gentoo resync : 15.12.2019

author: V3n3RiX <venerix@redcorelinux.org> 2019-12-15 18:09:03 +0000
committer: V3n3RiX <venerix@redcorelinux.org> 2019-12-15 18:09:03 +0000
commit: 7bc9c63c9da678a7e6fceb095d56c634afd22c56 (patch)
tree: 4a67d50a439e9af63947e5f8b6ba3719af98b6c9 /sci-chemistry
parent: b284a3168fa91a038925d2ecf5e4791011ea5e7d (diff)
90 files changed, 615 insertions, 2916 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 893a1088c3e2..6b2ad67562c0 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 1b33c2abb01e..a89d41a10537 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -2,5 +2,5 @@ AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab
 AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0
 AUX apbs-1.4.1-python.patch 3979 BLAKE2B b21633655df329f5d445c4e53140367b0a8a6cfbfafccba8943206ed9bae46839bae532e3efd19d75e89bc70a1fa59d05f3ed977b1a59f949649d3e89b887a96 SHA512 a38ca3bbf692f42268d192aff61949ece95d9b043ac10b4eec33e383773beec1c60425a12e84843a602e828528f6cf0ed6b8c90e99aeea679c5abc8c093c68ae
 DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a
-EBUILD apbs-1.4.1-r2.ebuild 3038 BLAKE2B 52199b0b53f146f7ed915b0cf65e48de40b39e5df10fde56ab89fb43324e3d98e66ba9d09a85d4cc209427d0cd0fc24f7472bc55393703b4c8aa2a13c3d23cdd SHA512 d5b3e8008db4f59618dc08d7e5289929a4852856aea51e2b08e6151d8530f6dab882a0b7229b079afd4ef336023b0f0a0ff19accce91f980fe2a6aea71a6399c
+EBUILD apbs-1.4.1-r2.ebuild 3032 BLAKE2B 7e8c4f17445e54a201d1d9279f80feee228f20d4d33a4596dfeee15f0ce066904c34c978db13a453e7e5589c356b26cfab2aa0bc80f38fa56dda8a8f7f025295 SHA512 ab8592cdf95689aecbadfee6f3ebd0b121f04e9e95dd5307f2d353c6e80609328a633417fe47d4a2f9e2572a965268354d99cf0aba5641aa6d42443d1d27f765
 MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
index b3c4f192894b..88910ddde996 100644
--- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
+++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
@@ -106,7 +106,7 @@ src_compile(){
 }
 
 src_test() {
-	python_export_best
+	python_setup
 	cd tests || die
 	LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die
 	grep -q 'FAILED' log && die "Tests failed"
diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest
deleted file mode 100644
index 2b830596d521..000000000000
--- a/sci-chemistry/aria/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST aria2.3.2_08.26.2013.tar.gz 1878602 BLAKE2B 3044192853c0ed0653d20fea959d3b01321f559845c555289658f93b65e9148f8cd0f59619e8690887b2811d613e6cc2f67b67af7d84ade4b8fc18403367086c SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e
-EBUILD aria-2.3.2_p20130826.ebuild 1930 BLAKE2B 129dfba9d6e9209e2d88a6c1357dd247d5089e18b9393f75fb23b2c1dcd98ea80768f20ba9f09e9b6b97213ab5140075c7d484aeb9cb4fa5ef116d248ad29644 SHA512 7a752e8c87b300b55ce0b50c0a3c45df26fc34f3205b55231f685ab76548077b7f70392c260cf23f5d09b91d2f7f172432771315227a4cecb069199596e33cea
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild
deleted file mode 100644
index c06c8d979bb6..000000000000
--- a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit eutils python-single-r1 versionator
-
-MY_P="${PN}$(get_version_component_range 1-2 ${PV})"
-DATE="08.26.2013"
-
-DESCRIPTION="Automated NOE assignment and NMR structure calculation"
-HOMEPAGE="http://aria.pasteur.fr/"
-SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2_${DATE}.tar.gz"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-tcltk/tix
-	dev-lang/tk:0=
-	>=dev-python/numpy-1.1[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP},tk]
-	>=sci-chemistry/cns-1.2.1-r7[aria,openmp]
-	>=sci-chemistry/ccpn-2.2[${PYTHON_USEDEP}]
-	sci-chemistry/clashlist
-	sci-chemistry/procheck
-	sci-libs/clashscore-db"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_nofetch(){
-	einfo "Go to http://aria.pasteur.fr/archives/aria2.3.2.tar.gz/view, download ${A}"
-	einfo "and place it into your DISTDIR directory."
-}
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-}
-
-src_test(){
-	export CCPNMR_TOP_DIR=$(python_get_sitedir)
-	export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-	${PYTHON} check.py || die
-}
-
-src_install(){
-	python_moduleinto ${PN}
-	python_domodule src aria2.py
-	python_moduleinto ${PN}/cns
-	python_domodule cns/{protocols,toppar,src/helplib}
-
-	if use examples; then
-		insinto /usr/share/${P}/
-		doins -r examples
-	fi
-
-	# ENV
-	cat >> "${T}"/20aria <<- EOF
-	ARIA2="$(python_get_sitedir)/${PN}"
-	EOF
-
-	doenvd "${T}"/20aria
-
-	# Launch Wrapper
-	cat >> "${T}"/aria <<- EOF
-	#!/bin/sh
-	export CCPNMR_TOP_DIR="$(python_get_sitedir)"
-	export PYTHONPATH="$(python_get_sitedir)/ccpn/python"
-	exec "${PYTHON}" -O "\${ARIA2}"/aria2.py \$@
-	EOF
-
-	dobin "${T}"/aria
-	dosym aria /usr/bin/aria2
-
-	dodoc README
-	python_optimize "${D}/$(python_get_sitedir)"
-}
diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/aria/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest
index 05fd5ff8103b..065022beda3e 100644
--- a/sci-chemistry/autodock/Manifest
+++ b/sci-chemistry/autodock/Manifest
@@ -1,4 +1,4 @@
 AUX autodock-4.2.6-buildsystem.patch 1500 BLAKE2B d295cdc7e46ecad118b7747aa26c97c5d08d54f28fecbb09e1c356fcf1e977164acb57dfa3ecc57fef28e4a37b6d16f9741c1fdb6c8f1c3b3a3b3d9085fd75f6 SHA512 08a7643e2973f2ebdd01c54acb1e3e0802ea3d7a33cbed4c03f58d29c7e13a246418feb4a61088dae18c3ab78db6fd5b3c11f9974dec59fe46dbf7cfbbe98c3a
 DIST autodocksuite-4.2.6-src.tar.gz 35438010 BLAKE2B 88e036ecc0492fb83f31b90fd0983ec57d889a61d17249f672a3e30e942f6c329dc2494088a8fc7c5bc39a5bdbb38fb1514f1750c7145374f202a928d477faa9 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb
-EBUILD autodock-4.2.6.ebuild 2178 BLAKE2B ba9efd6481e64f6a91836f72ba95fe532fb0adbf9a6bf37eecde2b83cc1d3738b076c1d41c28633b28499eca4a30c6994e6e417caba6d391bbc8561ab355456a SHA512 f8b186454cec3e7deb6078cfa659d15eeebdc7e4bcb36d03327603ecda063b8a383a032001b8db9ad849dddb2c5992ec57c4f0bb6d8031a89cdad44fb3d82acb
+EBUILD autodock-4.2.6.ebuild 2202 BLAKE2B f425ab34d6941523d6c8b1c8740b4b8a2aa89b49c965466af77c8dda0cc4ef3d24a9c5a40ad82156497f24f6d3afb341e697838446d96195fd6a990b909160b4 SHA512 516d12bbf27984ecd844bae777c408790f7288b08d025fc618920458181dc57abbe3442b69270c1209afa6ebb45b11e774f60e1721452d790119270157336252
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild
index 862cda1437b9..6cfe76fbbfd0 100644
--- a/sci-chemistry/autodock/autodock-4.2.6.ebuild
+++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -18,6 +18,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="examples openmp test"
+RESTRICT="!test? ( test )"
 
 RDEPEND=""
 DEPEND="test? ( ${PYTHON_DEPS} )"
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
deleted file mode 100644
index 92f35baaafb1..000000000000
--- a/sci-chemistry/ccpn/Manifest
+++ /dev/null
@@ -1,22 +0,0 @@
-AUX 2.3.1-parallel.patch 850 BLAKE2B 7a6368cde3e6352db8d61da151b5c4246e446453ad5ba4b164d2544c4aa044b224eec38dcdb5958360987ff03a01f99b293e257b210b0226406f9de05067b07f SHA512 0597e21c03baa27e2342249814fc0700b73cf2800173468574ef704d48f7e6e042ac6ae552bbb9e27fd4baca36cfaf60a1eac9813354916b3e8295a35b64dcdf
-AUX analysis 283 BLAKE2B c487800b5a09f3cc6d0e86ffadf22fae6d33c9dea95e0485ac51b0e49313bc4318fae1fd12c892ea1103c5089d65f967cdac43b0712c15d6eab90ecc3c2a07d1 SHA512 f2dd8216021201b0f9307f8bb82033c3ebb1c9f21450ae206e59ad6442b0cf0f8fc6e4817d4347eb78a9528ba1ef60bd5395708067352d11330215e5ce2568ff
-AUX dangle 279 BLAKE2B da9f1f48ea829315405b1fca6631ad0ae9aec70ad22b13ab2a344888a7a9e81d07feeb6a7dfc60e9b867b02c7a87c161d9c34cd9ad55e90f973e5aa9ea905529 SHA512 21fca09578aa13819a20f08ff414ca2b8d08d177a1ab09f8d85c53ae20fc6f38ab46e2933d72c239029b37ec5eebc3162f0c8e99f1ca1dd20aaa49277fac4e7d
-AUX dataShifter 282 BLAKE2B 6a16d423b13d96ee939289daa1d456f8861721d29893065d2abb2915559af08d7cfde890a152388ee1f184a2e3fde2ad9159d7d6b5256aba4b29589079d7101a SHA512 f1c4a87d0d4d1a613ce8c9eacd9e3ba5047f1205404140c0c68a354bb790397b7ec49426660a48601a305906b60a8957d218dbc5ad1d6d48beb7030772a199b7
-AUX depositionFileImporter 286 BLAKE2B 9c2cfb9424defd3043d6164b33a435675fa90307cf67f6eea0c5dfa88db702a6f0736cccb26314dca5ba672820a20a044ac00514bbbdf3f58c86611cf1f87ff2 SHA512 f7d7caa4b2b2d91eb5dc27ec0ccd6251dab94f6d8e318190b2f2b1b997f825d6cee1e3a38ee77f9358102dcdaf7d93c4d18c7250855446580abd459db31eec6d
-AUX eci 267 BLAKE2B 79cced29dcc1b50a1482641a64df5340ed0cce5791f7de245def0c8aeb57d12380bb082efa147de80dc14a7751e458df89a077d64a2f9ef24e8913540fb4c4ab SHA512 800b2624fe21c706a1bc30bc8fd4fefb9f4c18cb795266cb8afcb3db09776600785a453eed656b4b25b34fc5e39a0e7a599bff2417bedbd0ac6945d2ad900080
-AUX extendNmr 266 BLAKE2B fb5406150f66718cb2e90018e6403df446010c4fbeffd168bc662e7c9ddc5c6a5f75548a0f8f5e296e4ab10ee56f6997784ad0e7701e855bba107ea1ab74939c SHA512 b94d480c776bc2da31ed12419df1c3364036299553697b7d50eb0ebf073126041e8acd3f1c30051dc1dbc44fef9662001e718a29b8c7fcfc2ca19c0da90125ce
-AUX formatConverter 286 BLAKE2B 37fa628a08c1b5293171f41b8322c8003c72e6a26f9e58446e4090881ac05c186c2cde66bbd328a03a53237bd5169d48c69846ef3ea8331b16a0a08c2a0dc1c2 SHA512 a987b73b10614a2616b62589004ae1e321903af08efea62f6c74f2cf5b1e7053454a382107056250824373bce9f281ad0af2e8f6928cdf2e556e9638646cfcda
-AUX pipe2azara 290 BLAKE2B 6a366e968961119dee2d3e451d8c467b724bac5c011ef646b86807c7e71f8471e5b72c1a0b7059a6f88578e6f615c79dc370b48c0e7f06caa7e7dfb2013a7c3a SHA512 6f90a1720dc786d84576029cf77271e8eeb0b5c38506e93227064aafba1152a86762125d3bb9f26a741dcc215da87cf96ba9b8926568db79b56159f8839e8a80
-AUX xeasy2azara 288 BLAKE2B f79ab9f4add3f1c6574b64d3bdc52991ce798f273cf3989d1bd7b5ddcf219d99235b1be00453e29cad39f31fb7f46d5880d6709d40bd19a0947972a4cf0b5e6b SHA512 e9a3dedc155f9f7b163eead73099532653454a7f5f12042348abf87a4e8930cb8b0b66fd87ef9fcc3b395c92d7e4942829ec8f5e7a1c28c7b3ce51022b8fce6b
-DIST analysis2.4.1.tar.gz 36088236 BLAKE2B 8aaf4ffe5a8dc7a6b805a7a66e163cb03b0fc8a45617ebf892268a2f3658e49c48e3c2de4ea654a840eef2c01cf3a3f28f45e053697e68bbc83ce22d19a29cf3 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1
-DIST analysis2.4.2.tar.gz 36390919 BLAKE2B 5e7fa44b2029d834ef634b2cd9f2c34d7e6dbfd3e257b9344cff92d13750a21325a2a2f82eb072ae385c528a7406796959c8201edbc1422bc54a17e176d7db33 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b
-DIST ccpn-update-2.4.1-150226.patch.xz 10732 BLAKE2B 9f31bd16e7a866b016c5db8b837e3ee926d2db7cd3b15e7cd32fe00f7723e511214d36221ba86651e79223f0a1d30e2402aa446eb063a078b989102032ae743b SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb
-DIST ccpn-update-2.4.2-150325.patch.xz 2096 BLAKE2B 589c8129d2e1df6231412cd1398823208cbdc7307f63f3a5480a65e428aeb0b6411b9110ddd380ad37addd2ea9118bc6156662c5fd80a7eee362f53fd417e724 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873
-DIST ccpn-update-2.4.2-150413.patch.xz 3132 BLAKE2B f4d55e4b301df4500f29d281de2b274f7912d61d1ad54fedf992e76dd254e86dcb2e9d2a2f4d58ce028d4c9df6bedad847a9e72bef7627800c2d31cc7c43909e SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d
-DIST ccpn-update-2.4.2-150421.patch.xz 3788 BLAKE2B 125eed69e2593e0ab64e6d3cdcee026c4af067c3aa2e9742b033741cc65cc0391fb86c825b372c02dcd549ca260196fd4e8938516d218653d3db80f60ce9caf2 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648
-EBUILD ccpn-2.4.1_p150226.ebuild 4568 BLAKE2B ed7b8ce6ab7a0309bfb92aadf6039b68b1e5b889cebfd4aa23ea95584885fb8f1560a2b13e280adf0ccd10ec728309ccd2b35aa35af6df80bb4bf8e501553294 SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0
-EBUILD ccpn-2.4.2.ebuild 4569 BLAKE2B 9ad48cd3693d89a501645b59d3734f84fd9bc536f3140ca8b88d79defb9b9b70aa1a60b5a78a2b3da7ba5fdca3344d7a4f9772891c11df50cea77e16c6b2869a SHA512 f780549f9a4802482fdf47b963bfe0a7fce49fd029ebe1e1117500dcf2a296489da71e47e8c19ad6bb3a84d778f34bb0faff619b34259baae9f0d841a16ce827
-EBUILD ccpn-2.4.2_p150325.ebuild 4568 BLAKE2B ed7b8ce6ab7a0309bfb92aadf6039b68b1e5b889cebfd4aa23ea95584885fb8f1560a2b13e280adf0ccd10ec728309ccd2b35aa35af6df80bb4bf8e501553294 SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0
-EBUILD ccpn-2.4.2_p150413.ebuild 4568 BLAKE2B ed7b8ce6ab7a0309bfb92aadf6039b68b1e5b889cebfd4aa23ea95584885fb8f1560a2b13e280adf0ccd10ec728309ccd2b35aa35af6df80bb4bf8e501553294 SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0
-EBUILD ccpn-2.4.2_p150421.ebuild 4568 BLAKE2B ed7b8ce6ab7a0309bfb92aadf6039b68b1e5b889cebfd4aa23ea95584885fb8f1560a2b13e280adf0ccd10ec728309ccd2b35aa35af6df80bb4bf8e501553294 SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
deleted file mode 100644
index a1755eca7d7d..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk:0=[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}]
-		)"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/2.3.1-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS=""
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
deleted file mode 100644
index 6303b8d42837..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-#PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk:0=[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}]
-		)"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/2.3.1-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS=""
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild
deleted file mode 100644
index a1755eca7d7d..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk:0=[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}]
-		)"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/2.3.1-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS=""
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild
deleted file mode 100644
index a1755eca7d7d..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk:0=[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}]
-		)"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/2.3.1-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS=""
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild
deleted file mode 100644
index a1755eca7d7d..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk:0=[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}]
-		)"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/2.3.1-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS=""
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/files/2.3.1-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch
deleted file mode 100644
index fcf44707e082..000000000000
--- a/sci-chemistry/ccpn/files/2.3.1-parallel.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/ccpnmr2.3/c/Makefile b/ccpnmr2.3/c/Makefile
-index 01fb25a..8e8e1fe 100644
---- a/ccpnmr2.3/c/Makefile
-+++ b/ccpnmr2.3/c/Makefile
-@@ -5,22 +5,22 @@ all: compile
- compile: global structure analysis clouds dynamics bayes
- 
- global:
--	cd memops/global && $(MAKE)
-+	$(MAKE) -C memops/global
- 
--structure:
--	cd ccp/structure && $(MAKE)
-+structure: global
-+	$(MAKE) -C ccp/structure
- 
--analysis:
--	cd ccpnmr/analysis && $(MAKE)
-+analysis: global
-+	$(MAKE) -C ccpnmr/analysis
- 
--clouds:
--	cd ccpnmr/clouds && $(MAKE)
-+clouds: global
-+	$(MAKE) -C ccpnmr/clouds
- 
--dynamics:
--	cd ccpnmr/dynamics && $(MAKE)
-+dynamics: global
-+	$(MAKE) -C ccpnmr/dynamics
- 
--bayes:
--	cd other/cambridge/bayes && $(MAKE)
-+bayes: global
-+	$(MAKE) -C other/cambridge/bayes
- 
- clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean
- 
diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis
deleted file mode 100644
index 828ed4e64ae9..000000000000
--- a/sci-chemistry/ccpn/files/analysis
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle
deleted file mode 100644
index 6d8a42e615de..000000000000
--- a/sci-chemistry/ccpn/files/dangle
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter
deleted file mode 100644
index c083960f2f60..000000000000
--- a/sci-chemistry/ccpn/files/dataShifter
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter
deleted file mode 100644
index 09505ccc4925..000000000000
--- a/sci-chemistry/ccpn/files/depositionFileImporter
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@
diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci
deleted file mode 100644
index 54d913348718..000000000000
--- a/sci-chemistry/ccpn/files/eci
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $*
diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr
deleted file mode 100644
index a2fe4c997c7c..000000000000
--- a/sci-chemistry/ccpn/files/extendNmr
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@
diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter
deleted file mode 100644
index 6cb273612352..000000000000
--- a/sci-chemistry/ccpn/files/formatConverter
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara
deleted file mode 100644
index 5a3710a134a7..000000000000
--- a/sci-chemistry/ccpn/files/pipe2azara
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara
deleted file mode 100644
index 7b73714c2fa5..000000000000
--- a/sci-chemistry/ccpn/files/xeasy2azara
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-export TCL_LIBRARY=gentootcl
-export TK_LIBRARY=gentootk
-export PSIPRED_DIR=gentoousr
-gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/ccpn/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest
index 737afa52d7ae..f0d861fd3d5a 100644
--- a/sci-chemistry/chemical-mime-data/Manifest
+++ b/sci-chemistry/chemical-mime-data/Manifest
@@ -3,6 +3,5 @@ AUX chemical-mime-data-0.1.94-pigz.patch 481 BLAKE2B dee47e41645b5d196326fb7439e
 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-r2.ebuild 1340 BLAKE2B 34fb2296fd370aa2dc5ac9043db17c6c862d9c443f2e43c3043c25fd5a52170ef45e5237d6cc86cd96a7b2828c4e87035ef141403f4902e8bf971e9f454c8eab SHA512 bbbdb5aea48fef9f226fb2b7c94a9bc126e72647a94054ec58c307c159609855c655a070ddb8bb5fe110a77ec82b2cfeed965ff9ad8fd9c8d7a66aba9de9a8cc
-EBUILD chemical-mime-data-0.1.94-r3.ebuild 1003 BLAKE2B f9d2752e808ef67bfb8f48182133ff94c1365042954e6c51fdf5368d6374f94f4e8db99ff2c58df2c5c4125f14a1644300c913067060b325762cad6f1ab99c2e SHA512 127d2bf314e3852c7e1330f74c70ea6ddfc4f4ca379ec95bb46a21b1708c210292f8c1192757e6495029ab910a340d31304e805febae160675080863941e8294
+EBUILD chemical-mime-data-0.1.94-r3.ebuild 1007 BLAKE2B 20203fada235e55c4614a8f5f80271adb91ecb8e21e553aeaf3ef2d0bb9f94b78ae7f4905db9698f2d4a0971cc309eb863277261dae0cb4fc19d60cc6a8037c4 SHA512 421ee83448926cc336065c22f270d2c8d4f7fdd0517b684ecd4faa002b16bad0113d9de3fb88a548a7e35e028d3572932a7fc8907d516d3878cc4cafb1474131
 MISC metadata.xml 474 BLAKE2B c4d6ffbdf66f856fc9e404202d9a9956d8bbfaeb31eb1eb056300ca5049c02d0499ead32a2013080e397eba272bd3a290b81f343baab1fb40204364bfa5208ec SHA512 59cfe759a75bf49fb020652168434fb610c2d5ba56507945253f556b5542a119bc9c9dc4f2b71ceed93f6672b31e5713cc9d76c433e95b0a08c51e9e577bac00
diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild
deleted file mode 100644
index d9d29973585b..000000000000
--- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils fdo-mime
-
-DESCRIPTION="A collection of data files to add support for chemical MIME types"
-HOMEPAGE="http://chemical-mime.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-RDEPEND="
-	gnome-base/gnome-mime-data
-	x11-misc/shared-mime-info"
-DEPEND="${RDEPEND}
-	dev-util/intltool
-	dev-util/desktop-file-utils
-	dev-libs/libxslt
-	media-gfx/imagemagick[xml,png,svg]
-	media-gfx/inkscape
-	virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-turbomole.patch
-	"${FILESDIR}"/${P}-pigz.patch
-	"${FILESDIR}"/${P}-namespace-svg.patch
-	)
-
-src_prepare() {
-	# needed for convert/inkscape #464782
-	export XDG_CONFIG_HOME=$HOME/.config
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-update-database
-		--htmldir=/usr/share/doc/${PF}/html
-		)
-	autotools-utils_src_configure
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	ewarn "You can ignore any 'Unknown media type in type' warnings."
