPILERC) \$(RCFLAGS)
+ 
+ install:
+@@ -3596,8 +3572,7 @@
+ 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
+ 	\$(CD) $vmd_bin_dir ; \\
+ 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
+-	if [ ! -x "/bin/csh" ]; then \\
+-		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
++	if [ -x "/bin/bash" ]; then \\
+ 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
+ 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
+ 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
+--- a/src/Makefile.old	2020-09-09 18:22:46.234818925 +0200
++++ b/src/Makefile	2020-09-09 18:37:22.356511690 +0200
+@@ -647,7 +647,7 @@
+ vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX)
+ 	$(ECHO) "Linking " $@ "..."; \
+ 	$(CD) ../LINUXAMD64 ; \
+-	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
++	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
+ 	$(COMPILERC) $(RCFLAGS)
+ 
+ install:
+@@ -660,10 +660,6 @@
+ 	if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
+ 		$(MAKEDIR) "/usr/local/lib/vmd"/doc; \
+ 	fi
+-	-$(COPY) ../Announcement  "/usr/local/lib/vmd"
+-	-$(COPY) ../README        "/usr/local/lib/vmd"
+-	-$(COPY) ../LICENSE       "/usr/local/lib/vmd"
+-	-$(COPY) ../doc/ug.pdf        "/usr/local/lib/vmd"/doc
+ 	if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
+            $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
+ 	-$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
new file mode 100644
index 000000000000..295811db0580
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
@@ -0,0 +1,11 @@
+--- a/scripts/vmd/chemical2vmd.old	2020-09-09 18:40:56.795215443 +0200
++++ b/scripts/vmd/chemical2vmd	2020-09-09 18:41:09.648348701 +0200
+@@ -61,7 +61,7 @@
+ 
+ 
+ # Make a temp. file to store the load command
+-$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'};
++$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'};
+ sub tmpfile {
+     local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$;
+     local ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
new file mode 100644
index 000000000000..6ff1210c5426
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -0,0 +1,265 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+
+MY_PV="${PV/_alpha/a}"
+MY_P="${PN}-${MY_PV}"
+SRC_URI="
+	${MY_P}.src.tar
+	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
+"
+
+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"
+
+CDEPEND="
+	>=dev-lang/tk-8.6.1:0=
+	dev-lang/perl
+	dev-libs/expat
+	$(python_gen_cond_dep 'dev-python/numpy[${PYTHON_MULTI_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="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/chemical-mime-data
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+"
+
+S="${WORKDIR}/${MY_P}"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${MY_P}.src.tar from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-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 "to ${MY_P}.src.tar"
+}
+
+src_prepare() {
+	xdg_src_prepare
+
+	use cuda && cuda_sanitize
+
+	cd "${WORKDIR}"/plugins || die
+
+	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 "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch
+	eapply "${FILESDIR}"/${PN}-1.9.4-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
+}