gentoo resync : 04.07.2020

26 files changed, 74 insertions, 785 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 47701b13d982..08f6a519da1d 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest
index 065022beda3e..45cbb04a2703 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
+AUX autodock-4.2.6-buildsystem.patch 1480 BLAKE2B 3f1884ee05e062cb630b43fe3e8ecf6f827ada23d5d3060a5bb3d7e854f7c5e2d2b1f7a476c4effcdcbab4292b33fae093474773a31a6995465d00dbbb721246 SHA512 9c5b05f4831049c2c064358df26124526973110ddd31ffa7930f185694f9258dfce648085a96f05a2173aa61b4cdcda7a6fe170a56160708e031fb248f9e6bbe
 DIST autodocksuite-4.2.6-src.tar.gz 35438010 BLAKE2B 88e036ecc0492fb83f31b90fd0983ec57d889a61d17249f672a3e30e942f6c329dc2494088a8fc7c5bc39a5bdbb38fb1514f1750c7145374f202a928d477faa9 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb
-EBUILD autodock-4.2.6.ebuild 2202 BLAKE2B f425ab34d6941523d6c8b1c8740b4b8a2aa89b49c965466af77c8dda0cc4ef3d24a9c5a40ad82156497f24f6d3afb341e697838446d96195fd6a990b909160b4 SHA512 516d12bbf27984ecd844bae777c408790f7288b08d025fc618920458181dc57abbe3442b69270c1209afa6ebb45b11e774f60e1721452d790119270157336252
+EBUILD autodock-4.2.6.ebuild 2337 BLAKE2B 3302c9d3690f3faf97ef2265512de2c31b0b83752ed92375ecc822e42125eb50324a97197131b5280c71e1a165d1052f4250d06ed412d0b86034464168e9ef49 SHA512 3f215c0d54059f77da1623a9d5602e81e652d84382b327c3deee86f8cdb2d5392476d62288452881977f1582fa36474c648e7e519b5cf7fd7d1a926778697941
 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 6cfe76fbbfd0..b4dce2e439b4 100644
--- a/sci-chemistry/autodock/autodock-4.2.6.ebuild
+++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild
@@ -1,38 +1,56 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+# Tests require python2
+#PYTHON_COMPAT=( python2_7 )
 
-inherit autotools eutils python-any-r1 versionator
+inherit autotools readme.gentoo-r1 #python-any-r1
 
 MY_PN="autodocksuite"
 MY_P="${MY_PN}-${PV}"
 
 DESCRIPTION="A suite of automated docking tools"
 HOMEPAGE="http://autodock.scripps.edu/"
-SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz"
+SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(ver_rs 1- '')/${MY_P}-src.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="examples openmp test"
-RESTRICT="!test? ( test )"
+
+IUSE="examples openmp" #test
+#RESTRICT="!test? ( test )"
+
+# False positives caused by nested configure scripts
+QA_CONFIGURE_OPTIONS=".*"
 
 RDEPEND=""
-DEPEND="test? ( ${PYTHON_DEPS} )"
+DEPEND=""
+#DEPEND="test? ( ${PYTHON_DEPS} )"
 
 S="${WORKDIR}/src"
 
+DISABLE_AUTOFORMATTING="yes"
+DOC_CONTENTS="
+The AutoDock development team requests all users to fill out the
+registration form at:
+
+http://autodock.scripps.edu/downloads/autodock-registration
+
+The number of unique users of AutoDock is used by Prof. Arthur J.
+Olson and the Scripps Research Institude to support grant
+applications.
+"
+
 PATCHES=(
 	"${FILESDIR}"/${P}-buildsystem.patch
 )
 
 src_prepare() {
-	local i
+	default
 
-	epatch "${PATCHES[@]}"
+	local i
 
 	sed \
 		-e "s/\tcsh/\tsh/" \
@@ -58,15 +76,15 @@ src_compile() {
 	emake -C autogrid
 }
 
-src_test() {
-	elog "Testing autodock"
-	cd "${S}/autodock/Tests" || die
-	cp ../*.dat . || die
-	${EPYTHON} test_autodock4.py || die "AutoDock tests failed."
-	einfo "Testing autogrid"
-	cd "${S}/autogrid/Tests" || die
-	${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed."
-}
+#src_test() {
+#	elog "Testing autodock"
+#	cd "${S}/autodock/Tests" || die
+#	cp ../*.dat . || die
+#	${EPYTHON} test_autodock4.py || die "AutoDock tests failed."
+#	einfo "Testing autogrid"
+#	cd "${S}/autogrid/Tests" || die
+#	${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed."
+#}
 
 src_install() {
 	if use openmp; then
@@ -79,7 +97,7 @@ src_install() {
 	insinto /usr/share/${PN}
 	doins -r \
 		autodock/{AD4_parameters.dat,AD4_PARM99.dat} \
-		$(usex examples "autodoc/EXAMPLES" "")
+		$(usex examples "autodock/EXAMPLES" "")
 