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	ewarn "You can ignore any 'Unknown media type in type' warnings."
-}
diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild
index ae7e62e898fc..a25326ccb709 100644
--- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild
+++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 inherit autotools xdg
 
 DESCRIPTION="A collection of data files to add support for chemical MIME types"
-HOMEPAGE="http://chemical-mime.sourceforge.net/"
+HOMEPAGE="https://github.com/dleidert/chemical-mime"
 SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2"
 
 LICENSE="LGPL-2.1"
diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest
index ce072c27449c..aff262f69648 100644
--- a/sci-chemistry/cluster/Manifest
+++ b/sci-chemistry/cluster/Manifest
@@ -2,5 +2,4 @@ AUX 1.3.081231-includes.patch 245 BLAKE2B 6bbe0621d49bc7af8091a5594ebcd52d29d99c
 AUX 1.3.081231-ldflags.patch 842 BLAKE2B 67085c3dd9ca5e97b28481fbf06a0f9b6294bd519eb3639c54b10cd9b11a4c44a48dbfa907cdf9ff8ec68761164e82d415c44ad0c3a551842416759c76d4b7a9 SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4
 DIST cluster.1.3.081231.src.tgz 8860 BLAKE2B 4bfc6fe9efa3dbde106ad12df7b23990a748fee5446f16fe4e3cf9232697313bd513366a2283ac732cf0c7306ac65af578155328d0b04e4b5b99536553c9b903 SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac
 EBUILD cluster-1.3.081231-r1.ebuild 664 BLAKE2B 1bb02947160c9306e9fbeb3fbc8197327b4e19d0ee585170ec2769f578e781ca092015f05f368923f9aae5887a491d9e8029db0e36731aa033d18c5691e15582 SHA512 2179d4beb99e86945b2afa8b0951da4f2c59ad13a0070429d7c0a24e0d363ee0a7f12a3710655305be332cec4744e3b22167e1c99986fcb1e22dec2fc46e6d59
-EBUILD cluster-1.3.081231.ebuild 646 BLAKE2B f15642c24f170c1f042a7b695aff41005b4b22c66e14ffa6002c3609864221934933f2e939516b20ccde2ddf53c5a219f11bbf8357094d8d2fbfaa66e9bf0750 SHA512 2bafc4cec0e46ad3749a5b005f629340bc2b0ec8e3fd062da5f20edcccb67597c6a3b1cb5c7045a2d3796de3b488f78ca7b53678c911d63f9dfaf0ff290f9a73
 MISC metadata.xml 661 BLAKE2B 602330745970373b72472999d013a804a343da0ea3c2a1ef948d3fea97dfbb1f1533a0322d1b8295a19ea377725d503c36f37316f5168ea815053afde8388b50 SHA512 449c8965bd2f3039effcf1d6fc15fea1708cf5987aee36a4b8c470f85b59f7b04884a796a353f17fd890aa9d2e4ee7b1c25ed969febabaa54e577f8be31ed889
diff --git a/sci-chemistry/cluster/cluster-1.3.081231.ebuild b/sci-chemistry/cluster/cluster-1.3.081231.ebuild
deleted file mode 100644
index e9d3b8999e1e..000000000000
--- a/sci-chemistry/cluster/cluster-1.3.081231.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Build lists of collections of interacting items"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
-
-SLOT="0"
-LICENSE="richardson"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}"/${PN}1.3src
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-ldflags.patch \
-		"${FILESDIR}"/${PV}-includes.patch
-	tc-export CXX
-}
-
-src_install() {
-	dobin ${PN}
-	dodoc README.cluster
-}
diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
deleted file mode 100644
index fb9785137012..000000000000
--- a/sci-chemistry/cns/Manifest
+++ /dev/null
@@ -1,16 +0,0 @@
-AUX 1.2.1-allow-gcc-openmp.patch 926 BLAKE2B 05278c040466c8d0c6f6ef2684457fa3b96309eec75d21cdc4f49f33c491d966d8a1ae77d128c54eaabacbf305071871c85eb82ac99748c2a3cae0a68092d7db SHA512 cdaae39096625ff1b84ec76b36d2ec3f2e4e4e532d347fa3f0d3e0aa239e2477301de6c768f14788a9b599694568422009bc1c0298ad677cab28d463e0ea8524
-AUX 1.2.1-aria2.3.patch 658 BLAKE2B 22bf941d31729220a8a1e7cae3dbd164502a6815ddb26452c1409aa65ab9f8145f98f280cf7ee2fb91466d4452f82b20297ebe6a3504569c6cc65dc8be8bb6bd SHA512 54758723bc4900673dff73e3aa4d9ead803c44ee3af514259b21c73f7495aaa077e29efe381e674d2a6c5c8d888d7c9cf4d4a998b6c4b6d91de488dc4526f7e4
-AUX 1.2.1-gentoo.patch 2071 BLAKE2B bc9e5bf684d8a82550a386a0e56aeb58105c224d2d7c9e7ade19fe7002222483052ff4730e5d03828a832314b2f6d24cf121a27471405aad2d8de637c4d97f32 SHA512 ecc545e66859d3a88c38cfd40abc278fdd8fca520d63b8d8ab3f2301352962cc70ba436078edec793fda90212fe44c0d333163d64c37afd65e19240f1044feb7
-AUX 1.2.1-ifort.patch 5346 BLAKE2B e3b5be17eba98c6749f8f82dd7ed7569e044cb54fc203da1e1e595ba32b31850b1c159dad46b67379cf2ae2544933bc7e05f57e76ecf166b72573bb9a1ab553b SHA512 738ac365cdf77f5fe0d1b93e1a3b55453b589854822ca18220d32f912c799f8ca133317419f39baf1f8376126b5dc4ea073a19e2c0e05ddb970008bddaed93f3
-AUX 1.2.1-parallel.patch 641 BLAKE2B b297b2c73b22cb6383d28117f6ece1c11f9eb35f80b13cc632732b838c461135b845498e3df8c9aae107749c71e84728c689425e077a9047ae7356403a9def02 SHA512 0d0b43cb055a6d594fcd26d118d1ed9dba86d7e7e99beaf430fa42eb81a1d073622e14cd08377ee9dbd3b68b8b99f80c28ac6c26eb93ffa1ba28ee239a0bdf89
-AUX 1.3_p7-delete.patch 448 BLAKE2B 1b678ecb54ed31c73805b9665c441b1bc5fbd965ce3a09d161096796381fe531c06046bc3be38cd371279bf1a935aefd6b058a1c66856e03e4132ffe230dc74d SHA512 54767ba82bb20190497b92d729b3a3c4ce245fe2b3574a9fef5aa303e19462728953bec7925384fbcf5eb760023fb2b0da19f3162721fe51b1b9733817e7b80a
-AUX 1.3_p7-gentoo.patch 2581 BLAKE2B 7a65fdf4c787b5adbf1730ecbbf74950ca29cdefa62f7a6dab085f0e85e773e117746559e6ec9f97cca36a8e0464b71ed92b33d18ab0babf2dd2566fc0a1b35e SHA512 235b5890c9c0aa9bfac0034e35c3641968b5b1f600bbbfa81240fe405f28910a00184b6fa2ec7a993883ba6db95f1fa9e44cb4b7b9e61ab3d9dcfa26869e1a4c
-AUX cns_solve_env_sh 7070 BLAKE2B 733dc170c5bb009e4774486b95aeb18811cbf339ffda3ff1ee3e8b6b703c782996b291ed0a1aaee6fd314a86b429183fc5a632136bbe3e13524176325828801e SHA512 b012e46706f39d934ff27e4b381907ddd25ca1fbc0112c320b117d68cca3e81f571bfd1821b49477dc16bfd8a0a943c43469fe847cf99e6ab2d08ef238bada31
-AUX cns_solve_env_sh-1.3_p7 7332 BLAKE2B cc4a96591f5bb7716d981525a923413f5f723774cc6253e7483b0ef849a6c57e0fd31e27d4848fd2656e50d83935416a6de62016f9a054bc48313454df9c5548 SHA512 afe2f24c85eff265659e5b2ba2edab519c3193d30b2dcd815bc91a929fd4f4a9167148f8248237569f809d627a8fa623a46fe82d3e0a2cb1827bed910ce565cb
-DIST aria2.3.1.tar.gz 1833973 BLAKE2B 4bf51626a4283452e75a834d0160a4204efd5a35ee8b07329f2a4f933ceea23e53177e6ed19bc9cc158b2a00491d20c75d443bdc04e7feb2d7eda3dc006818e1 SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5
-DIST aria2.3.2.tar.gz 1836270 BLAKE2B 725b0db2b5de36d1b132c5073b8a91f26fa19b48549f4c899041a2b140127524f660c4faeb8c35e94d3d19c24b0252f379de0e85c8fb08b86fc7834252239fb9 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa
-DIST cns_solve_1.21_all-mp.tar.gz 32748040 BLAKE2B 7c82fd9cddc56a00d791d6d5525491b91525962f000c2fdfb02a3ab81305c0c026c115c2328dac99ac7b30146ca591620f4f42019938fb49e7ce52235b281121 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857
-DIST cns_solve_1.3_all.tar.gz 64167735 BLAKE2B 3901a597eb0deac7f2fad173e15d78bfcd753c4019739e22c8851194c9446305cd92bcff73f7f06dc21b6d055852863993412296e1e555ef0b3b730052934cbd SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37
-EBUILD cns-1.2.1-r8.ebuild 6595 BLAKE2B 4a1b1f74950f5795a1fb78631808d3b9cff8cb5beb4a2c3bc939e2813fd3805e4a79a94d7903add989231185e23fef4dfffdc1efa531a1694ef1f82e82b91fe7 SHA512 7984a1aa41357c54363ab69480ce0324c89998adfa6085fa4c03c47d101bd82c6fe5e71154360d2583af0c63921222bbf70bcb2a6939771ed44e9fa8c16c6b07
-EBUILD cns-1.3_p7-r1.ebuild 5821 BLAKE2B d8e730c053d96c3321e60f7724fb61de96b4b6b1f720a4c97c8f6c03b6b44b3a5a9fce22f252606c097ffcfebbca2745225f0cbaf75ef1a4e4a21af055790366 SHA512 01befafeacfa8fe2450e0e5090c67d041813c362f50c4deb1ca3e0e5801b793b86b5acc7f9bb4f0e72baeb259fd40f3a6eb620890182774b82db40bc04695997
-MISC metadata.xml 954 BLAKE2B 69065a98205d1c37abcc868279491caf3fa82fc209f25b8570385302a7efb14f1e13e23eedaae5db86fecdd56c9cf3d5bfeb0e425dd824c3f1fa5150a9641aad SHA512 af24c501f427f9473a9ef8ec90dfd14b2abb0856e8bde8bb1c664fe49a23032895c4d28d06112791b78880be1ef9b781efe60c26bee5d8e9a40a40b41713159b
diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild
deleted file mode 100644
index c9d9a80f36af..000000000000
--- a/sci-chemistry/cns/cns-1.2.1-r8.ebuild
+++ /dev/null
@@ -1,232 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="
-	${MY_P}_all-mp.tar.gz
-	aria? ( aria2.3.2.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-FORTRAN_NEED_OPENMP=1
-
-S="${WORKDIR}/${MY_P}"
-
-RESTRICT="fetch test"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "into your DISTDIR directory."
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	get_fcomp
-}
-
-get_bitness() {
-	echo > "${T}"/test.c
-	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
-	case $(file "${T}"/test.o) in
-		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
-		*32-bit*|*ppc*|*i386*) export _bitness="32";;
-		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
-	esac
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${PV}-parallel.patch
-
-	get_bitness
-
-	if use aria; then
-		pushd "${WORKDIR}"/aria* >& /dev/null
-			# Update the cns sources in aria for version 1.2.1
-			epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-			# Update the code with aria specific things
-			cp -rf cns/src/* "${S}"/source/ || die
-		popd >& /dev/null
-	fi
-
-	# the code uses Intel-compiler-specific directives
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
-		use openmp && \
-			append-flags -fopenmp && append-ldflags -fopenmp
-		COMP="gfortran"
-		[[ ${_bitness} == 64 ]] && \
-			append-fflags -fdefault-integer-8
-	elif [[ $(tc-getFC) == if* ]]; then
-		epatch "${FILESDIR}"/${PV}-ifort.patch
-		use openmp && \
-			append-flags -openmp && append-ldflags -openmp
-		COMP="ifort"
-		[[ ${_bitness} == 64 ]] && append-fflags -i8
-	fi
-
-	[[ ${_bitness} == 64 ]] && \
-		append-cflags "-DINTEGER='long long int'"
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die
-	sed \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		-i "${S}"/cns_solve_env || die
-	sed \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		-i "${T}"/cns_solve_env_sh || die
-
-	einfo "Fixing shebangs..."
-	find "${S}" -type f \
-		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-	if [[ $(tc-getFC) =~ g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# Set up the compiler to use
-	ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		F77=$(tc-getFC) \
-		LD=$(tc-getFC) \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FCFLAGS} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		compiler="${COMP}" \
-		install
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	csh -c \
-		"export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		-e "/^g77on/d" \
-		-i "${S}"/cns_solve_env || die
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		-e "/^g77on/d" \
-		-e "/^g77off/d" \
-		-i "${T}"/cns_solve_env_sh || die
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		-i "${S}"/cns_solve_env || die
-	sed \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		-i "${T}"/cns_solve_env_sh || die
-
-	newbin "${S}"/*linux*/bin/cns_solve* cns_solve
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*linux*/utils/Makefile || die
-
-	dobin "${S}"/*linux*/utils/*
-
-	sed \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		-i "${S}"/bin/cns_web || die
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web}
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
-	doins "${S}"/bin/cns_info
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh
-	newins "${T}"/cns_solve_env_sh cns_solve_env.sh
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/*
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix || die
-}
-
-pkg_postinst() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild
deleted file mode 100644
index 327d14b2488e..000000000000
--- a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild
+++ /dev/null
@@ -1,215 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="
-	${MY_P/p7}_all.tar.gz
-	aria? ( aria2.3.1.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-FORTRAN_NEED_OPENMP=1
-
-S="${WORKDIR}/${MY_P/p7}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "into your DISTDIR directory."