 	DOCS=(
 		RELEASENOTES
@@ -88,15 +106,9 @@ src_install() {
 		autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf
 	)
 	einstalldocs
+	readme.gentoo_create_doc
 }
 
 pkg_postinst() {
-	elog "The AutoDock development team requests all users to fill out the"
-	elog "registration form at:"
-	echo
-	elog "\thttp://autodock.scripps.edu/downloads/autodock-registration"
-	echo
-	elog "The number of unique users of AutoDock is used by Prof. Arthur J."
-	elog "Olson and the Scripps Research Institude to support grant"
-	elog "applications."
+	readme.gentoo_print_elog
 }
diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
index ae44ffeb3159..443dfcd868ce 100644
--- a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
+++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
@@ -1,11 +1,11 @@
- src/autodock/Makefile.am | 6 +++---
- src/autogrid/Makefile.am | 4 ++--
+ a/autodock/Makefile.am | 6 +++---
+ b/autogrid/Makefile.am | 4 ++--
  2 files changed, 5 insertions(+), 5 deletions(-)
 
 diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am
 index 799a3c4..911897b 100644
---- a/src/autodock/Makefile.am
-+++ b/src/autodock/Makefile.am
+--- a/autodock/Makefile.am
++++ b/autodock/Makefile.am
 @@ -459,7 +459,8 @@ endif
  
  BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h
@@ -28,8 +28,8 @@ index 799a3c4..911897b 100644
  
 diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am
 index b531099..b78b380 100644
---- a/src/autogrid/Makefile.am
-+++ b/src/autogrid/Makefile.am
+--- a/autogrid/Makefile.am
++++ b/autogrid/Makefile.am
 @@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \
  BUILT_SOURCES = default_parameters.h
  