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	get_fcomp
-}
-
-get_bitness() {
-	echo > "${T}"/test.c
-	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
-	case $(file "${T}"/test.o) in
-		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
-		*32-bit*|*ppc*|*i386*) export _bitness="32";;
-		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
-	esac
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${PV}-delete.patch
-
-	get_bitness
-
-	if use aria; then
-		pushd "${WORKDIR}"/aria* >& /dev/null
-			# Update the cns sources in aria for version 1.2.1
-			epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-			# Update the code with aria specific things
-			cp -rf cns/src/* "${S}"/source/ || die
-		popd >& /dev/null
-	fi
-
-	# the code uses Intel-compiler-specific directives
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		use openmp && \
-			append-flags -fopenmp && append-ldflags -fopenmp
-		COMP="gfortran"
-		[[ ${_bitness} == 64 ]] && \
-			append-fflags -fdefault-integer-8
-	elif [[ $(tc-getFC) == if* ]]; then
-		use openmp && \
-			append-flags -openmp && append-ldflags -openmp
-		COMP="ifort"
-		[[ ${_bitness} == 64 ]] && append-fflags -i8
-	fi
-
-	[[ ${_bitness} == 64 ]] && \
-		append-cflags "-DINTEGER='long long int'"
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die
-	sed \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		-i "${S}"/cns_solve_env || die
-	sed \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		-e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \
-		-e "s:^limit:^ulimit:g" \
-		-i "${T}"/cns_solve_env_sh || die
-
-	ebegin "Fixing shebangs..."
-		find "${S}" -type f \
-			-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die
-		find . -name "Makefile*" \
-			-exec \
-				sed \
-					-e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \
-					-e "s:/bin/ls:ls:g" \
-					-e "s:/bin/rm:rm:g" \
-					-i '{}' + || die
-	eend
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-
-	# Set up the compiler to use
-	ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		F77=$(tc-getFC) \
-		LD=$(tc-getFC) \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FCFLAGS} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		compiler="${COMP}" \
-		install
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	cat >> "${T}"/66cns <<- EOF
-	CNS_SOLVE="${EPREFIX}/usr"
-	CNS_ROOT="${EPREFIX}/usr"
-	CNS_DATA="${EPREFIX}/usr/share/cns"
-	CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3"
-	CNS_LIB="${EPREFIX}/usr/share/cns/libraries"
-	CNS_MODULE="${EPREFIX}/usr/share/cns/modules"
-	CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar"
-	CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb"
-	CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal"
-	CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr"
-	CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray"
-	CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal"
-	CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr"
-	CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib"
-	EOF
-
-	doenvd "${T}"/66cns || die
-
-	# Don't want to install this
-	rm -f "${S}"/*linux*/utils/Makefile || die
-
-	sed \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		-i "${S}"/bin/cns_web || die
-
-	newbin "${S}"/*linux*/bin/cns_solve* cns_solve
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	dobin \
-		"${S}"/*linux*/utils/* \
-		"${S}"/bin/cns_{edit,header,import_cif,transfer,web}
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/*
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix || die
-}
-
-pkg_postinst() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch
deleted file mode 100644
index 42b9b0572231..000000000000
--- a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- source/xfft.f.orig	2008-08-03 00:36:52.000000000 -0700
-+++ source/xfft.f	2008-08-03 00:37:06.000000000 -0700
-@@ -514,7 +514,7 @@
-       LOGICAL QHERM
-       DOUBLE PRECISION XRCELL(9), MAPR
- C local
--!$    integer omp_get_max_threads, kmp_get_stacksize
-+!$    integer omp_get_max_threads
-       LOGICAL DONE
-       DOUBLE PRECISION ZERO
-       PARAMETER (ZERO=0.0D0)
-@@ -537,7 +537,7 @@
-       NBPP=1
- ! The following command is only relevant for the ifort compiler (if -openmp option is used).
- ! If your compiler is not ifort, and gives an error, just comment the next line out:
--!$      if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23)
-+!       if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23)
- ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, 
- ! and 2**22 bytes (4Mb) for 64bit.
- ! This may be low for big structures, which leads to segmentation faults!
diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch
deleted file mode 100644
index 8c6939d8eb92..000000000000
--- a/sci-chemistry/cns/files/1.2.1-aria2.3.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/cns/src/cns.f b/cns/src/cns.f
-index a3c2cbe..51a34f8 100644
---- a/cns/src/cns.f
-+++ b/cns/src/cns.f
-@@ -470,6 +470,7 @@ C local
-       INTEGER      HNLEN, TMP, PTRSZ, STLEN
-       CHARACTER*(1) CNSPTMP
-       CHARACTER*(4) ST
-+!$    integer omp_get_max_threads
- C
- C write header
-       WRITE(6,'(10X,A)')
-@@ -526,6 +527,9 @@ C
-       WRITE(6,'(10X,7A)')
-      & ' Running on machine: ',HOSTNM(1:HNLEN),
-      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
-+!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
-+!$   &  ' threads'
-+!$C (to change use setenv OMP_NUM_THREADS x)
- C
-       CALL GETNAM(USERNM,12,TMP)
-       WRITE(6,'(10X,2A)')
diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch
deleted file mode 100644
index 2b47bfcc7d86..000000000000
--- a/sci-chemistry/cns/files/1.2.1-gentoo.patch
+++ /dev/null
@@ -1,63 +0,0 @@
---- cns_solve_1.21/instlib/source/Makefile.proto	2000-09-07 20:35:33.000000000 +0200
-+++ cns_solve_1.21/instlib/source/Makefile.proto.new	2009-07-14 09:18:37.000000000 +0200
-@@ -11,6 +11,8 @@
- 
- SHELL=/bin/sh
- 
-+cns_string=`date "+%y%m%d%H%M"`
-+
- # commands
- RM = /bin/rm
- 
-@@ -25,26 +27,20 @@
- 
- # rule for the fortran routines
- $(OBJS): 
--	@ echo "compiling: $(@:.o=.f)"; \
--	  $(F77) -c $(F77FLAGS) $(@:.o=.f)
-+	$(F77) -c $(F77FLAGS) $(@:.o=.f)
- 
- # rule for the dynamic memory allocation C routines
- dmemory.o: dmemory.c
--	@ echo ; echo "compiling: $?"
--	@ $(CC) -c $(CCFLAGS) $?
-+	$(CC) -c $(CCFLAGS) $?
- 
- # rule for the machine specific C routines
- machine_c.o: machine_c.c
--	@ echo ; echo "compiling: $?"
--	@ $(CC) -c $(CCFLAGS) $?
-+	$(CC) -c $(CCFLAGS) $?
- 
- # rule for the executable itself
- ../bin/cns_solve: $(DEPENDS) 
--	@ echo ; echo "linking: cns_solve"; echo
--	@ cns_string=`date "+%y%m%d%H%M"`; \
--	  $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
--	                                      $(LDFLAGS) \
--	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
-+	$(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
-+	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
- 	  if [ -x cns_solve-$$cns_string.exe ]; \
- 	    then echo "created executable file cns_solve-$$cns_string.exe"; \
- 	         echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \
---- cns_solve_1.21/instlib/utils/Makefile	2004-08-30 00:40:35.000000000 +0200
-+++ cns_solve_1.21/instlib/utils/Makefile.new	2009-07-14 09:50:27.000000000 +0200
-@@ -22,14 +22,14 @@
- 	make clean
- 
- .f:
--	$(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
-+	$(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
- 
- .c:
--	$(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
-+	$(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
- 
- .l:
- 	lex $(@).l
--	$(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
-+	$(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
- 
- relink:
- 	@ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile`
diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch
deleted file mode 100644
index ba44bebd1b68..000000000000
--- a/sci-chemistry/cns/files/1.2.1-ifort.patch
+++ /dev/null
@@ -1,126 +0,0 @@
-diff --git a/source/angledb.f b/source/angledb.f
-index 28ad657..eaa847d 100644
---- a/source/angledb.f
-+++ b/source/angledb.f
-@@ -1416,10 +1416,10 @@ C include files
- C local variables
-       INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS
-       INTEGER THETYPE, CURPSIS, CURPHIS
--      INTEGER CLASSINDEX
-+      INTEGER CLASINDEX
-       DOUBLE PRECISION K1, CUTOFF
-       CHARACTER*4 THENAME
--      CHARACTER*20 CLASSNAME
-+      CHARACTER*20 CLASNAME
- C begin
- C
-       IF (ANGLEDBFLAG) THEN
-@@ -1450,10 +1450,10 @@ C
-            ELSE IF (WD(1:4).EQ.'CLAS') THEN
-                 OLDCLASS = CURANGLEDBCLASS
-                 CALL NEXTWD('class name =')
--                CLASSNAME = WD(1:20)
-+                CLASNAME = WD(1:20)
-                 ANGLEDBMODE = NEW
-                 DO COUNT = 1, NANGLEDBCLASSES
--                     IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN
-+                     IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN
-                           ANGLEDBMODE = UPDATE
-                           CURANGLEDBCLASS = COUNT
-                      END IF
-@@ -1472,7 +1472,7 @@ C
-                      END IF
-                      NANGLEDBCLASSES = NANGLEDBCLASSES + 1
-                      CURANGLEDBCLASS = NANGLEDBCLASSES
--                     ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME
-+                     ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME
-                      ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS
-                 END IF
- C
-@@ -1733,16 +1733,16 @@ C
-      &                         HEAP(ANGLEDBTPTR))
-                      ELSE IF (WD(1:4).EQ.'CLAS') THEN
-                           CALL NEXTWD('Class name>')
--                          CLASSNAME = WD(1:20)
--                          CLASSINDEX = 0
-+                          CLASNAME = WD(1:20)
-+                          CLASINDEX = 0
-                           DO COUNT = 1, NANGLEDBCLASSES
-                                IF (ANGDBCLASSNAMES(COUNT).EQ.
--     &                              CLASSNAME) THEN
-+     &                              CLASNAME) THEN
-                                     PRINTTHISCLASS(COUNT) = .TRUE.
--                                    CLASSINDEX = COUNT
-+                                    CLASINDEX = COUNT
-                                END IF
-                           END DO
--                          IF (CLASSINDEX.EQ.0) THEN
-+                          IF (CLASINDEX.EQ.0) THEN
-                                CALL DSPERR('ANGLEDB',
-      &                              'unknown class. Using first.')
-                                PRINTTHISCLASS(1) = .TRUE.
-diff --git a/source/rama.f b/source/rama.f
-index c5d14f2..3063e7b 100644
---- a/source/rama.f
-+++ b/source/rama.f
-@@ -1468,11 +1468,11 @@ C include files
- C local variables
-       INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS,
-      &     THETYPE, CURPSIS, CURPHIS,
--     &     CURCHIS, CURTHTS, CLASSINDEX
-+     &     CURCHIS, CURTHTS, CLASINDEX
-       INTEGER CLEN
-       DOUBLE PRECISION K1, CUTOFF
-       CHARACTER*4 THENAME
--      CHARACTER*50 CLASSNAME
-+      CHARACTER*50 CLASNAME
- C begin
- C
- C this is used by READRAMA2 to hold the selection
-@@ -1503,10 +1503,10 @@ C
-            ELSE IF (WD(1:4).EQ.'CLAS') THEN
-                 OLDCLASS = CURRAMACLASS
-                 CALL NEXTWD('class name =')
--                CLASSNAME = WD(1:50)
-+                CLASNAME = WD(1:50)
-                 RAMAMODE = NEW
-                 DO COUNT = 1, NRAMACLASSES
--                     IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN
-+                     IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN
-                           RAMAMODE = UPDATE
-                           CURRAMACLASS = COUNT
-                      END IF
-@@ -1525,7 +1525,7 @@ C
-                      END IF
-                      NRAMACLASSES = NRAMACLASSES + 1
-                      CURRAMACLASS = NRAMACLASSES
--                     RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME
-+                     RAMACLASSNAMES(CURRAMACLASS) = CLASNAME
-                 END IF
- C
- C set force constant for current class,
-@@ -1954,18 +1954,18 @@ C
-      &                         HEAP(RAMAATOMPTR), 0)
-                      ELSE IF (WD(1:4).EQ.'CLAS') THEN
-                           CALL NEXTWD('Class name>')
--                          CLASSINDEX = 0
-+                          CLASINDEX = 0
-                           DO COUNT = 1, NRAMACLASSES
--                               IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME)
--     &                              CLASSINDEX = COUNT
-+                               IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME)
-+     &                              CLASINDEX = COUNT
-                           END DO
--                          IF (CLASSINDEX.EQ.0) THEN
-+                          IF (CLASINDEX.EQ.0) THEN
-                                CALL DSPERR('RAMA',
-      &                              'unknown class. Using first.')
--                               CLASSINDEX = 1
-+                               CLASINDEX = 1
-                           END IF
-                           CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR),
--     &                         HEAP(RAMAATOMPTR), CLASSINDEX)
-+     &                         HEAP(RAMAATOMPTR), CLASINDEX)
-                      ELSE
-                           CALL DSPERR('RAMA',
-      &                         'Expected ALL or CLASs.')
diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch
deleted file mode 100644
index dfaa40021d66..000000000000
--- a/sci-chemistry/cns/files/1.2.1-parallel.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto
-index 0d0dd3e..ae9e422 100644
---- a/instlib/source/Makefile.proto
-+++ b/instlib/source/Makefile.proto
-@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o
- 
- # the default is to make the cns executable
- cns_solve:
--	@ make -k printflags       F77BUG="$(debug)" DEBUG="$(debug)"
--	@ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
--	@ make -k exepurge
-+	@ make printflags       F77BUG="$(debug)" DEBUG="$(debug)"
-+	@ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
-+	@ make exepurge
- 
- # rule for the fortran routines
- $(OBJS): 
diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch
deleted file mode 100644
index cbddf4289158..000000000000
--- a/sci-chemistry/cns/files/1.3_p7-delete.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp
-index b64467a..5f727db 100644
---- a/utils/cluster_struc.cpp
-+++ b/utils/cluster_struc.cpp
-@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) {
-         for (int i = 0; i < nrstruc; i++) {
-           delete[] neighbor[i];
-         }
--        delete[] neighbor, neighborcount;
-+        delete[] neighbor, delete[] neighborcount;
-         return 5;
-       }
-       if (rmsd < cutoff) {
diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch
deleted file mode 100644
index 7942c55abfb9..000000000000
--- a/sci-chemistry/cns/files/1.3_p7-gentoo.patch
+++ /dev/null
@@ -1,80 +0,0 @@
-diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto
-index 0d0dd3e..dd4b680 100644
---- a/instlib/source/Makefile.proto
-+++ b/instlib/source/Makefile.proto
-@@ -11,6 +11,8 @@
- 
- SHELL=/bin/sh
- 
-+cns_string=`date "+%y%m%d%H%M"`
-+
- # commands
- RM = /bin/rm
- 
-@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o
- 
- # the default is to make the cns executable
- cns_solve:
--	@ make -k printflags       F77BUG="$(debug)" DEBUG="$(debug)"
--	@ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
--	@ make -k exepurge
-+	@ make printflags       F77BUG="$(debug)" DEBUG="$(debug)"
-+	@ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
-+	@ make exepurge
- 
- # rule for the fortran routines
- $(OBJS): 
--	@ echo "compiling: $(@:.o=.f)"; \
--	  $(F77) -c $(F77FLAGS) $(@:.o=.f)
-+	$(F77) -c $(F77FLAGS) $(@:.o=.f)
- 
- # rule for the dynamic memory allocation C routines
- dmemory.o: dmemory.c
--	@ echo ; echo "compiling: $?"
--	@ $(CC) -c $(CCFLAGS) $?
-+	$(CC) -c $(CCFLAGS) $?
- 
- # rule for the machine specific C routines
- machine_c.o: machine_c.c
--	@ echo ; echo "compiling: $?"
--	@ $(CC) -c $(CCFLAGS) $?
-+	$(CC) -c $(CCFLAGS) $?
- 
- # rule for the executable itself
- ../bin/cns_solve: $(DEPENDS) 
--	@ echo ; echo "linking: cns_solve"; echo
--	@ cns_string=`date "+%y%m%d%H%M"`; \
--	  $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
--	                                      $(LDFLAGS) \
--	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
-+	$(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
-+	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
- 	  if [ -x cns_solve-$$cns_string.exe ]; \
- 	    then echo "created executable file cns_solve-$$cns_string.exe"; \
- 	         echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \
-diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile
-index 98de84f..4f32b34 100644
---- a/instlib/utils/Makefile
-+++ b/instlib/utils/Makefile
-@@ -22,17 +22,17 @@ utils:
- 	make clean
- 
- .f:
--	$(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
-+	$(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
- 
- .c:
--	$(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
-+	$(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
- 
- .cpp:
--	$(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK)
-+	$(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK)
- 
- .l:
- 	lex $(@).l
--	$(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
-+	$(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
- 
- relink:
- 	@ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile`
diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh
deleted file mode 100644
index 34e1a2b635cf..000000000000
--- a/sci-chemistry/cns/files/cns_solve_env_sh
+++ /dev/null
@@ -1,221 +0,0 @@
-#!/bin/sh
-#
-# This file sets up the appropriate environmental variables and paths
-# for CNSsolve. In the case of the same machines with different versions
-# of the OS, backward compatibility is assumed - ie. a later version will
-# be setup for a previous version of the OS if nothing else is available.
-#
-#   written by: Paul Adams
-#
-#   copyright Yale University
-#
-# ==========================================================================
-#
-# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
-#
-# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
-
-	CNS_SOLVE=_CNSsolve_location_
-
-#
-# ==========================================================================
-#
-# full expansion of the CNS_SOLVE variable prior to use.