diff --git a/sci-chemistry/gperiodic/Manifest b/sci-chemistry/gperiodic/Manifest
index 1e70b609648b..8f6e9217df37 100644
--- a/sci-chemistry/gperiodic/Manifest
+++ b/sci-chemistry/gperiodic/Manifest
@@ -1,11 +1,3 @@
-AUX gperiodic-2.0.10-makefile.patch 2266 BLAKE2B b59eb8c878b821e15086f074a06eabf8be2ad694e6f7e11358232d4efd8c2e9512c2cada8cb11ac3e6678fee0620d6f0c77bb14e190dae6db8d38f4400616696 SHA512 f2e8369e7ad35e546f70191a18e07961f5000c354f0624ca5bd0a7bf77f6a8fb5e3fa299688ffccba8fbd1c7e0e28de9e214a030f5a6d2909c72f26772ac2b73
-AUX gperiodic-2.0.10-nls.patch 508 BLAKE2B 6ae02c56b235a79ad3400edc7a79d9f7e0daf5a67e2a51fff65db94ad2eb14f3ef800f3b774fb3747b221bdbc5ffccbd2419fe3cab2fbd432f4c25921bf7a68e SHA512 1c5a6f067ac9e6f9b1073bc97c3f5ae133f7f1f84e54ee30a9898cb658b31db20c4c483cc9557bd43db3eec2ce9a82df49611fb4d692e5b004b08461cb149a43
-AUX gperiodic-3.0.1-makefile.patch 3196 BLAKE2B f0862f3b205f41aaec9cb1574a34bb8ba77ef01f12c7d9878dbf9f9ab076ef56eb56f2de2c12200d563930eb0533d4beacb3625f9b58661eb76c23accced3199 SHA512 fd2f17a2f83c32387769ecf5d42599a41fd2c5775cefe5fcf5c9f3fcc0f3d5e077c524bcb1467c0fe6176304f78a4ba7ff377da9d92cbd57e576f5aceb5d13e4
-AUX gperiodic-3.0.1-nls.patch 488 BLAKE2B d325dded4249cbbceb45bcac7e20eade635e50d2ed410f6a6c5141b169ccf05fcf090b98a56b8efa8b21519e32a5113adc87665a29188be4608ce68c6a35299a SHA512 acd270f4c8e4cd271f2d48ea48e716195cb39e14ea09a41dc48787756f4f5806fea3bb3cf5072aac49f897c610a36fcbe89de433efefab845f7462d4693a5eef
-DIST gperiodic-2.0.10.tar.gz 131213 BLAKE2B bd846dd64afa07e038008e6fe0563f5743767f3a1fba1aad0122ae644c7fb9279657609733bc4e6d4f4dcf988aff6096431ba1b71d02a328e01376ae00ff9bcb SHA512 23d0074ad5b0f9e25e8eee63f8c375e2448b1ee7c00f89e965b7dd8ce3f60f20251d7699a2f7a767228316144b946a5ac204a3e478c395767133f7fc801b51ba
-DIST gperiodic-3.0.1.tar.gz 375347 BLAKE2B fb10c7d3484e822e636a8aca245ab2a68a95cfebbb433df03a643a1155f300d2cdca49ddb5713d298c69a25123abbf72e17fdd51f69c9b031d05153937b283fc SHA512 3bf47359dda1a029f3528ea04d28cd75909bceb535f6e1dc6c90f5a17b668e0dd98900ddd83633649383ff4e2fc588265275e0e4a27897ecc4ac6db4e93befc1
 DIST gperiodic-3.0.3.tar.gz 451559 BLAKE2B b91995046b9905a534e3b6f530aee0ad2b4e6ac42cd11755ea182fdaaf8970f34b1aea8a33870abb8767837606a42a0cf0d76c9a689236aa39fba686e1521ee8 SHA512 7226063cf7977f4283a199d4a3d1842d6c9be60c53f5a005541eb26f35cd6538b29f086dc13c28225779e1849a12d1c39150897055c03902cb00adc011bc1ce8
-EBUILD gperiodic-2.0.10-r2.ebuild 980 BLAKE2B b5ba74641f0f3ae67d8bb727d25d73f05f2f9cd900863264c358ab41be3cfeb9fddd39b17d6eb017238add96318e12d7a6067be57024bbd5b21882ec6e526823 SHA512 3d70210080fbeb3d8689202f21b6aa25f78a4309abe4e72859ec4cb1b66a4a97db5e854b09fec1919e67947c4916a467fe86ccca9538b8e622e18598c820f87c
-EBUILD gperiodic-3.0.1.ebuild 1252 BLAKE2B 852805406f9d9d35f2e70166ec0b49eb557494b86cf028147bf0b2e2fa69450eaec73b3a1e974e001c7c67ddb95b01b14fd6d4a58c9e025e7b9c7adfc4da8c25 SHA512 942525b7106bac0451a802c4a896baf83b310a52c206ee043877f255b1abfa2592ed440dd2554cae5bcdefe210a519927e3fa387d47ad96be36a6701855a9a3e
-EBUILD gperiodic-3.0.3.ebuild 882 BLAKE2B bdf7520bda855a1538578ac7cb46de5717a461a913493e8f1d1003178348f98af5c7cbff9ba12d0a662b68f23bae750f14276db9a804c4dfbfdc4af1346a7ef6 SHA512 60ff9a7394a9e3a141b9f2a214d9abc2bd5996062baa77e6f341e73a1e69a9aa9b3f5e121e0fffc751deb04d41713b3024cb5e9c219383384fd7004a4c360e6e
+EBUILD gperiodic-3.0.3.ebuild 881 BLAKE2B 7413f3d080b148fd09ae289e4032475eb73470ae6822710f854781bb01f9dbe21e53a9d11828894468c7b14581998f43ff28809da12faf273988e0418f2280cf SHA512 7a9dfb58b2c2be95fcc72d37a6585bd4bd244721751b545ef07ef276b0fddba88e6c19ee06d726ca5d3c45dbb70cba12d39b4948c9a9ad149859b690fb97d3c7