-#
-export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
-#
-# ==========================================================================
-#
-# set the number of threads for SGI multiprocessors
-# if this causes a problem on other systems it can be commented out
-#
-export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1
-#
-# ==========================================================================
-#
-# get the machine architecture
-#
-if [ -d $CNS_SOLVE ]; then
-  if [ ! "$CNS_ARCH" ]; then
-    export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
-  fi
-else
-  export CNS_ARCH; CNS_ARCH='unknown'
-fi
-#
-# system variables (this is needed for openmp)
-#
-ulimit -s unlimited
-# ==========================================================================
-#
-# general environmental variables
-#
-export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
-export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
-export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
-export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
-export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
-export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
-export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
-export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
-export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
-export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
-#
-# general user aliases
-#
-cns_web () { $CNS_SOLVE/bin/cns_web; }
-cns_header () { $CNS_SOLVE/bin/cns_header; }
-cns_info () { cat $CNS_SOLVE/bin/cns_info; }
-cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
-if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
-  cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
-else
-  cns_edit () { $CNS_SOLVE/bin/cns_edit; }
-fi
-run_tutorial () { "csh -f tutorial.csh"; }
-#
-# g77 compilation and use
-#
-g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
-g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
-#
-# developer aliases
-#
-run_tests () { $CNS_SOLVE/bin/run_tests; }
-run_diffs () { $CNS_SOLVE/bin/run_diffs; }
-maketar () { $CNS_SOLVE/bin/maketar; }
-create_patch () { $CNS_SOLVE/bin/create_patch; }
-#
-#
-# ==========================================================================
-#
-# to do expansions - unset noglob just in case user has it otherwise
-#
-set +f
-#
-# try to set up appropriate path
-#
-# first strip off any trailing information (eg. _g77)
-#
-CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
-#
-cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
-cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
-cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
-cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
-cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
-#
-# if we are looking for a specific type of setup then limit search
-#
-cns_dirs=""
-if [ ! "$CNS_G77" ]; then
-  if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
-    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
-  fi
-else
-  CNS_ARCH="${CNS_ARCH}_g77"
-  if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
-    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
-  fi
-fi
-#
-# first look for an exact match (with os version)
-#
-#
-cns_found=0
-if [ -n "$cns_dirs" ]; then
-  for cns_dir in $cns_dirs ; do
-    cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
-    if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-      if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
-           $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then
-        cns_archenv=$cns_dir
-        cns_found=1
-      fi
-    fi
-  done
-#
-#
-# now look for an exact match (without os version)
-#
-  if [ $cns_found -eq 0 ]; then
-    for cns_dir in $cns_dirs ; do
-      if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-        if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
-             $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
-          cns_archenv=$cns_dir
-          cns_found=1
-        fi
-      fi
-    done
-  fi
-#
-# now look for a backwards compatible match (with os version major/minor)
-#
-  if [ $cns_found -eq 0 ]; then
-    for cns_dir in $cns_dirs ; do
-      if [ $cns_found -eq 0 ]; then
-        cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
-        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-          if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
-	    osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
-            if [ $osv_test -eq 1 ]; then
-              cns_archenv=$cns_dir
-	      cns_found=1
-            fi
-          fi
-        fi
-      fi
-    done
-  fi
-#
-# now look for a wildcard match on cpu
-#
-  if [ $cns_found -eq 0 ]; then
-    cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
-    cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
-    for cns_dir in $cns_dirs ; do
-      if [ $cns_found -eq 0 ]; then
-        cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
-        cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
-        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-          if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
-               $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
-  	    cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
-            if [ $cpu_test -eq 1 ]; then
-              cns_archenv=$cns_dir
-	      cns_found=1
-            fi
-          fi
-        fi
-      fi
-    done
-  fi
-fi
-#
-# if found set environment
-#
-if [ $cns_found -eq 1 ]; then
-  #
-  # set installation and source directory
-  #
-  export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
-  export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
-  #
-  # path for CNSsolve utility programs
-  #
-  if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
-    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
-  fi
-  #
-  # path for CNSsolve executable if installed
-  #
-  if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
-    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
-  fi
-fi
-#
-unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
-unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
-unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
-#
diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7
deleted file mode 100644
index 12368f87b596..000000000000
--- a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7
+++ /dev/null
@@ -1,229 +0,0 @@
-#!/bin/sh
-#
-# This file sets up the appropriate environmental variables and paths
-# for CNSsolve. In the case of the same machines with different versions
-# of the OS, backward compatibility is assumed - ie. a later version will
-# be setup for a previous version of the OS if nothing else is available.
-#
-#   written by: Paul Adams
-#
-#   copyright Yale University
-#
-# ==========================================================================
-#
-# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
-#
-# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
-
-	CNS_SOLVE=_CNSsolve_location_
-
-#
-# ==========================================================================
-#
-# full expansion of the CNS_SOLVE variable prior to use.
-#
-export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
-#
-# ==========================================================================
-#
-# get the machine architecture
-#
-if [ -d $CNS_SOLVE ]; then
-  if [ ! "$CNS_ARCH" ]; then
-    export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
-  fi
-else
-  export CNS_ARCH; CNS_ARCH='unknown'
-fi
-#
-# ==========================================================================
-#
-# system variables for OpenMP
-#
-# The default stack sizes are usually insufficient, especially when
-# CNS is compiled using OpenMP. If the stack sizes are too
-# small segfaults may occur. Recommended setting for "stacksize":
-limit stacksize unlimited
-#
-# KMP_STACKSIZE is specific for Intel ifort, icc:
-##setenv KMP_STACKSIZE 256m
-#
-# OMP_STACKSIZE is used by all compilers:
-setenv OMP_STACKSIZE 256m
-#
-# Uncomment the following line and change as appropriate to set the number 
-# of processors (threads) to use. 
-###setenv OMP_NUM_THREADS 4
-#
-# ==========================================================================
-#
-# general environmental variables
-#
-export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
-export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
-export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
-export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
-export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
-export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
-export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
-export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
-export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
-export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
-#
-# general user aliases
-#
-cns_web () { $CNS_SOLVE/bin/cns_web; }
-cns_header () { $CNS_SOLVE/bin/cns_header; }
-cns_info () { cat $CNS_SOLVE/bin/cns_info; }
-cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
-if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
-  cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
-else
-  cns_edit () { $CNS_SOLVE/bin/cns_edit; }
-fi
-#
-# g77 compilation and use
-#
-g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
-g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
-#
-# developer aliases
-#
-run_tests () { $CNS_SOLVE/bin/run_tests; }
-run_diffs () { $CNS_SOLVE/bin/run_diffs; }
-maketar () { $CNS_SOLVE/bin/maketar; }
-create_patch () { $CNS_SOLVE/bin/create_patch; }
-#
-#
-# ==========================================================================
-#
-# to do expansions - unset noglob just in case user has it otherwise
-#
-set +f
-#
-# try to set up appropriate path
-#
-# first strip off any trailing information (eg. _g77)
-#
-CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
-#
-cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
-cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
-cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
-cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
-cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
-#
-# if we are looking for a specific type of setup then limit search
-#
-cns_dirs=""
-if [ ! "$CNS_G77" ]; then
-  if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
-    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
-  fi
-else
-  CNS_ARCH="${CNS_ARCH}_g77"
-  if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
-    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
-  fi
-fi
-#
-# first look for an exact match (with os version)
-#
-#
-cns_found=0
-if [ -n "$cns_dirs" ]; then
-  for cns_dir in $cns_dirs ; do
-    cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
-    if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-      if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
-           $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then
-        cns_archenv=$cns_dir
-        cns_found=1
-      fi
-    fi
-  done
-#
-#
-# now look for an exact match (without os version)
-#
-  if [ $cns_found -eq 0 ]; then
-    for cns_dir in $cns_dirs ; do
-      if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-        if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
-             $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
-          cns_archenv=$cns_dir
-          cns_found=1
-        fi
-      fi
-    done
-  fi
-#
-# now look for a backwards compatible match (with os version major/minor)
-#
-  if [ $cns_found -eq 0 ]; then
-    for cns_dir in $cns_dirs ; do
-      if [ $cns_found -eq 0 ]; then
-        cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
-        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-          if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
-	    osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
-            if [ $osv_test -eq 1 ]; then
-              cns_archenv=$cns_dir
-	      cns_found=1
-            fi
-          fi
-        fi
-      fi
-    done
-  fi
-#
-# now look for a wildcard match on cpu
-#
-  if [ $cns_found -eq 0 ]; then
-    cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
-    cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
-    for cns_dir in $cns_dirs ; do
-      if [ $cns_found -eq 0 ]; then
-        cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
-        cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
-        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
-          if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
-               $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
-  	    cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
-            if [ $cpu_test -eq 1 ]; then
-              cns_archenv=$cns_dir
-	      cns_found=1
-            fi
-          fi
-        fi
-      fi
-    done
-  fi
-fi
-#
-# if found set environment
-#
-if [ $cns_found -eq 1 ]; then
-  #
-  # set installation and source directory
-  #
-  export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
-  export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
-  #
-  # path for CNSsolve utility programs
-  #
-  if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
-    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
-  fi
-  #
-  # path for CNSsolve executable if installed
-  #
-  if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
-    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
-  fi
-fi
-#
-unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
-unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
-unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
-#
diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml
deleted file mode 100644
index 67326b6bd798..000000000000
--- a/sci-chemistry/cns/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="aria"> Support patch for sci-chemistry/aria</flag>
-  </use>
-  <longdescription>
-Crystallography and NMR System (CNS) is the result of an international
-collaborative effort among several research groups. The program has 
-been designed to provide a flexible multi-level hierachical approach for the
-most commonly used algorithms in macromolecular structure determination. 
-Highlights include heavy atom searching, experimental phasing (including 
-MAD and MIR), density modification, crystallographic refinement with maximum
-likelihood targets, and NMR structure calculation using NOEs, J-coupling, 
-chemical shift, and dipolar coupling data.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/ksdssp/Manifest b/sci-chemistry/ksdssp/Manifest
index 8691e1e8a7c1..29e85fc38b85 100644
--- a/sci-chemistry/ksdssp/Manifest
+++ b/sci-chemistry/ksdssp/Manifest
@@ -1,4 +1,3 @@
 DIST ksdssp-040728.shar 104347 BLAKE2B f77ba1fd83e9dd959dabf49818c541605eb8fba895880dbd8324cd02a0528d7961ced200de4b64c18c897a18e9f78474293a9f95fee9beace36f5faba61fcaa2 SHA512 17c32bea1f32acfd31353d0378fe2a664a8922db8b929da4b9b10ac279013946911acd2a26ab3ab227ae160352c8313dcf742fae8c139a90ac11f772f17a1689
 EBUILD ksdssp-040728-r1.ebuild 916 BLAKE2B 7d2461015ee5646fc30b2ce61f52c63b01340b32a8b79e70eff1c3762cf7e82967063abee0b12195e4ff2db6afd4f13b501faec4116a464de10fb63e376e0318 SHA512 90eeb66be6665ca20bbe2dfdf1515d4ff44480dba23c47511501750749f903c2a1f80394e7c026b0ed99f4e545dcf3d70c64bcf8f21b49d945ed6e99878b5d30
-EBUILD ksdssp-040728.ebuild 859 BLAKE2B ee6ce02895ff0dc3d6880d6dce5d92002f413fa1ac9d42096d27fd2339b50c80f18d34133aa52308e165c786af6a4ad024da1c9ad8d89c8a3168847eed626faf SHA512 9c75d28ec520923f51d9b985d4de7f99a65496797bd897d837e9d6a2abc92fa73e90832451f0c5ee198c6d0bccb2ad79b9189e93dab8efdd40070c2555c325a2
 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/ksdssp/ksdssp-040728.ebuild b/sci-chemistry/ksdssp/ksdssp-040728.ebuild
deleted file mode 100644
index 9dcb38c517d6..000000000000
--- a/sci-chemistry/ksdssp/ksdssp-040728.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit toolchain-funcs
-
-DESCRIPTION="ksdssp is an open source implementation of dssp"
-HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html"
-SRC_URI="mirror://gentoo/${P}.shar"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD"
-IUSE=""
-
-RDEPEND="sci-libs/libpdb++"
-DEPEND="
-	${RDEPEND}
-	app-arch/sharutils"
-
-S="${WORKDIR}"/${PN}
-
-src_unpack() {
-	"${EPREFIX}"/usr/bin/unshar "${DISTDIR}"/${A}
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \
-		BINDIR="${EPREFIX}/usr/bin" \
-		.TARGET="${PN}.csh" \
-		.CURDIR="${S}" \
-		CC="$(tc-getCXX)" \
-		LINKER="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		${PN} ${PN}.csh
-}
-
-src_install() {
-	dobin ${PN}{,.csh}
-}
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
index d4b7e143cac0..ed5b2ebbe93c 100644
--- a/sci-chemistry/mdtraj/Manifest
+++ b/sci-chemistry/mdtraj/Manifest
@@ -1,3 +1,3 @@
 DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76
-EBUILD mdtraj-1.9.1.ebuild 889 BLAKE2B fd2423ca08f4666101c409c52be19c717d222c19da08424c2923e91bb9ad6961c64b3fb97a6b71e1d5a9a9cd568f0325510943c388c35c59049f4597ce0cca02 SHA512 61c0a2351c18155aec9bf5fcd6a3f7b2e319c096f493866f94789b11bfbef4a6bbfe849a111acad74503bb30d327c10e15b34338f752763f77e3033b2e287680
+EBUILD mdtraj-1.9.1.ebuild 913 BLAKE2B 219e598b0f693590a70c7221fb247587d17eb0214838e45517a099fcbcd936d342735a02da84ca81c74c6ab11ece7fe31cfc74d5610e728d79437867a2d12f9a SHA512 e169ea7efef0a9531657ee793a1bba5e020f3d5d013b8ffed5e6198d2057d98e0961fc734edfefe0b9592d60d22fd6d67c631c071073ce75d1359ea5dbfd774e
 MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
index 2ac95db2c57d..889d5e8e0b26 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -15,6 +15,7 @@ SLOT="0"
 LICENSE="GPL-2"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-python/setuptools[${PYTHON_USEDEP}]
diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest
index 1c85a8486821..28f2def46ff2 100644
--- a/sci-chemistry/molden/Manifest
+++ b/sci-chemistry/molden/Manifest
@@ -1,14 +1,8 @@
 AUX molden-4.7-implicit-dec.patch 225 BLAKE2B 5d3a911b27bac3b1041d6b85599468ce6f0b0b8a52a118bf1d8d4ab5e22b7c0bcda0dd9f14241fd8e9bc0b79c966a07da1d40c38839086496f11edf1ff733516 SHA512 9a76dfdd434849532a8625459663ca81d8a948b20f7ea8296ae8d25a51f6c28b3cab2691be0f7683ff5d5b7ed8d84211ac26a5bb22c27891863a1c04299d8fea
-AUX molden-4.8-ambfor.patch 480 BLAKE2B 59db88a3a997ebb0f6d99b30cd46ddbf3d4cfac43adf2b47bc189db44e5b6077ee5e296abd792f8e131f1c15c5586020252b0acc0ed2a590670abf047e339c1c SHA512 9fe52f994e621e4ce578a8cdfa9074ceda522c2426c4b15c4d1de38832eef936de54bd07021489e0e12f420b25179b7a3cb615512d77d4457d9e7c9adae0f475
 AUX molden-4.8-ldflags.patch 866 BLAKE2B ba4e859d0706e17e926b3f55ed03bac5d50dcb0c5f3ddd8f5dd829cd75880bfe64f6f509d3d76acbbe0613c17348df70527be34abb084f19c46ce6f0e11f5964 SHA512 427ec1da9e71b2097164f8fb7448713961f7fdb63b8a51dee23490d6d305129dd12a9e782033588304406dd35aa18ceb7040c32fa09ea38b339f9dc47e0a24a9
-AUX molden-4.8-overflow.patch 714 BLAKE2B fe94c6192632388f9e88f68abf2c9467e11fec068d13f510217870a897f4ac685fc5651a8a60db2f1b72d967275b34f84aeb9d598cad7d8323ace3d66ec44b36 SHA512 ecc4f4501166a4ed4a1c451901d3aed49e3ad7fd3833cb4419a62b1864e689399ca68562fbc82784813881a003a405d4eea5d0e351a9181cbb164beb702d3765
 AUX molden-5.0-ambfor.patch 523 BLAKE2B 1443a26ff5fbaab3092a6df6a5ab0d514547d59788030ea1c761b8867cf042ff53f6382b85c7aa5383a85504c99e625e9e9c13cd96e1c52a2e05347286be474a SHA512 f531d3bd50374bf658e710f2e4b649559503b378ab663f03cd9259b9105b6c25eab61318bb3d02814425ecb596802569aa3281741d611d4e1c8fc4da771fd481
 AUX molden-5.0-overflow.patch 341 BLAKE2B c7285c87c0741ecf6bce3bad89883ed6e7720cb72a479c9bea7ad8a1dabcc1ae8894f6811e2d537555a00cb9138a7b579dee631221efb3a721b77b446abcb82d SHA512 342b7531179b8a3c3aedff085022d972bd795d2c56ebf4b49fce5ff60e6cc9ea48ed18258af53042ad72aae400f694aec9692bc0b1abfa960bc100ee02f57981
 AUX molden-5.5-gcc8.patch 328 BLAKE2B e098e680a5b75ff09fbaecf44609055584b0f1c49edc0ea16b81dbff68b06883dc6317340b3dc6b26836958d1f561b3aed383964f7c65126079f74b3023f96dd SHA512 cc1a8c08b9081ff138aedda11887295f0eb31b97174ce45bffae8e563318388035948775f03d39823280103ea522a20939b6294e3d3721e599e6790e4a5695e2
-DIST molden4.8.tar.gz 2969701 BLAKE2B 943bfd7bd8dde2da8e171f4a0f5e570ec1a064ef92e6ae4f6cbc48289e42c4660e021965670c132328e575d2ca388fccf7f8ae77d4f7342b55fe5522f2f63c6e SHA512 11f2406e54a077d044369b5eee4a8a1c1b10f052188d33d4162af0151a1e76a1d5274d8788bbc3610905ff271b0bd2100990b77540a0290ad608bd5c29b839e3
-DIST molden5.0.tar.gz 3063244 BLAKE2B 857f3276e45d05f92f291b0189cdcb7aeacd9ede0eeaf1ebe6b6942d397bbdd83812b4a5c8163be75a5a3c7bd0b29c9304d29ae596e04ba9bfbb30960e899326 SHA512 bf45849bf4efb67bc552767c28a6df6e5106a7d8ac2d73db2c7218412fb6cd2f2785c2be83a8589a5664ba9c0ca052cef5eb155c665ee1f3d6c7fe208f806a6b
 DIST molden5.5.tar.gz 4934764 BLAKE2B 6ce71f928ed9aacf8fe9830c4c36a675f81d63e97d08e96519ff74d172540ae0a9af25ca966d6c02cdcbbc43633a0ef80be9d31ef98a80d59a8e1a13374c2f51 SHA512 45269d2c7a52b3b2bf4fdb5f4ca3912637b3414ff9dfcd0d4f23815b3dcf7a53ffee717420d4fbf286b71c972539e756a440f5e37b7b7325ab312c25fc6c47b0
-EBUILD molden-4.8-r2.ebuild 1726 BLAKE2B ed9494e53f93b3de114e1032c88658628efe0e30af1b8670a32b090f7b6bd720c9a0795a4a4e5ba1fc7d6f50439b8f6b85e671854e1ae79e18d952356dce0483 SHA512 ca0772ada2086f91150f8a0ab2a86c9a9a6169a89e2c8c0f6b4ab4d368906f5d5d2807cd228e1f42292c6562d980a0e206f568433b396d23c7846beb65dd6f5a
-EBUILD molden-5.0.ebuild 1733 BLAKE2B 2d5e3657c53ae6f7ca67996d63ec98776d1de5330ae050b8d8191289d6800298bdccc1361b57df4573f2e99d2688edc09234a72b2c29431e482406c37bcf213e SHA512 0584ad6f157bab063a79b8e095dedec04e6a2f1d05d5483027dc8c7b0b8455956140ae69f9d6749b47ce69db30d62d391e9f7a7e00dba696d73687861d6bd604
 EBUILD molden-5.5.ebuild 1639 BLAKE2B 7f3b42046e10a433442cc664c6552c9f74ca5bc142da2bc5fe813cc7deb78d4cb1e9231c0554b0ec3d500f72c6104595c053555f66c28e982394fc973bda8455 SHA512 185d8c4004d0023b3663f13b793fb99a6f17573c1dfdc87602b97f0735cb4a52f4c9f7f833f01ccbf837f311ded87f61418c16d918955a67c9c962d149f3d054
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/molden/files/molden-4.8-ambfor.patch b/sci-chemistry/molden/files/molden-4.8-ambfor.patch
deleted file mode 100644
index 1ececa7f57e9..000000000000
--- a/sci-chemistry/molden/files/molden-4.8-ambfor.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur molden4.8/ambfor/makefile molden4.8.new/ambfor/makefile
---- molden4.8/ambfor/makefile	2009-12-19 06:14:32.000000000 -0500
-+++ molden4.8.new/ambfor/makefile	2010-02-25 22:33:41.000000000 -0500
-@@ -32,7 +32,7 @@
- 	$(LDR) -o ambmd md.o verlet.o allocmd.o $(OBJS) $(LIBS)
- 
- ambfor.o:	ambfor.f
--	${FC} -c -g -ffast-math -funroll-loops -m32 -o ambfor.o ambfor.f
-+	${FC} $(FFLAGS) -c ambfor.f -o ambfor.o 
- 
- allocmd.o:	alloc.c
- 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch
deleted file mode 100644
index 7cbd7f436f57..000000000000
--- a/sci-chemistry/molden/files/molden-4.8-overflow.patch
+++ /dev/null
@@ -1,38 +0,0 @@
- xwin.c |   10 ++++++----
- 1 files changed, 6 insertions(+), 4 deletions(-)
-
-diff --git a/xwin.c b/xwin.c
-index f395909..092edff 100644
---- a/xwin.c
-+++ b/xwin.c
-@@ -13552,7 +13552,7 @@ void NewActiveStruct()
- #ifdef CRAY
-     _fcd ztr;
- #else
--    char ztr;
-+    char ztr[4];
- #endif
- #endif
- 
-@@ -13650,8 +13650,10 @@ void NewActiveStruct()
- */
- 	clfpstr->ihashz = 0;
- #else
--	strncpy(&ztr,HetAtm[j],3);
--	parhet_(&j1,&ztr);
-+	if (HetAtm[j] != NULL) {
-+	   strncpy(ztr,HetAtm[j],3);
-+	   parhet_(&j1,ztr);
-+	}
- #endif
- #endif
-     }
-@@ -27353,7 +27355,7 @@ char *errstr;
- 	UpdateZME();
- 	RedrawScroll(&zscroll);
-     }
--    strcpy(ZMEerr,errstr);
-+    strncpy(ZMEerr,errstr,MAXZMEERR);
-     RedrawStatus();
- }
- 
diff --git a/sci-chemistry/molden/molden-4.8-r2.ebuild b/sci-chemistry/molden/molden-4.8-r2.ebuild
deleted file mode 100644
index f00761130395..000000000000
--- a/sci-chemistry/molden/molden-4.8-r2.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils fortran-2 flag-o-matic toolchain-funcs
-
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
-HOMEPAGE="http://www.cmbi.ru.nl/molden/"
-SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
-
-LICENSE="MOLDEN"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="opengl"
-
-RDEPEND="
-	x11-libs/libXmu
-		virtual/glu
-	opengl? (
-		media-libs/freeglut
-		virtual/opengl )"
-DEPEND="${RDEPEND}
-	x11-misc/gccmakedep
-	app-editors/vim"
-	# vim provides ex, which the build system uses (surf/Makefile, at least)
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-ambfor.patch \
-		"${FILESDIR}"/${P}-overflow.patch \
-		"${FILESDIR}"/${P}-ldflags.patch \
-		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
-	sed \
-		-e 's:makedepend:gccmakedep:g' \
-		-e "s:/usr/include/sgidefs.h::g" \
-		-i surf/Makefile || die
-	sed 's:shell g77:shell $(FC):g' -i makefile || die
-}
-
-src_compile() {
-	# Use -mieee on alpha, according to the Makefile
-	use alpha && append-flags -mieee
-
-	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
-	# unfortunately a bash bug prevents us from doing typeset and
-	# assignment on the same line.
-	typeset -a args
-	args=(
-			CC="$(tc-getCC) ${CFLAGS}" \
-			FC="$(tc-getFC)" \
-			LDR="$(tc-getFC)" \
-			FFLAGS="${FFLAGS}" )
-
-	einfo "Building Molden..."
-	emake -j1 "${args[@]}"
-	if use opengl ; then
-		einfo "Building Molden OpenGL helper..."
-		emake -j1 "${args[@]}" moldenogl
-	fi
-}
-
-src_install() {
-	dobin ${PN} g${PN}
-	if use opengl ; then
-		dobin ${PN}ogl
-	fi
-
-	dodoc HISTORY README REGISTER
-	cd doc
-	uncompress * && dodoc *
-}
diff --git a/sci-chemistry/molden/molden-5.0.ebuild b/sci-chemistry/molden/molden-5.0.ebuild
deleted file mode 100644
index 52f4ccdcfed0..000000000000
--- a/sci-chemistry/molden/molden-5.0.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils fortran-2 flag-o-matic toolchain-funcs
-
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
-HOMEPAGE="http://www.cmbi.ru.nl/molden/"
-SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
-
-LICENSE="MOLDEN"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="opengl"
-
-RDEPEND="
-	x11-libs/libXmu
-		virtual/glu
-	opengl? (
-		media-libs/freeglut
-		virtual/opengl )"
-DEPEND="${RDEPEND}
-	x11-misc/gccmakedep
-	app-editors/vim"
-	# vim provides ex, which the build system uses (surf/Makefile, at least)
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-ambfor.patch \
-		"${FILESDIR}"/${P}-overflow.patch \
-		"${FILESDIR}"/${PN}-4.8-ldflags.patch \
-		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
-	sed \
-		-e 's:makedepend:gccmakedep:g' \
-		-e "s:/usr/include/sgidefs.h::g" \
-		-i surf/Makefile || die
-	sed 's:shell g77:shell $(FC):g' -i makefile || die
-}
-
-src_compile() {
-	# Use -mieee on alpha, according to the Makefile
-	use alpha && append-flags -mieee
-
-	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
-	# unfortunately a bash bug prevents us from doing typeset and
-	# assignment on the same line.
-	typeset -a args
-	args=(
-			CC="$(tc-getCC) ${CFLAGS}" \
-			FC="$(tc-getFC)" \
-			LDR="$(tc-getFC)" \
-			FFLAGS="${FFLAGS}" )
-
-	einfo "Building Molden..."
-	emake -j1 "${args[@]}"
-	if use opengl ; then
-		einfo "Building Molden OpenGL helper..."
-		emake -j1 "${args[@]}" moldenogl
-	fi
-}
-
-src_install() {
-	dobin ${PN} g${PN}
-	if use opengl ; then
-		dobin ${PN}ogl
-	fi
-
-	dodoc HISTORY README REGISTER
-	cd doc
-	uncompress * && dodoc *
-}
diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest
index 473739395db5..6ab473c01cc1 100644
--- a/sci-chemistry/moldy/Manifest
+++ b/sci-chemistry/moldy/Manifest
@@ -1,4 +1,4 @@
 AUX 2.16e-as-needed.patch 3226 BLAKE2B 777b34d43da82b036e401c398d0f59a5f268905a399f38277be73ba6bdaefd6f1de2ec748302edfc68c6389acb22fa50d72b465522b1f2d5bbd14eca289d7595 SHA512 b32461bb052c908106f0f8d74be4eba52daa41ba592a7ba6083edc2a54c4a14003cf33560572e57f2b370ad5ea1f703e388855e8e7fa67ccec40e3015a8f5803
 DIST moldy-2.16e.tar.gz 488410 BLAKE2B 44ff1dacc66922ba11297ca54c645f209b782b8cde50e427d54d1d249a93b718eeb865357ea47b820801fdbca325d5f0d6027fe11ce6e0a842e77d1970a0467c SHA512 b672f4e5c8843277d1b66eedf5f7ad87be0b4c014e0d6bfda4ef941cd9bfeec68d94a361e28531cc3794ee2e4a6937f15c462c69f9adcfcfe5254c3c677fe877
-EBUILD moldy-2.16e-r2.ebuild 1811 BLAKE2B 1e03c508b0a5376efd64559517798bff39339e3815cb65bea7cbe7d72e622d40f49760a6872846e369fe0ef07a7e4040b5fcfceab26278c1b52f13bd8fad15aa SHA512 6f6280a30cef11539d27b6efa5326f3ca5b365e179dbc3f3e2b5b237b92e66786f4969ebd7ff1d67b3e3f53f2c52a3bc46ccb5ba45078db17e7d325c4640fff0
+EBUILD moldy-2.16e-r2.ebuild 1804 BLAKE2B 3c4865ada8baec131c5bb92e6856e3526a4aea05cb754423bf7cb896992c6e2732ad42b31808059c602549de7fd5054de780cfbe85218056c975f7c4c5fbda90 SHA512 5b8b76efa8f2132b50abd4ce3f0a137a8ed433c4e88b5b60df7043df00d5c78696c08dcfaade590842625429fa67656fa2d4537b158bedfb54da1eb79224bdcf
 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
index 8ba71f621898..0d3399860306 100644
--- a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
+++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
@@ -61,7 +61,7 @@ src_install() {
 	if use examples; then
 		rm Makefile.in configure.in config.h.in
 		insinto /usr/share/${PN}/examples/
-		doins *.in *.out control.* || die
+		doins *.in *.out control.*
 	fi
 	if use doc; then
 		insinto /usr/share/doc/${PF}/pdf
diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest
index d70775668870..9b7a014b2025 100644
--- a/sci-chemistry/molequeue/Manifest
+++ b/sci-chemistry/molequeue/Manifest
@@ -1,4 +1,4 @@
 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.ebuild 1479 BLAKE2B f00bb04fa08a720367daa464399daa71f47c4fe34263dc699811cc9ea0683a065d06a30e8be9d0ccd46071329829cae739a8c3fa5773998c1c3b8fb6d53653a1 SHA512 a6a5643849c85231652e9d1ff1c93e599a539eca0cc5572bab8ae9b837cc2f6ad8f5c04d96774493187f3f3cb216f163e7990a9d62abb60caefcde9ad610aedb
+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.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
index 71e253b4283a..0a2c4acc3e53 100644
--- a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
+++ b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
@@ -15,6 +15,7 @@ SLOT="0"
 LICENSE="BSD"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="+client doc server test +zeromq"
+RESTRICT="!test? ( test )"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}
 	server? ( client )
diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest
index be99a3ca0878..c7a1874bb71c 100644
--- a/sci-chemistry/molsketch/Manifest
+++ b/sci-chemistry/molsketch/Manifest
@@ -1,5 +1,5 @@
 AUX molsketch-0.3.0-_DEFAULT_SOURCE.patch 661 BLAKE2B 48e877f41de2b27d1c6bbdac34d68893b58bf22e3d2ca8fa3e777f950f6906b100471b0a1287205e65bb5e97e9b3bd40b64377f513750ec039ebffdddbd0ea22 SHA512 9fd409ca55d5df0c61e84d3d9941f4855b7dcd32fd7521f24204570858dc6205c70ca4c645c5eee31bdc446a315e02081fa947677a4f22addce16ec4dad64c10
 AUX molsketch-0.4.1-more-quotes.patch 478 BLAKE2B 857f6a6f2514a4322f2a178aed0232f6f18d06831fea72ac8bbfa2cb806cdb2f73f2daeb4e9b8326be9dbd96518047c24f2721c3509d1551d90cfa80ca0105a8 SHA512 015344abb4aaa7f214e4e8a7eebe1a7a8f4d43b8a76a9c5f984fc4c5cf8da450430330543fe69d481ceec25c5a59ee332439654fd4ce82ce080aa4883cc1d113
 DIST Molsketch-0.4.1-src.tar.gz 1499842 BLAKE2B 22584f012e838037f9e23c16da6c63984604002884d279b2b6012d80eb08af9ee18b4d364fa29327572854fccad34840f97413b29b487cfbeb6496a2a8003d17 SHA512 263b088c2b8d01c1f13802b18aea6f6784580fe1a806de45b0e1ecd9f29024350e01a611bdeed1891938acc733a42746203d345d3be13ebaf4c309413e86bf26
-EBUILD molsketch-0.4.1-r1.ebuild 1359 BLAKE2B 2c455402f624b9fadf848b8e4f9ecbcf0d89f453f284bd907a55ef2118f6099af46d907216bf40319f5fece28b3d00c294286cdf82137f0a807299b707e05e50 SHA512 e1ecf0c0a0412cee651839204cd80039216a81bbd28cd37c23197a8270ce97e26b2df644b4b9144f139d7b8243b3437a2f13301c184152ad89fcf9778d6eaf82
+EBUILD molsketch-0.4.1-r1.ebuild 1383 BLAKE2B 58fa01d7f55eaf1394e2f44738b20395c9ca979076bf6ff32ae8db524f8d1d0b30e2da2a019e92d29de61e95d4077bc2aff47d8aa21b022fc20deeaab8ef3f86 SHA512 f41c9caa896b44939521a5badcf584de071bfd64c05524b8b1d7a9333a1579c83847a3f0151cd7c16cd213bf1739ac40a760638b92faac18e22d6d7d27e76256
 MISC metadata.xml 609 BLAKE2B 07b5bc6ee3fbbbd071bac3959e4f42a6d38cb6dff2ca6e86f9d6e0108c9f3370dc1a99ea5b4a26b58769d45d064e85e9c0c5c6cacf980b68def32e7c63b1cf54 SHA512 34417299d583ff8a830dbe5e4898e999c3a4d72f11cc032f1274e12ad9dfb424d7d8eaaa2e5dac8efb748d7da68691e4ea1b4b1a426407b8dadc740ba109d61c
diff --git a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild
index c34e60a0106c..87dc43370de6 100644
--- a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild
+++ b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -17,6 +17,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 DEPEND="
 	>=sci-chemistry/openbabel-2.2
diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest
index c9c16933c73c..6b1e2c080a55 100644
--- a/sci-chemistry/nmrglue/Manifest
+++ b/sci-chemistry/nmrglue/Manifest
@@ -1,4 +1,4 @@
 AUX nmrglue-0.5-nohyper.patch 1408 BLAKE2B 8e91e270183ce8f4c361fd3577dc4942b2afab81ee8f59df5c8dd9056dbf639653d2e84f9dc04026636dda98e28a244586ba5bc2cd4ed5c43c8a31d0c0cab4d1 SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd
 DIST nmrglue-0.5.tar.gz 142604 BLAKE2B 9a018a73bea46176fc06042013cb23b3eeb962df8a595388da536d17f1d2d4d550065c5492df28de860ea1290314d2fa1110af349be0c2a8b1b31677b3e4afbc SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2
-EBUILD nmrglue-0.5-r1.ebuild 726 BLAKE2B f67232037b0cc6e96837387790d96a530aac385decb8f53317f4ea28221e798c6f1e61cce20e4665df92826291f3e730d8aac1c819fba562c77c6b6b13e6d7b4 SHA512 a896e0d38e5772ec35ec9da9ef198cde44b1b88adfb58d3df1229b3e04bff8e066a330549d852e0abbcd05163dd8f61c42953550ccd6368d72cc30b59b98f976
+EBUILD nmrglue-0.5-r1.ebuild 753 BLAKE2B 37b2d1f011c7cf4f44fbf4468154384173d40310c519b9a10c49cd684291c912add9abc9ea1b19254302a520a1dc3b204b80ad23056f78bc59d0f993c99fe3a4 SHA512 6242503f01772bf425bd6665b51f2a00288f1c352ac7b9f1ecc154a9c5ed99e19c58ddf09dd4e0a9cf9f5991fcdbe208b06300290c968ebd2d16f2894487562d
 MISC metadata.xml 1338 BLAKE2B 480651ef6112e93e3c70e734f4ca7d7b24653109f503fab6a340c9dc246b881b5ab103b90f8ffbc92a6d5352b399c15a33072292e549b4ffcc2689f049996cfd SHA512 7defa016b2c5f51327f282ef8dbb5f99767e554112baf10d72a6c86462d86bf7bd3129226340bbdb00f9e95b2349fc3594b6d0d8cd0175457bbb5f034e31aa7c
diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
index 939e9307cc50..97ddc5611088 100644
--- a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
+++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
@@ -15,6 +15,7 @@ SLOT="0"
 LICENSE="BSD"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-python/matplotlib[${PYTHON_USEDEP}]
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index f7fb369c0129..2681ad9f8d71 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 706 BLAKE2B 085b2f5a1678c02a6a8efc5f760dc43ef311774a47d80c87efb75111ac750ec6bf520286fa74325eca71138eecff4b2772ab087d4de1b9b9a5f1c81806d6be87 SHA512 04884d47a9549d2c107bbeb9c36edbe18ee68a7edd447fce405f39a4297bdacf3f81ddf4c5c19e9728355f07960b836e684087573b3a2b7892225de8b7beaea1
 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 2181 BLAKE2B dab9ccf7576cc1b24eb6d7566f487b4f6d6711797cb6b15800d120f2226d3fa19977908bcae3535177fb7f938365673518266bae2f3eb4eb0cbc48c6850af7d0 SHA512 4d0783e28d81d0c8f61dcf9f4d8f8acc835de48d3d7299d555ef939bd447d120c722aab97efd1981e0148485e80956632119eeb07ca6d67328a9435ce81b86ac
-EBUILD openbabel-2.4.1.ebuild 2013 BLAKE2B b7fe713786600ac7efc9b4541663b8049c0145863cd6efc397dbed8a858cb006746e8ae6ddb4b9148023d5bf3a7f1cca76a4327577a5f9809c8e17d5a4f78945 SHA512 2eddc590968cb39a8c87563eb724669742b795bbf1861d85d9892e87fa9137b989f36ba435f98fe1b8151a142aa73a73df49ab5ef5ad1617e2d3875ad655ee1e
+EBUILD openbabel-2.4.1-r1.ebuild 2208 BLAKE2B 388a26c0e190f24a10081eaa0fb901fab153b05fe67cd82734a75265cdb9f18877f58ae5db0f9d0cf8b8ee0158ef967ee5eb2079245ea3b9becf41d5118439dd SHA512 e6dbdbaea505c769e6e639b8135c6da460a2918f02f72c817263425ff9618583642324a9aef3226713e20a3c500a6963b56602a289620581519c41f023822dac
+EBUILD openbabel-2.4.1.ebuild 2037 BLAKE2B 8004d9f684cb960e9dfc933a97b9f2c5d7219323d6e2368086cc02d878d7b26dc444e335a532a02e8a3c7dd2b68f4ffaa3b15e2cfc74482fae06d5af594c3ec7 SHA512 126480882f9af4a12981609c7897da380cb89479b4df7e69ef4e1d6456f1eda1e4842243f23f0829fa17ed6103b9dbf7012f95e290dffb332d62f378bc4af0ca
 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 0834c411ef29..2d53613d1d29 100644
--- a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
@@ -18,6 +18,7 @@ SLOT="0/5.0.0"
 LICENSE="GPL-2"
 KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE="doc openmp test wxwidgets"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-cpp/eigen:3
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
index 4606746af57d..b76a75d78d9b 100644
--- a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -16,6 +16,7 @@ SLOT="0/5.0.0"
 LICENSE="GPL-2"
 KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE="doc openmp test wxwidgets"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-cpp/eigen:3
diff --git a/sci-chemistry/p3d/Manifest b/sci-chemistry/p3d/Manifest
index a9db6f559b15..8edb957e6d33 100644
--- a/sci-chemistry/p3d/Manifest
+++ b/sci-chemistry/p3d/Manifest
@@ -1,4 +1,4 @@
 DIST p3d-0.4.3.tar.gz 7213577 BLAKE2B b614957be16ede7567bd6412d183b3cb79638a5033672afd725cafaf393e306d5d227e1bca444ea17d60a3cd3bb5d3b2c910f2bfc68a118d3bffcd29944b4c29 SHA512 b4cf472b849ece96fe0b2b7f633c496fe3d12bf8cb82a2af10180ce5c27c5465dd0c16cb912d22c56c933b68c06e7de28c0c640da29eaa6bc6f95009bf10277f
 EBUILD p3d-0.4.3-r1.ebuild 649 BLAKE2B 9d2730c029ad4a75ed58af5cec21bc050e482064e915c2da565cc5c0035d562ba38b121f43731a28a42d49dfc81fd43b0996698d2e457d16da2872d9cd01b6cd SHA512 e979d59ce970454ef0f8de72bb616b658b489c657bcc3077c2002b6389d00ff4515128da8f549eee5c2ed345d3e229f36de8ff5002e3a21ee5c744d63042295a
-EBUILD p3d-9999.ebuild 528 BLAKE2B 529e0bd09acbb397f643eb1a9b091ebabf8121d5404f530a93c001dc5ea233727780fa626867fc857c3524802ce403e469ed3a9e8ec4bb9f862672c5dc140e43 SHA512 e8cdafe07f73c5b2b1f5573270214abf574d349f922f4514b3f00e00e09ecca731d35d1fe10ec7ee05ea95cc8154e26b876b031b68dcff2470acb810ae46ce07
+EBUILD p3d-9999.ebuild 521 BLAKE2B 4d493463768caa477059286c3d14584d5ba779e7b88dd98125db6e96c0ef658cc3ca4aeae67103f9366a80e055dcfdfed1764d1281777b3e2922916c30a21002 SHA512 0484f573edd3b3df049d884f387e9d062bc6590a228ec70c88c99c70e72f24d94d29d53c5f5cfd0a71e1669590c3c1810eda4a5e9a62c218e1df808c863d2d9a
 MISC metadata.xml 1151 BLAKE2B db264a2a0e24aedec15301bb5a6bfe6b83d815e5dc146ccdbcc427d97c0b78ba98050bbc06d230988e1643be858a56469271b92b118bea373a7e284a54f18fb0 SHA512 322b35766a1e71129165a8559fe3caac109dfa85be2b0fa630fa249b28cf603e86f152c47835020ff1f5f0d12b7cbbff8758c08248522a7d2b1188812ec99722
diff --git a/sci-chemistry/p3d/p3d-9999.ebuild b/sci-chemistry/p3d/p3d-9999.ebuild
index f5eb1e8c1b42..5dd3fdc9a942 100644
--- a/sci-chemistry/p3d/p3d-9999.ebuild
+++ b/sci-chemistry/p3d/p3d-9999.ebuild
@@ -22,6 +22,6 @@ src_install() {
 
 	if use examples; then
 		insinto /usr/share/${PN}
-		doins -r pdbs exampleScripts || die
+		doins -r pdbs exampleScripts
 	fi
 }
diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest
deleted file mode 100644
index 7f53bcc9a2a9..000000000000