 MISC metadata.xml 550 BLAKE2B eeb2153919fb1045284131b22a26e22feb0c4671296ed2ba223b0d5f8632d5e73070ef9bf8fbff52c228ad3c9eae23a701b5d3f15e0fb11c5cb0fc148297c1bd SHA512 a847a617e38f540ac53851c97bb30bb3b64d7ca3dac8a89b9a1e70521081cb8e2ee0183c9f9fdfd099532add7dd017cbff53d3b67c7624adc4264953b646e2e4
diff --git a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch
deleted file mode 100644
index abdb5caae4f2..000000000000
--- a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch
+++ /dev/null
@@ -1,64 +0,0 @@
-Respect CC, CFLAGS, LDFLAGS
-Fix install paths
-Fix parallel build
-Drop DEPRECATED flags, bug #391099
-
---- Makefile
-+++ Makefile
-@@ -1,6 +1,5 @@
--CC := gcc
--CFLAGS := `pkg-config --cflags gtk+-2.0` -I. -DG_DISABLE_DEPRECATED -DGDK_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED
--LIBS :=`pkg-config --libs gtk+-2.0`
-+CFLAGS += `pkg-config --cflags gtk+-2.0` -I.
-+LIBS +=`pkg-config --libs gtk+-2.0`
- bindir ?= /usr/bin
- datadir ?= /usr/share
- enable_nls ?= 1
-@@ -8,12 +7,11 @@
- .c.o:
- 	$(CC) -c $(CFLAGS) $(CPPFLAGS) $<
- 
--all: 
--	make gperiodic
--	make -C po/ all enable_nls=$(enable_nls)
-+all: gperiodic
-+	$(MAKE) -C po/ all enable_nls=$(enable_nls)
- 
- gperiodic: gperiodic.o
--	$(CC) $(CFLAGS) -o gperiodic gperiodic.o $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o gperiodic gperiodic.o $(LIBS)
- ifeq ($(strip),1)
- 	strip gperiodic
- endif
-@@ -23,24 +21,21 @@
- gperiodic.o: gperiodic.c gperiodic.h table_data.h
- 
- install:
--	mkdir -p $(DESTDIR)$(bindir)
--	install -m 755 gperiodic $(DESTDIR)$(bindir)
--	mkdir -p $(DESTDIR)$(datadir)/applications
--	install -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications
--	mkdir -p $(DESTDIR)$(datadir)/pixmaps
--	install -m 644 gperiodic.png $(DESTDIR)$(datadir)/pixmaps
--	install -m 644 gperiodic-crystal.png $(DESTDIR)$(datadir)/pixmaps
--	make -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
-+	install -D -m 755 gperiodic $(DESTDIR)$(bindir)/gperiodic
-+	install -D -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications/gperiodic.desktop
-+	install -D -m 644 gperiodic.png $(DESTDIR)$(datadir)/pixmaps/gperiodic.png
-+	install -m 644 gperiodic-crystal.png $(DESTDIR)$(datadir)/pixmaps/gperiodic-crystal.png
-+	$(MAKE) -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
- 
- uninstall:
- 	rm -f $(bindir)/gperiodic \
- 	      $(datadir)/applications/gperiodic.desktop
- 	      $(datadir)/pixmaps/gperiodic.png \
- 	      $(datadir)/pixmaps/gperiodic-crystal.png
--	make -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
-+	$(MAKE) -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
- 
- clean:
- 	rm -f *.o gperiodic
--	make -C po/ clean
-+	$(MAKE) -C po/ clean
- 
- .PHONY: install uninstall clean
diff --git a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch
deleted file mode 100644
index de0bea04dc14..000000000000
--- a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch
+++ /dev/null
@@ -1,20 +0,0 @@
- po/Makefile |    2 ++
- 1 files changed, 2 insertions(+), 0 deletions(-)
-
-diff --git a/po/Makefile b/po/Makefile
-index d7d7d78..179dad6 100644
---- a/po/Makefile
-+++ b/po/Makefile
-@@ -26,10 +26,12 @@ endif
- 
- install: 
- 	$(MAKE) all
-+ifeq ($(enable_nls),1)
- 	for f in $(FILES_MO) ; do \
- 		mkdir -p $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES ; \
- 		install -m 644 $$f $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES/$(PACKAGE).mo ; \
- 	done
-+endif
- 
- uninstall:
- 	for f in $(FILES_MO) ; do \
diff --git a/sci-chemistry/gperiodic/files/gperiodic-3.0.1-makefile.patch b/sci-chemistry/gperiodic/files/gperiodic-3.0.1-makefile.patch
deleted file mode 100644
index a7a402a1a781..000000000000
--- a/sci-chemistry/gperiodic/files/gperiodic-3.0.1-makefile.patch
+++ /dev/null
@@ -1,66 +0,0 @@
- Makefile | 36 ++++++++++++++----------------------