--- a/sci-chemistry/parassign/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST PARAssign_Linux_x64_86.tgz 76693208 BLAKE2B 9141b7f3e6b50efd84cfc2af13c170946220b3f02f90422c4759a6aab8073a0d28cf44e045f305f392055816e50052826dd403f1d71ff7edb04950bf5dfc5f2b SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79
-EBUILD parassign-20130522.ebuild 1375 BLAKE2B cc8f36979dab81d6f1d19112631e37365ed4408943fc5173aabd3c9e4db53e5c155123d1874438d5caabbd9dae6328b6f2e494ed6285d6b66b516cb6f95d93cb SHA512 7634d41463024be7606e63cd6fda1a9645c5fea48922232e1b404fe486416e89a454ea63220772ba75a327cf4c03140beef332f857c3a283063cd4687abadd46
-MISC metadata.xml 1646 BLAKE2B 91f42dd65912632e8f19f6a2dfd6a5e4ea7e2be8c270516db4c5477841a78263352ec9f52c971e6a70e3ee32e86d952505068167cce62ec80e40b3b5d6566173 SHA512 73b07789bffc4fb45c5c3ca5c6b3e7fc75e358fc8a73b2cc2d76e8faf5bc1f2765fb1dcbdb2dcc34a21123d3f99bd8fc61ec3ca4a10e6887f26863b93fc1db1f
diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml
deleted file mode 100644
index f230593f73e9..000000000000
--- a/sci-chemistry/parassign/metadata.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-The use of paramagnetic NMR data for the refinement of structures of proteins 
-and protein complexes is widespread. However, the power of paramagnetism for 
-protein assignment has not yet been fully exploited. PARAssign is software that 
-uses pseudocontact shift data derived from several paramagnetic centers attached
-to the protein to obtain amide and methyl assignments. The ability of PARAssign 
-to perform assignment when the positions of the paramagnetic centers are known 
-and unknown is demonstrated. PARAssign has been tested using synthetic data for 
-methyl assignment of a 47 kDa protein, and using both synthetic and experimental
-data for amide assignment of a 14 kDa protein. The complex fitting space 
-involved in such an assignment procedure necessitates that good starting 
-conditions are found, both regarding placement and strength of paramagnetic 
-centers. These starting conditions are obtained through automated tensor 
-placement and user-defined tensor parameters. The results presented herein 
-demonstrate that PARAssign is able to successfully perform resonance assignment
-in large systems with a high degree of reliability. This software provides a 
-method for obtaining the assignments of large systems, which may previously have
-been unassignable, by using 2D NMR spectral data and a known protein structure.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/parassign/parassign-20130522.ebuild b/sci-chemistry/parassign/parassign-20130522.ebuild
deleted file mode 100644
index c49d09b2ab0a..000000000000
--- a/sci-chemistry/parassign/parassign-20130522.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 python-r1
-
-DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)"
-HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration"
-SRC_URI="PARAssign_Linux_x64_86.tgz"
-RESTRICT="fetch"
-
-SLOT="0"
-LICENSE="Apache-2.0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/scientificpython[${PYTHON_USEDEP}]
-	sci-biology/biopython[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}"/PARAssign_Linux_x64_86/
-
-src_prepare() {
-	sed \
-		-e '1i#!/usr/bin/python2' \
-		-i code/*py || die
-
-	if use x86; then
-		sed \
-			-e "s:munkres64:munkres:g" \
-			-i modules/setup.py || die
-	elif use amd64; then
-		sed \
-			-e "s:munkres:munkres64:g" \
-			-i code/*py || die
-	fi
-	cd modules || die
-	rm *o *c || die
-	distutils-r1_src_prepare
-}
-
-src_compile() {
-	cd modules || die
-	distutils-r1_src_compile
-}
-
-src_install() {
-	python_foreach_impl python_doscript code/* || die
-
-	dodoc PARAssign_Tutorial.pdf README
-
-	cd modules || die
-	distutils-r1_src_install
-}
diff --git a/sci-chemistry/povscript+/Manifest b/sci-chemistry/povscript+/Manifest
index 17c8df756f7c..02b58a98d2f0 100644
--- a/sci-chemistry/povscript+/Manifest
+++ b/sci-chemistry/povscript+/Manifest
@@ -1,6 +1,4 @@
 AUX povscript+-2.1.2.2.19-libpng15.patch 542 BLAKE2B 1fcc229fd3e90a1c567ea42bd87b4b9de281b4976016a0c990f3a66ba2d9d3d8b7eacb80c1caf31326a4c35ff33863d9495b857163ee86bf7060e44debbe19f6 SHA512 5f795238f95adfa0712c92afda669d461cc292b358aa51907ceea1c2d5e5e470d1817d75f461a46efb962ffefafa2606400d32c1f681192f8e161d6e23ee5224
-DIST molscript-2.1.2pov2.19.tar.gz 845101 BLAKE2B c6b6219ad88df0a481fc4cfb96fe6340fe068cb16b2602a9328672bffccb6534d0dde56553f0d3cca42279ac1f2e02190adbea39d83af30667a74c4c6073d0eb SHA512 11796552a889ae309ebac31047440732921cd300d89ad284beb3655e2797fe1a68adf9a5a7e54e6668ea240c5b0897c22f65d839870ee43591854976000ab05f
 DIST molscript-2.1.2pov2.20.tar.gz 822930 BLAKE2B da050db5124d04e7c0e2c06b0e666d631f214b4519b41ac4b4775dbdbf5be2608f5417f13fad45c36f796d486a8d9211d2fd3d9403afa1b6d27e52b4f0a7f248 SHA512 f7cae4d9b583a05962742ee36ec717f0ecac6bb88086bcfa484b51b0d2e16a15920bc7c09d9d777453d7ef7b81be444924d15a889e4725bfca7bf517d4e52db2
-EBUILD povscript+-2.1.2.2.19.ebuild 1244 BLAKE2B d5881ff5b01720fc963724313dadb41c12b3d3a5f15a66792edf92abc2cdef31c6f402456faad65270e74bcbfa0aecc00602ab4d883585dd55f53e99d4d82329 SHA512 b3e58b153ee8a5e1145f87c24742de76518a6e0792185256b2d8463782a93e37357801bda4a586054576cde9040d39ac140a68af796c1661cbe1f06e4d448694
 EBUILD povscript+-2.1.2.2.20.ebuild 1263 BLAKE2B 11784b37663618506624aa8f3f9b034ee01c387dbb286c226b01c35fcbf6075bb355ed96d7663f8c46feb9da08d2c92ef06521f1b64d0e9a50ffb3453957d2bb SHA512 54cebb95ef03430d1071a894b2a47f118ae0e952bcacc0f80f3d727aa18912d4701a116c97469bf2a37b28e01fa5fe51cf7aa02fe2fb69134bf98465210d4770
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild
deleted file mode 100644
index ed9dc48f4d5c..000000000000
--- a/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils versionator
-
-V1=$(get_version_component_range 1 ${PV})
-V2=$(get_version_component_range 2 ${PV})
-V3=$(get_version_component_range 3 ${PV})
-V4=$(get_version_component_range 4 ${PV})
-V5=$(get_version_component_range 5 ${PV})
-
-MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5}
-
-DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more"
-HOMEPAGE="https://sites.google.com/site/timfenn/povscript"
-SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz"
-
-LICENSE="glut molscript"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-libs/glib:2
-	media-libs/freeglut
-	media-libs/giflib
-	>=media-libs/libpng-1.4
-	sci-libs/gts
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg
-	virtual/opengl
-	x11-libs/libX11"
-DEPEND="${RDEPEND}"
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-libpng15.patch
-}
-
-src_install() {
-	emake DESTDIR="${D}" install
-	cd "${D}"/usr/bin
-	mv molscript povscript+
-	mv molauto povauto+
-}
-
-pkg_postinst() {
-	elog "You must install media-gfx/povray to use the POV backend,"
-	elog "which is one of the main features of this over molscript."
-}
diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest
index 2ec37e80f5d1..316132cafba5 100644
--- a/sci-chemistry/psi/Manifest
+++ b/sci-chemistry/psi/Manifest
@@ -9,5 +9,5 @@ AUX psi-3.4.0-format-security.patch 1021 BLAKE2B 58aebbd7d8d8fd8c78c8cce7ad28574
 AUX psi-3.4.0-parallel-make.patch 445 BLAKE2B e98ee4f5d0feb639058c3b589c6eb6747b35386276f48a6775ab40833364d0feadc55fb4f91abb58009b83f8122fbb119f0588acc13eabb5fb9857af202ac3d5 SHA512 bf574c6c9c1e1ffc8747fb51896b8f9d8b29c4796b0a06529a58a2ab1ed5ee0a4270fe071eb86ca745bad2c760701c4d9eb7f269cd390f6d9cadf4065962e52e
 AUX use-external-libint.patch 1359 BLAKE2B 24fe9d7eb369f6c6846915cd87471d4f2bcf66da09105d73c4b75cebfa7138d318d5dfca653368d80eb5b39a31eabde60da5b439786ed00d95b31b90e56a44ed SHA512 8b4749b0c449dbc89067eec466d3d557da86e7f2d950cc0a94409e158a31a3fb8ceafefd090168acd97975ff3ccc7859e6f2df3c2cd57a3571b79f71aca6fff7
 DIST psi-3.4.0.tar.gz 7413072 BLAKE2B de8b5e0fb1692780446385bf13f6b9984f5be8d441730babacf6f59dd18be6e13b1cff17170cec87def1f743d7e634354b57afbc046e6f34c79c9fc52c31b146 SHA512 b13d2464502545cceec3a3b6048b505b918da26730c1614617b04ee6c1d637c9f799ef7fd92ad9554fa2db87617004aa810a6a81400a04df3c06787d51654ca6
-EBUILD psi-3.4.0-r2.ebuild 1935 BLAKE2B 419b171d833160c8abcc7920f9f2d594eaa885e564a5ed9bfaedeeb17719ad94c55e1946e507020c8af578428b49b34d0f4458628f04b1675141bfad0aab5771 SHA512 75c1615bb6510bfa0ef2a771a78a4d262dfac80ce5c597d69cba1c030e0a3db90902d3a9330ce9d2440918e2ee649fc44bca9c7453ff5099d592188d8142bfda
+EBUILD psi-3.4.0-r2.ebuild 1959 BLAKE2B b40aa3f7ea09f433373dafca0b535e4de2b302af81864212f8b989989ef7970657531e62f4c35e7501728da011a3266738a9af8fc0e145329e6994566513d3ca SHA512 414ba2b293b6b1edd8d82096706db88cc105602688c6b85a119c3b1ecd0ef2209f83d19efc1b982a85fb04533406d9faf9483f83b90b568f49304a732755e552
 MISC metadata.xml 352 BLAKE2B a7c80467e6e67207a2a03e98071d1bbcec5024a528848f615ab38233c888a78032a9fe7a04dbf278964f9f9cb52d010ad592b1fe40436cb7839a1f2bfd4a375a SHA512 0ef2b193bcadef21bcad1e3fd3745b37f75bd65fe44645c667c99634d9047b28c82504002ed6967cf1cc2d5c8c43f5757ad08264613088ca36c7e94ac683b7e2
diff --git a/sci-chemistry/psi/psi-3.4.0-r2.ebuild b/sci-chemistry/psi/psi-3.4.0-r2.ebuild
index 34dd75b6c1df..f40a13060173 100644
--- a/sci-chemistry/psi/psi-3.4.0-r2.ebuild
+++ b/sci-chemistry/psi/psi-3.4.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=4
@@ -13,6 +13,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="amd64 x86"
 IUSE="static-libs test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	!sci-visualization/extrema
diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest
deleted file mode 100644
index 80c9aafbaa8f..000000000000
--- a/sci-chemistry/pymol-plugins-psico/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST pymol-plugins-psico-3.1.tar.gz 76136 BLAKE2B d1218b0d9da9326a47fb5e0d6268c43ee2d6266066260b83686aa664c500609fb87d61886a83d46a59a2270c3671cfdb7e2f3f761f7898b52932d5f92b2b4b31 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e
-EBUILD pymol-plugins-psico-3.1-r1.ebuild 982 BLAKE2B 9a95ce4fc98f64a72f8ada9630597aa37931dbcbd33b163bd1e2a40964e2c8de753378a5650d5a2e04f54ddafbc808709269608d924a923cd2185ad30c4ba529 SHA512 33c405c0e95a1f040c58c8ed68d314dd6fee488fd92a5acf45014c692a0fe5d2168f46799a918683543e2e285e6c0decd9b94daf26aee1d98bc3f15a6841bb5a
-MISC metadata.xml 359 BLAKE2B 209861a26fe54237d677fedc834fa833880ec97916f743df270b4e3a9e851f1233dd51756133a083cbd455bb4f682c63fb3c245ee5e934ef9f6278e74cb9de46 SHA512 1c94755813187e50e66f575868d2deabf6448e39bc6829ecdb60a29a4de5a37c58d28bdc7b21551f906101469614b2672949658220e5edea0fc4f10bad8d4116
diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml
deleted file mode 100644
index 29f0c024a2f1..000000000000
--- a/sci-chemistry/pymol-plugins-psico/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">speleo3/pymol-psico</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild
deleted file mode 100644
index 0fca945ebee8..000000000000
--- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 vcs-snapshot
-
-DESCRIPTION="Pymol ScrIpt COllection"
-HOMEPAGE="https://github.com/speleo3/pymol-psico/"
-SRC_URI="https://github.com/speleo3/pymol-psico/tarball/${PV} -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD-2"
-IUSE="minimal"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-biology/biopython[${PYTHON_USEDEP}]
-	sci-libs/mmtk[${PYTHON_USEDEP}]
-	sci-chemistry/pymol[${PYTHON_USEDEP}]
-	!minimal? (
-		media-libs/qhull
-		media-video/mplayer
-		sci-biology/stride
-		sci-chemistry/dssp
-		sci-chemistry/mm-align
-		sci-chemistry/pdbmat
-		sci-chemistry/theseus
-		sci-chemistry/tm-align
-		sci-mathematics/diagrtb
-	)"
-
-pkg_postinst() {
-	if ! use minimal; then
-		elog "For full functionality you need to get DynDom from"
-		elog "http://fizz.cmp.uea.ac.uk/dyndom/dyndomMain.do"
-	fi
-}
diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest
index 1c2c7b89f8cb..7d477d91d72f 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-r1.ebuild 1567 BLAKE2B 09376d6d533a61e61fc3e118e2a6f52d18e72cf1efc79d0fa06515aa2e62b36a6be73d5b7c986c4b4431ba97518b0ebced17931aabe55fc4c7265bfba0022213 SHA512 4b334b6c1c64a8495d716e4d9032f79c24201e07b87a8a555412677c70e5794456c662364c9b3d839b65248cf8f31f091540575f6ba5a72518964e9078a3ab32
+EBUILD relax-4.0.0-r1.ebuild 1591 BLAKE2B 58569336b45732cafd601b30e8ef2db0666eceb49c4d5ee5b45aeec1cfec7cf4505f1b77c532bbfc550c2111e439bc8cf5b3fc686bd6216c0627cbad6dd5c0ba SHA512 fbb5be5c93e7dafe75f9c3a13a0d849fbf494a7018a35389b9284251f8231c1174c3cf1469ba24781ca030bc729ecb225edffed9db6305c83b37299fe373bc4c
 MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e
diff --git a/sci-chemistry/relax/relax-4.0.0-r1.ebuild b/sci-chemistry/relax/relax-4.0.0-r1.ebuild
index c08c298b59f4..5a99d4554ba7 100644
--- a/sci-chemistry/relax/relax-4.0.0-r1.ebuild
+++ b/sci-chemistry/relax/relax-4.0.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -17,6 +17,7 @@ SLOT="0"
 LICENSE="GPL-2"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
diff --git a/sci-chemistry/surf/Manifest b/sci-chemistry/surf/Manifest
index 4eb052684bb0..5a66f3575403 100644
--- a/sci-chemistry/surf/Manifest
+++ b/sci-chemistry/surf/Manifest
@@ -1,3 +1,3 @@
 DIST surf-1.0.tar.Z 74347 BLAKE2B 543696838470f8b263d3841e177bb9054eb24a1ff0978fa09d9617e32a3a3e6b0662b37c1faa83fa449321276c8b3dd4aed80e978ea3c8315ed5b11f37196a73 SHA512 55b0e771f880931e43d677498ef4cdd92e5f57980d90b686b13c7ae612c8d695353a6f3b5ad0dab184d44e67d8cc5244e7b3f45b4f067c4174ed4399c184d435
-EBUILD surf-1.0.ebuild 822 BLAKE2B 36d7470b934c3be20aa12016336f04e96a1a2a9bbb8917dc546ca2e60b57e50d9daf1936082fd7df38f6fd702c1a108d9f53240f2885d88705cafd4fd22f086b SHA512 94b7de7a59085f10b60c3aa8ab5280a441239cb63ea3723d15dac949295a07d401c820c5b24e7ff1d03571086c6a1ead3a43d2688a17d6ab4928c9728270f706
+EBUILD surf-1.0.ebuild 796 BLAKE2B 3e66904e8e7fd63a6577a64c011ced32e73031807a7470c9895c172743759133e7423404a4107c5f99d127124d2bb14457ff882627ace6e524257200b67bcef2 SHA512 774ac12030accc1959b6eb22bd52ddd32b3a4b53ade020a5e36d58d160c0b5c3beed3c49eb8ae13b02d68dc95a21675063eb4b9c4262f804bf60a700c0d0b31b
 MISC metadata.xml 261 BLAKE2B 509ce9958149f9cd522a2c68dd0d23ed851d19d02494611456592897093378d180a6006cddf1575fd60106119e72726255c49db2e10fde1b370bdf2f3cf8c94a SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7
diff --git a/sci-chemistry/surf/surf-1.0.ebuild b/sci-chemistry/surf/surf-1.0.ebuild
index 138830fe777c..5b6ff83975fd 100644
--- a/sci-chemistry/surf/surf-1.0.ebuild
+++ b/sci-chemistry/surf/surf-1.0.ebuild
@@ -33,11 +33,10 @@ src_compile() {
 		&& emake \
 			CC="$(tc-getCC)" \
 			OPT_CFLAGS="${CFLAGS} \$(INCLUDE)" \
-			CFLAGS="${CFLAGS} \$(INCLUDE)" \
-			|| die
+			CFLAGS="${CFLAGS} \$(INCLUDE)"
 }
 
 src_install() {
-	dobin ${PN} || die
-	dodoc README || die
+	dobin ${PN}
+	dodoc README
 }
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index e170171ba4f4..582201b861ab 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,11 +1,13 @@
 AUX vmd-1.9.1-cuda-device_ptr.patch 894 BLAKE2B 96aeab7c2b9d29e5cd3558e69d1365d6b7dc2d78284bb1185d63a57300a83a4c7c0b8f1c1718027ff33333d34bba116d6898fbee74ab23dfd1a77c560160d659 SHA512 9a561773562873dad077f0f2903299952cb935c69ae4bd1463a5f79d6f27ae3845ac5a24ee295ff3569d9c65ae00a9fe3974f4ead003109246f97d130c2c48bf
 AUX vmd-1.9.2-format-security.patch 550 BLAKE2B d50d05d8697c345f5888b1344c827be1282c5b2e06cfddac022d562688550a728a91a943f9b31c4247f683dcd062ab8fe8ed360aa97a202f20af0467a3148cd3 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d
 AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00
+AUX vmd-1.9.3-tmpdir.patch 673 BLAKE2B 074456a8a68a36f16a804aeb8caee9abf14505cb76a2661b03ad97119bf4afb13a994c9cf22eeb952a79a980fcf03bd3dee5c93cf63bf82a19831f71bcbd83c2 SHA512 f7f570c729259f9133fb6411047266312c3d5f802d4cffe316cfdc4094f0fd0830c3eaae6408f56ea17dadba283e1a1fdf86fec858a5211b1c00ed927f160ea4
 DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51
 DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba
 EBUILD vmd-1.9.2.ebuild 7155 BLAKE2B 734137c1a02d76da109d35faf11f29138a8e48dda6d84b7151f93f2095481127f136a5f8954a80912c85ae7031a01c3374783a042bf5461fd9d1049b577a082b SHA512 3f9fc1f4cc8f6f5031de74a8211db2a9e11d07de110689832d408c343a307ba25efa354f5862d4e6d8d06d3d18b567820401fc9fcdc8818f65a33ea24a3c657b
 EBUILD vmd-1.9.3-r1.ebuild 7512 BLAKE2B cfd3259efcf3457e520f8f9ebf809373a99b6d6d5d3ab36192bf7ddd694835d7dd5c113957591d9041b583e58ac419f6cb8649f24ded0e62c89cabf056d45020 SHA512 cb0fc6cbc37c39351d51a3535569adaa69f4aee81942c0eeb83fbd7f1ca5aa3005bc8c87a74002869cc4fd81fb917601ae1bfd0a3dfd474fcf345f696cfd7d21
+EBUILD vmd-1.9.3-r2.ebuild 7693 BLAKE2B e6a96e06546f562448d4c77ca4f5626c878b69a1385edf1ed5f1b01d388aae2f19a710cadd3c3da66974bbc6d3c5c075e220b83faee8b5d626d15c73d372737a SHA512 8ab709222532622b87720fefc80e0c057c23bad5a26bb812cf7539705493c04202980545639bd8e62ef855fca9c850c0e7d825b3ec323aca6fc9a5cdf837d84d
 EBUILD vmd-1.9.3.ebuild 7110 BLAKE2B d8ad6f495aaacdc4727e2c0e5d950a9670478aba7b55e62ed7074f06ad26151468f0f55a0786ce9dba80a181e7c36e912eaeaaa9ad7ae660739c65f482337c97 SHA512 c0eba398b6a815a59c9d8708dc796273ad3211ddc8e02aee8333f00f42f095c4d8999aaa246665ceb9282d2053c0631dc3c8ed7b60981d88ff9f8a2badf6b89a
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch
new file mode 100644
index 000000000000..22712abf30b8
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch
@@ -0,0 +1,22 @@
+--- a/scripts/vmd/vmdinit.tcl~	2016-10-27 05:46:34.000000000 +0200
++++ b/scripts/vmd/vmdinit.tcl	2019-12-03 16:29:01.894002827 +0100
+@@ -197,7 +197,7 @@
+       set env(TMPDIR) /tmp
+     }
+     default {
+-      set env(TMPDIR) /usr/tmp
++      set env(TMPDIR) /tmp
+     }
+   }
+ }
+--- a/scripts/vmd/chemical2vmd~	2000-07-03 19:30:23.000000000 +0200
++++ b/scripts/vmd/chemical2vmd	2019-12-03 16:28:49.316861178 +0100
+@@ -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 ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
new file mode 100644
index 000000000000..02ad806afbeb
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
@@ -0,0 +1,266 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python2_7 )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
+	${P}.src.tar
+"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	>=dev-lang/tk-8.6.1:0=
+	dev-lang/perl
+	dev-libs/expat
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/netcdf:0=
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	${PYTHON_DEPS}
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
+	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
+	sqlite? ( dev-db/sqlite:3= )
+	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
+	xinerama? ( x11-libs/libXinerama )
+"
+DEPEND="${CDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	dev-lang/swig
+"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/chemical-mime-data
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
+	elog "Place both into your DISTDIR directory"
+	elog
+	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
+	elog "file may get downloaded as a compressed tarball or not. In that case"
+	elog "you will need to ensure you uncompress the file and rename it"
+	elog "as ${P}.src.tar"
+}
+
+src_prepare() {
+	xdg_src_prepare
+
+	use cuda && cuda_sanitize
+
+	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
+
+	cd "${WORKDIR}"/plugins || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${S}" || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
+	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
+	eapply "${FILESDIR}"/${P}-tmpdir.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags::g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
+		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+	if use cuda; then
+		sed \
+			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+		sed \
+			-e '/compute_/d' \
+			-i configure || die
+		sed \
+			-e 's:-gencode .*code=sm_..::' \
+			-i src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
+		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
+		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+
+	EMAKEOPTS=(
+		TCLINC="-I${EPREFIX}/usr/include"
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
+		TCLLDFLAGS="-shared"
+		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
+		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
+		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
+		NETCDFDYNAMIC=1
+		EXPATINC="-I${EPREFIX}/usr/include"
+		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
+		EXPATLDFLAGS="-shared"
+		EXPATDYNAMIC=1
+	)
+	if use gromacs; then
+		EMAKEOPTS+=(
+			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+			TNGINC="-I${EPREFIX}/usr/include"
+			TNGLDFLAGS="-shared"
+			TNGDYNAMIC=1
+		)
+	fi
+	if use sqlite; then
+		EMAKEOPTS+=(
+			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+			SQLITEINC="-I${EPREFIX}/usr/include"
+			SQLITELDFLAGS="-shared"
+			SQLITEDYNAMIC=1
+		)
+	fi
+}
+
+src_configure() {
+	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+	use tachyon && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
+		PYTHON_LIBRARY="$(python_get_LIBS)" \
+		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
+
+	perl ./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins || die
+
+	emake \
+		${EMAKEOPTS[@]} \
+		LINUX
+
+	# build vmd
+	cd "${S}"/src || die
+	emake
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins || die
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib
+
+	# install vmd
+	cd "${S}"/src || die
+	emake install
+
+	# install docs
+	cd "${S}" || die
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd || die
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}"/vmd.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	# Open PDB files with VMD
+	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}
diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest
index 0858402306b0..53ff74f8d77e 100644
--- a/sci-chemistry/votca-csg/Manifest
+++ b/sci-chemistry/votca-csg/Manifest
@@ -1,14 +1,18 @@
 DIST votca-csg-1.4.1.tar.gz 347702 BLAKE2B 8c98804bafd75148fa72a9e119d4448ab9b04fb6f305e1e162a18013871d03778873a50670ce06bb218fc063f51ad67efc4a182c2d7bb46f91b59e30181b71d6 SHA512 87f2798c9b5f2d82ae1c158238f7a3b7007c7ceb7ce82503f0b002f605f2cc0b5ca4c8ef24fab571efae63a81e7a60bc476b5433962c239de4f5d42bae3c10ea
 DIST votca-csg-1.4.tar.gz 346527 BLAKE2B 8f0a41f9aa9fd865e2e544d5fd587d93d631edc2dabab8edfc3461582da2e0401a266a42be1c0f1e6647502cdcccee55b5bba891aa156394012b8b5e1b06f7e8 SHA512 26318644c7af2dfa1b81242b27ffac98f2180c3a1f05581bc50a00f644cec4b19ffbaf41c9d941a4714171b56ae93fe41f1a663cd0593ae2b0be2da379119d9b
+DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 3559452182c325d5df72918ec6e12122c8214df9733d779c123ff199597fe47fc493fd75adf1f5dbc6b55016373863378ba3cc69fb6b61bc1531c6e591d8131c
 DIST votca-csg-1.5.tar.gz 429164 BLAKE2B da04bd9ce8e879e9a961006256e03d160fa49fe77aa2f1eff0986b338296b04137bb087ecfabb7f2fc855b0ccd83dc4ddddfd65c43303bf5f2eef0519d27b0ec SHA512 c5a77ded3c9b2582494bea55b464689d566d4155713af823dccc6999f98438444d51fae3948144f82c2aaf3914eee740fe21e8828af689d37ab0b5ffea0605fa
 DIST votca-csg-manual-1.4.1.pdf 1282641 BLAKE2B 370b7c8997649555fd2360b999cf381c340a74c3747afda23d0e9d346367cc6d14d4e9a0e9ac82184945427d30050dd623dd1b6d8218c6ff3d2f17331987aaae SHA512 e89f41af05eaeb9ea499e8625cc98e2632ec647ec2d8c9c9052dcd4d2935d082b29b51495514e3e06e73ce42b8cda7017fc523a013569378e2bc86bf88ad32d4
 DIST votca-csg-manual-1.4.pdf 1281983 BLAKE2B 5659c2e327ba7bb00fac15adfb578288d546b509366863f593776a62dd3064662535d4fd525f1063f5ccaf47446822f13fefd7f66aa9d68cd1a4a7c99d66a790 SHA512 2e1f4a4375d83df9bd357d4d17e79d26a3a31c9177f008de86721427ffc6f43a5000ec840691108b52a8aecf962321ba6363cd975c7445d7230ee5b0b151b3fa
+DIST votca-csg-manual-1.5.1.pdf 1263719 BLAKE2B 29e2ce27215787a1121e45ec1e88ce7c61ba81709a2519aa0959eede505498b9aaf4f38666bb1a4f97837c98b862e7ed02405da07294a7ec76cc80390fe72e0d SHA512 7d9fb4c635383e1b9c9547691f8729e19f273fcafc4dab2a6b438b3ce98ea05bd31887d09bc4edc86ceb0b04d71a4371aed7aadc3ba6864f7be2ef3328ede642
 DIST votca-csg-manual-1.5.pdf 1273566 BLAKE2B edfa2adb942d968cf79499e89342b7aaab64edfbfb6e02f76a66201df0920a58acc17bf4e2e4846d104519df163223c27f283cc5798ec7b64d9317a7728ff8c4 SHA512 da298ab0c27000ccf7fb5793c4252c4e17a969709db2649a5acb56af6208b954312c46a2ea8399cdb879b699e72a0ded0b2fe1bcd26431c6625f36b09c0267a5
 DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 BLAKE2B e9acf8e421f6fce4d97be2d51fb559979c6fd3e6b042525cedf32cadeab1dddc5b1aaf80bbbfd387da3bce71672759c2e84d317c789f616dc71834c72a581fff SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90
 DIST votca-csg-tutorials-1.4.tar.gz 6348417 BLAKE2B 612fcbc4457a57be74e5306bf86d6e031ea8cd55ebe3f4d246c0876e272e6e6dd535c8dd2f24f7593cb1ef31fbc18111269d29cb69120368ddef7b1b7d25825c SHA512 f3eb28a133ebc04eed07f84d5962943cb9c547c1099638127f15e0015dfdf3f0b25aab4c97d009d6040bf1d69d408cc178edd6e803d33bf1d831e12dca0671c7
+DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c
 DIST votca-csg-tutorials-1.5.tar.gz 5947774 BLAKE2B d497f1e9282c4cacc070d09d901ad8f5d3042ab3a279aa4d1c3bcd3184dc22231d1f2a75ba0ffe245e6f6300fb740e562b24c8039594ec01307491a6068b55f6 SHA512 00447380fa887178ad02cc4e1425a04fc2fd2babdd4790d387fcd4aa2734dc14dacf4b4444d420937aa0a5b53e90741b44f9a4bca31bdcdae10fbfb8323e9848
 EBUILD votca-csg-1.4.1.ebuild 3204 BLAKE2B e447a6859d7ee4d722701f96634667529bd183f10dd4affeb2713023edfe52ab73988df7ef912963bd154b893bd2d401d2fd110a729040a2a2c52ec5fd44985c SHA512 df94c127269df2a2eaa9643005eeeae6925b458fbb0cb4d1661757a49e5ab4926a613c532e4df4475b34768e904d2388270c868c9ad675cd110e2b1737153e3d
 EBUILD votca-csg-1.4.ebuild 3200 BLAKE2B 041deefd8fc208525c636d00665f7ea70d0efafb78fa98a3437823fb550e6c39a29d33e94860c3d8f01dbbdb050dd568c63dc1099d4da620f9044545850f40d1 SHA512 939608311d071b6abf8cc26dd73c9713c41476772bb37b41fc77fb3a02672989664b8a06e5465b2825285c3365ad3d70879e5c24a1c698cbb3c8ab6d2341fe31
+EBUILD votca-csg-1.5.1.ebuild 2546 BLAKE2B ef9552a84560fa785dab1752939be518dd310967077263f45334dfa942b5d2e8c0ad6d184e8721ba7e9ea1bf4465dbf6fe4a5745e4c90475dc71926a5ea960aa SHA512 be9245c6359e241944619366574bafe5216ee2ca096ee69fcf190caff4b8ff9ff7433f2961b166a25bc1c05ef7c76c59ebe32447ab10d75a10398498c507d964
 EBUILD votca-csg-1.5.ebuild 2544 BLAKE2B e76bd6372f66745230d307d6214e031367f83ddf673e3f3a3e8e5263053de49e102c415baed7c6e709f164d6b994363540d4152f5202660c4b87894b8837cf37 SHA512 66a240156d31a389a91cd8a8e9f5e65236005683fef5d01657386297fb812706bcd43933cbf0d7d6fa9fa8456fe216e45ae651ebb52309ed845cd9dde076f02c
 EBUILD votca-csg-9999.ebuild 2540 BLAKE2B 7391ae1af857c92b688fab507417c875189725d8f121296aaefccecc903501cc6c50561b0a7a4f834d5713f2bdd75b2325594fbbc32e6d0a0d814cf5c7ca7b14 SHA512 fc36ac2de479e2766722b3eb64d8f4eb43233c9625c67124d2ec583e21e22f1c77d6bee2a71d9c3b35451eeb0c6ddc729f4726e8b56f7e45b2c64a9f45fd94ae
 MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1
diff --git a/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild
new file mode 100644
index 000000000000..8ae77aec9f51
--- /dev/null
+++ b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils multilib
+
+IUSE="doc examples extras +gromacs hdf5"
+PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )"
+if [ "${PV}" != "9999" ]; then
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+		doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf )
+		examples? (	https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
+else
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
+	KEYWORDS="~amd64"
+	PDEPEND="${PDEPEND} doc? ( ~app-doc/${PN}-manual-${PV} )"
+fi
+
+DESCRIPTION="Votca coarse-graining engine"
+HOMEPAGE="http://www.votca.org"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+
+RDEPEND="
+	~sci-libs/votca-tools-${PV}
+	>=dev-cpp/eigen-3.3
+	gromacs? ( sci-chemistry/gromacs:= )
+	hdf5? ( sci-libs/hdf5 )
+	dev-lang/perl
+	app-shells/bash:*"
+
+DEPEND="${RDEPEND}
+	doc? (
+		app-doc/doxygen[dot]
+		dev-texlive/texlive-latexextra
+		virtual/latex-base
+		dev-tex/pgf
+	)
+	>=app-text/txt2tags-2.5
+	virtual/pkgconfig"
+
+DOCS=( README.md NOTICE CHANGELOG.md )
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use examples; then
+			EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git"
+			EGIT_BRANCH="master"
+			EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_configure() {
+	mycmakeargs=(
+		-DWITH_GMX=$(usex gromacs)
+		-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5')
+		-DWITH_RC_FILES=OFF
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	newbashcomp scripts/csg-completion.bash csg_call
+	for i in "${ED}"/usr/bin/csg_*; do
+		[[ ${i} = *csg_call ]] && continue
+		bashcomp_alias csg_call "${i##*/}"
+	done
+	if use doc; then
+		[[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf"
+		cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html
+		dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html
+	fi
+	if use examples; then
+		insinto "/usr/share/doc/${PF}/tutorials"
+		docompress -x "/usr/share/doc/${PF}/tutorials"
+		rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake*
+		doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/*
+	fi
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Please read and cite:"
+	einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). "
+	einfo "https://dx.doi.org/10.1021/ct900369w"
+	einfo
+}
diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest
index aa724622e435..13065a99df56 100644
--- a/sci-chemistry/votca-csgapps/Manifest
+++ b/sci-chemistry/votca-csgapps/Manifest
@@ -1,8 +1,10 @@
 DIST votca-csgapps-1.4.1.tar.gz 21066 BLAKE2B 8e1d25957b7c62d2182872de4d0c50c90fefdf699ec5e9e785916791e9cc06db2dbcbbdbaf7afe6921e34179e12dfa2326eb9464261801e48177ec69126ae2bb SHA512 80881ac173b56b07825c484f98c598de8d74bb8a54b888f06cc3a20d15670b49059e50adc210308e21ee4ea9038cf564c08d7ab33c4a43864acb1de97bc3fcef
 DIST votca-csgapps-1.4.tar.gz 21072 BLAKE2B 30c2f6692544741bfbec09efea2f68ae48cd4716e61e40d3da12a17ad941f2947cc6a8477229b80e420e217a95adff4152a07215e2e913e71736b61ba1ac226a SHA512 325c99606f17d7bb00e2cc3b1545f31dd4cf1fbc0d216f2da2c48e06b2011c9f99096643a6c6efd794a169de056f803f791c156afec4a73e41c58bc4ca1055f9
+DIST votca-csgapps-1.5.1.tar.gz 26006 BLAKE2B 8651978c15087fc7332fe229cfc33d8c4257faf46d72f7ac5fbaaf5f31133c4df3d97cae2b18730b5700e742c27e3db39696fdfe910ed884952ba0f832220c3d SHA512 4f83a46f16eb0a4cb9acc6c0d9523fa746dcf670107355c95fc02daa6ca91fb4f8d5e48bc920d8c13a9445390a25415f7217979903ea86f890df1d4704944c28
 DIST votca-csgapps-1.5.tar.gz 25975 BLAKE2B 185e759d658c6f763da2d26770766ec8ee05017b4c6a67e13915de04fbf2ecf268f2f800c5e18ef0f38c615340b0db163e886dc98a9395a69359f94dc8773f60 SHA512 20dda9d07ef2f33c9decff2766ece8f24cf2562993b4dfb7dd637d84325b835a6ecd30d34c5cfb9c428dbf72c2b5dfe9fd49d266182704b981db151c3c4ea2e4
 EBUILD votca-csgapps-1.4.1.ebuild 653 BLAKE2B 208ae3538fcf42296a4a1077d222a9d6f752648834dc8f74941546fa2bdffb6fd9ea60ad31d124b8de52c3f59c089f48d4395b5166989fec19191076570e1bf0 SHA512 13ab1d118aea4f16664566f4e13965cc46a9e67e37157e23ad8c76a68d5db89b8db5b95104c23cf9cc16f78315dc9f632708cbd3920a545d964e2226dc6f9ff2
 EBUILD votca-csgapps-1.4.ebuild 649 BLAKE2B 4b219583f5d5a1f7f4ed7635b4fedce2619d6a0b13bcab7bde2f88cf177a9478fefcb71974deacc09eded4f278ae27c95bd2aa387c79ad4ae2268c2ff0f40a94 SHA512 b6400f2a28ce0c2953495c00aeaab0bfd15c52df28a5e6575b0f568c9a777678495b591cbce58fa61e1d54149fa3f684c6f9f99aaa82127e2eedcc67f6259ed8
+EBUILD votca-csgapps-1.5.1.ebuild 668 BLAKE2B c1a715dcf42281b13819c20b51fc0c16f0435059e4f1dcfe83babd15eda4dc179d50ffe4a6252cd3155aec9545f2e5fc3bba728e2a6f739097422f5c6d94f247 SHA512 23d3ed6be1ea715a367f6203c9431598068ec7b1494865e594a67bfc55bc0f65e86914ad04cff7eff5a9e83fb79cae46fb4abd7997752a1a72dd90a68e173f97
 EBUILD votca-csgapps-1.5.ebuild 666 BLAKE2B de904c4c69f9b223466bc97f646a861a5e1ff64d061389a1a1ac845e7351f9626226354c7c080d7a52ef5db2eddf397b2bf48ce042e168a881cb12da14338333 SHA512 e768e56d45d9e8b4ce2c01358b9de4b876a7a4149947445d388a4a1cffb6ac6882b17cdd794b17eee7abdb75d34c4e108f399c28fbca5ae0b11bbe5d57e07202
 EBUILD votca-csgapps-9999.ebuild 665 BLAKE2B 23030fd2ba47629a9285fc8c9b436bb45614ba3ca8198592aea4189e5d2ae005d88b96a745e6de4db8f913e37e73e07f33a15ec0ef5dda9932a99159286711d4 SHA512 a72ac9569a69e4d94180fd45daf1d06496ea8e253f97a4ec877eb66db62bb7b600ab122909994504b5f677d3424a79e9e663dfa8f5c8d5a5b1388bee325aa524
 MISC metadata.xml 457 BLAKE2B 9d392be6c061ebd3d975308065fcdec4ee061268f4b8b79e122b183d2e4f7259fdb9e165b8b3f030f1edbbc4f112757b1de7a50929ac112d5633143f9585699a SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563
diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild
new file mode 100644
index 000000000000..a4a0669224d6
--- /dev/null
+++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit cmake-utils
+
+if [ "${PV}" != "9999" ]; then
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
+else
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
+	KEYWORDS="~amd64"
+fi
+
+DESCRIPTION="Extra applications for votca-csg"
+HOMEPAGE="http://www.votca.org"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE=""
+
+RDEPEND="
+	>=dev-cpp/eigen-3.3
+	~sci-chemistry/${PN%apps}-${PV}"
+
+DEPEND="${RDEPEND}"
+
+DOCS=( README )
diff --git a/sci-chemistry/votca-ctp/Manifest b/sci-chemistry/votca-ctp/Manifest
index dae27c257d5e..4aa7aa917476 100644
--- a/sci-chemistry/votca-ctp/Manifest
+++ b/sci-chemistry/votca-ctp/Manifest
@@ -1,5 +1,8 @@
+DIST votca-ctp-1.5.1.tar.gz 1345994 BLAKE2B 6e927c5d57abfff335412bdac085c9dd81696503310e58a89bf2207b07f9d9900d11d20176a11fbde6d6cdfa97f50faa5e877889e35201ad9ed5dd93dbc158cb SHA512 686d7193cdd6a763197dd4f332554c9c6c2022c539191d0a243e70450aa2a4c7048fff3c06636aee09525516fb3717fe49934d5daf2dfcdcbc08be416cc4b6c0
 DIST votca-ctp-1.5.tar.gz 1345419 BLAKE2B 148846b9118cabfa541eb4fe0129e366d0c447e2daf969833beb5df91ca7b43f0262c5845303ccf05ed8d3f9e2c2a5e0f876ec97c2601419ed04a28d56640494 SHA512 bc4dbddcefb473015a6513f44f4fddd5995a8598f82505e81b3c50ae771e64e8c979f39a347ab2deb55054e7efffad28b5ff3f73d2c1b8905bcaf6f007ff2959
+DIST votca-ctp-manual-1.5.1.pdf 948647 BLAKE2B 4afec48d0e6bb29dc86d4d22fce74a8d2197d6b7a1ed35a5b09af84c5bbc0fc49b91e045c85e5b5ab79beb5a7de1db78a15e395a1a5faf4c11cc1b58c1ffca97 SHA512 b4ae79b2da0037cc325fdff3b0fd8d142d6bfdad5bc11991cee314f40f105bcdcb1189d17679a84eb37da7a9bb686d0c5ee57c7796a0c6b787b70d53222dbc17
 DIST votca-ctp-manual-1.5.pdf 970539 BLAKE2B 8646215a4c2cd7be6d4c03820f00b8067e15c27f51fb6678540026cff1af0e28dffa528423ad47a4047a8f84fc1078d503a56a4a235e004735f0276ec1a6a33e SHA512 a315c1b4b37461f4f0d30ead1fec2ca33ff23d81c9d5e4d888ef7d7dd722f68f9596826f828f8a76841d6dde6889f623b73d9fe0f8a6c5a7cec1c16a83cf9030
+EBUILD votca-ctp-1.5.1.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84
 EBUILD votca-ctp-1.5.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84
 EBUILD votca-ctp-9999.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84
 MISC metadata.xml 453 BLAKE2B a61c365529a1c877e5bad44f6e2f0a24a8797956e9e3a5b3d4649c58c27df9301b50c84bb5767ca52a151e2b509f46a92cd3f17c1020fb7bedf7fb2fe708b48d SHA512 53ace87a281559ae8881b8b010c76801696521de930dcfaf12a5e320456cb4a21a55a7873d173bdb5cc740f3cdbccf1daf62bc83579342f4f23329df7dbd2dba
diff --git a/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild b/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild
new file mode 100644
index 000000000000..892997f7af3e
--- /dev/null
+++ b/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit cmake-utils multilib
+
+IUSE="doc"
+if [ "${PV}" != "9999" ]; then
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+		doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
+else
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
+	KEYWORDS=""
+fi
+
+DESCRIPTION="Votca charge transport module"
+HOMEPAGE="http://www.votca.org"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+
+RDEPEND="
+	~sci-libs/votca-tools-${PV}[sqlite]
+	>=dev-cpp/eigen-3.3
+	sci-libs/gsl
+	~sci-chemistry/votca-csg-${PV}"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+if [ "${PV}" != "9999" ]; then
+	DEPEND="${DEPEND}
+	doc? (
+		app-doc/doxygen[dot]
+		dev-texlive/texlive-latexextra
+		virtual/latex-base
+		dev-tex/pgf
+	)"
+fi
+
+DOCS=( README.md NOTICE CHANGELOG.md )
+
+src_configure() {
+	[[ ${PV} = *9999* ]] && mycmakeargs=(
+		-DBUILD_XTP_MANUAL=$(usex doc)
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	if use doc; then
+		[[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf"
+		cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html
+		dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html
+	fi
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Please read and cite:"
+	einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)"
+	einfo "https://dx.doi.org/10.1021/ct200388s"
+	einfo
+}
diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest
index 6d10a9af7b2b..8f2cf4195de6 100644
--- a/sci-chemistry/votca-xtp/Manifest
+++ b/sci-chemistry/votca-xtp/Manifest
@@ -1,11 +1,14 @@
 DIST votca-xtp-1.4.1.tar.gz 15214413 BLAKE2B 0f6e67179e2ee1fa8ab79ca0c2d810f9867dab474b50d49316aaed33a01b5cf93a129558792fff2851b8f1b7794ab423c25e4b6f6bce6809520ff40234b14e93 SHA512 1a3f5df3dc9a7f532464ef84ff4f4f8e60b9495529f349ab5e496595e73fff8f4678b8276b2c5733dd3f692ca03220e7d0bc4a82163017572428c0d1dd5f91fd
 DIST votca-xtp-1.4.tar.gz 15214266 BLAKE2B 435ba1603495d904ccce20b4fa665d3a1c62fc04005ea89cf83b431240fb78f8a44f09ad619af331802e43ca3d05b20a4c6bbbb0c75360940d4f786c0030fd7a SHA512 ffc32260331862393e199f7ab643b1008ee4f800cd017f175550a079afaa20e5c929cb8599bc0c2a2328253051895de7b979f5fec044243abc680a0dc87a69b9
+DIST votca-xtp-1.5.1.tar.gz 14634849 BLAKE2B 84ee9fc531a530ba276a6fd3eccc78dd25c27346db76871f33fe307dde451956bf091b636dd5594bf3b8b24a727fe7e5a730fb85cd2cbb0e5605705996e69bd2 SHA512 8fb6891e84d4d685e26287344554b705c607e7cb9f497c00ac9cd8328e50210c56706abdb7004b83d4addbfbc7b35c3526b4feabf75f681362b3b7a39c54b668
 DIST votca-xtp-1.5.tar.gz 14637712 BLAKE2B af04de706f0d100968928459a03b6a94a94a211b3f5bd056d123756d40760fb0ada70add429ed5b86e211dbdd3b91aa4cf12e51a260638766d04158e7b5a1201 SHA512 693f34004749edfbabcd0a19dc23b3de3c09858c7c0dfe1e420b92632397971e3687489c1074a489d4d2fd337ddc5749c419869db104c65736e7c01bf12cd140
 DIST votca-xtp-manual-1.4.1.pdf 1066873 BLAKE2B 8cbd4b55b013794a19a8b5867b929b8e2d9084e6780d777b2a2bbaea23006f4f4ec5b26bd4a07c59e1c6726f23471eb1756b668636e0c4e656a0807e64197586 SHA512 fdf1147f24785524f5e96020fcd29c32bbeef520eebf6afba32b59d7e777d586c452919478d2734c3f021e558b1147b945cdbc0833402be2b16e5af3a8e37f5f
 DIST votca-xtp-manual-1.4.pdf 1064006 BLAKE2B e4f0c20c6d40a5f58b863258cc122e5a7cf376b7138927c0a6bdd400841c330fc013287513258f6f68609e39f0bf39b965fd099171594c5e2730fba82a2488d4 SHA512 96d7f59dbcc3a6efdc297237025217d5a56d2c81e491d90680786ea4769a5ebbea379df3b06c4847307ee30accd7415e316dee4730361262f5aff73d2f5d387e
+DIST votca-xtp-manual-1.5.1.pdf 912290 BLAKE2B 4511885f5506f542d639b5c7d2bb2e6f4f24df8d7929959ff707ae9c28c357346ebc7cde072f742309f3ef8a6b00a51d0873071cdc4cbcd291670fca788f46a7 SHA512 b410ddad0566933a2c9ad386fb6f4df0e71b316a84bce8c841e94df8f438959f0967ade63d1146549d453c2ecdb48e3d8b1fd147e53888e1717c6db3d07ba061
 DIST votca-xtp-manual-1.5.pdf 923211 BLAKE2B 5d2c78260365c6339753e1663d707d642dea870183386f799e8fb34517fdb69680293b77356ae00c3ee6b66053c614b7174503e2e752790a56e7dd2976b3cb0a SHA512 86079339de1cb6e3d0487ad816e86deebe6a1bddcac1f06801e3f94eca2e19b30ec61b286f13429e257aa152129f5dbb4bbbc88ac9d58bf1a9aeb1c3f430d3e0
 EBUILD votca-xtp-1.4.1.ebuild 1622 BLAKE2B 1358e16a21b653584fefdf8eb673744f18ba75ef59ae5410c609857ca0b6d73676b5f7ca101dd24d2d58ca1547ca062941c71296ca57e45cdfed29052dfc7cb2 SHA512 bee48dc7a8c0caba3a9a7ed546ad690fb9fc22310f512bc613aa76b35f72b39f4a2b620ab2789237465ce07a0be7b8fbb444eccd45e795b0c1cc3667b046f978
 EBUILD votca-xtp-1.4.ebuild 1618 BLAKE2B bab1c2d4cd442bc2208f87ff16ed1218aaf6c34ccb229c63d9de14086055684ee9440102b0c9a5bf807ddad69d22ee1b680120f493f18891e8719211509a418f SHA512 affe412a6c4cb8139530d559ae4c12d519eb6b9190075743ed7806c2975a4647f48282893d71b4bef3477b0d35ee07815e416c33095be819967d235c9623a48a
+EBUILD votca-xtp-1.5.1.ebuild 1628 BLAKE2B a89ea389a31edce013d2e41eca4a0a818fd3f0b359aa9e770ecf3e04089b99063106d8b20562b36ad83fdc318c6cc6ffc119a589d995db08175e704ff7ce53f1 SHA512 a90fd6523ef6d42af25b99509718511cf0303bef2e0b083b6e4e8cbb5160bf1cc802b0e60a682c7bd1301f5b17cbaf78c2d2e593d2528f9c24b5f6c3c1aa984f
 EBUILD votca-xtp-1.5.ebuild 1626 BLAKE2B 15b3e63d11348ac376e15769b6106c98144a0ce88bbc7149fcf98bede2f7a29ee4ea066cea67fadf14e60e6dbc6745de4bffa4cf11d6ce6f08d5631fad0af347 SHA512 ac39f8f262a40683ff267dd13ea17cdfb9bd3ba62d698e8e20c98ee1adce53bd002a10dd7805a4ba419ca80a4a3ffd0b3b5c8f9e4b040182eaa6ffd069df114e
 EBUILD votca-xtp-9999.ebuild 1622 BLAKE2B 0c99db3dbba224f0485838e5fddb8b857fd13d5e5d798bbaa4b64f89ffcbb1bbbb55a626ff601efd583bf32270c4a8be21a4f8357e6a67e1d8f3feac7c2eccdc SHA512 31a8520c2438ecd0407748b65d363c5ebf2027b71b19fd90810f75b25cf5ea90ed7eedde354fb17dbd0f087963b0b23923f29a9d028d899668fd90eda0806231
 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e
diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.5.1.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.5.1.ebuild
new file mode 100644
index 000000000000..3d34efdc74c2
--- /dev/null
+++ b/sci-chemistry/votca-xtp/votca-xtp-1.5.1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils multilib
+
+IUSE="doc"
+if [ "${PV}" != "9999" ]; then
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+		doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
+else
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
+	KEYWORDS="~amd64"
+fi
+
+DESCRIPTION="Votca excitation and charge properties module"
+HOMEPAGE="http://www.votca.org"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+
+RDEPEND="
+	~sci-libs/votca-tools-${PV}[sqlite]
+	>=dev-cpp/eigen-3.3
+	~sci-chemistry/votca-csg-${PV}
+	sci-libs/ceres-solver
+	sci-libs/libxc"
+
+DEPEND="${RDEPEND}
+	>=app-text/txt2tags-2.5
+	virtual/pkgconfig"
+
+if [ "${PV}" != "9999" ]; then
+	DEPEND="${DEPEND}
+	doc? (
+		app-doc/doxygen[dot]
+		dev-texlive/texlive-latexextra
+		virtual/latex-base
+		dev-tex/pgf
+	)"
+fi
+
+DOCS=( README.md NOTICE CHANGELOG.md )
+
+src_configure() {
+	[[ ${PV} = *9999* ]] && mycmakeargs=(
+		-DBUILD_XTP_MANUAL=$(usex doc)
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	if use doc; then
+		[[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf"
+		cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html
+		dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html
+	fi
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Please read and cite:"
+	einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)"
+	einfo "https://doi.org/10.1021/acs.jctc.8b00617"
+	einfo
+}
author	V3n3RiX <venerix@redcorelinux.org>	2019-12-15 18:09:03 +0000
committer	V3n3RiX <venerix@redcorelinux.org>	2019-12-15 18:09:03 +0000
commit	7bc9c63c9da678a7e6fceb095d56c634afd22c56 (patch)
tree	4a67d50a439e9af63947e5f8b6ba3719af98b6c9 /sci-chemistry
parent	b284a3168fa91a038925d2ecf5e4791011ea5e7d (diff)