- 1 file changed, 14 insertions(+), 22 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 7e86dc4..9bd4fe8 100644
---- a/Makefile
-+++ b/Makefile
-@@ -14,8 +14,8 @@ enable_nls ?= 1
- 	$(CC) -c $(CFLAGS) $(CPPFLAGS) $<
- 
- all: 
--	make gperiodic
--	make -C po/ all enable_nls=$(enable_nls)
-+	$(MAKE) gperiodic
-+	$(MAKE) -C po/ all enable_nls=$(enable_nls)
- 	intltool-merge -d po gperiodic.desktop.in gperiodic.desktop
- 
- gperiodic: gperiodic.o
-@@ -29,24 +29,16 @@ gpdata.o: gpdata.c gperiodic.h
- gperiodic.o: gperiodic.c gperiodic.h table_data.h
- 
- install:
--	mkdir -p $(DESTDIR)$(bindir)
--	install -m 755 gperiodic $(DESTDIR)$(bindir)
--	mkdir -p $(DESTDIR)$(datadir)/applications
--	install -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications
--	mkdir -p $(DESTDIR)$(datadir)/pixmaps
--	install -m 644 icons/gperiodic.png $(DESTDIR)$(datadir)/pixmaps
--	install -m 644 icons/gperiodic.xpm $(DESTDIR)$(datadir)/pixmaps
--	mkdir -p $(DESTDIR)$(mandir)
--	install -m 644 gperiodic.1 $(DESTDIR)$(mandir)
--	mkdir -p $(DESTDIR)$(iconsdir)/hicolor/16x16/apps
--	mkdir -p $(DESTDIR)$(iconsdir)/hicolor/32x32/apps
--	mkdir -p $(DESTDIR)$(iconsdir)/hicolor/48x48/apps
--	mkdir -p $(DESTDIR)$(iconsdir)/hicolor/64x64/apps
--	install -m 644 icons/hicolor/16x16/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/16x16/apps
--	install -m 644 icons/hicolor/32x32/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/32x32/apps
--	install -m 644 icons/hicolor/48x48/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/48x48/apps
--	install -m 644 icons/hicolor/64x64/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/64x64/apps
--	make -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
-+	install -D -m 755 gperiodic $(DESTDIR)$(bindir)/gperiodic
-+	install -D -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications/gperiodic.desktop
-+	install -D -m 644 icons/gperiodic.png $(DESTDIR)$(datadir)/pixmaps/gperiodic.png
-+	install -D -m 644 icons/gperiodic.xpm $(DESTDIR)$(datadir)/pixmaps/gperiodic.xpm
-+	install -D -m 644 gperiodic.1 $(DESTDIR)$(mandir)/gperiodic.1
-+	install -D -m 644 icons/hicolor/16x16/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/16x16/apps/gperiodic.png
-+	install -D -m 644 icons/hicolor/32x32/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/32x32/apps/gperiodic.png
-+	install -D -m 644 icons/hicolor/48x48/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/48x48/apps/gperiodic.png
-+	install -D -m 644 icons/hicolor/64x64/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/64x64/apps/gperiodic.png
-+	$(MAKE) -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
- 
- uninstall:
- 	rm -f $(bindir)/gperiodic \
-@@ -58,10 +50,10 @@ uninstall:
- 	      $(iconsdir)/hicolor/32x32/apps/gperiodic.png \
- 	      $(iconsdir)/hicolor/48x48/apps/gperiodic.png \
- 	      $(iconsdir)/hicolor/64x64/apps/gperiodic.png
--	make -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
-+	$(MAKE) -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR)
- 
- clean:
- 	rm -f *.o gperiodic gperiodic.desktop
--	make -C po/ clean
-+	$(MAKE) -C po/ clean
- 
- .PHONY: install uninstall clean
diff --git a/sci-chemistry/gperiodic/files/gperiodic-3.0.1-nls.patch b/sci-chemistry/gperiodic/files/gperiodic-3.0.1-nls.patch
deleted file mode 100644
index 4420ca68e585..000000000000
--- a/sci-chemistry/gperiodic/files/gperiodic-3.0.1-nls.patch
+++ /dev/null
@@ -1,20 +0,0 @@
- po/Makefile | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/po/Makefile b/po/Makefile
-index d7d7d78..c596e5b 100644
---- a/po/Makefile
-+++ b/po/Makefile
-@@ -26,10 +26,12 @@ endif
- 
- install: 
- 	$(MAKE) all
-+ifeq ($(enable_nls),1)
- 	for f in $(FILES_MO) ; do \
- 		mkdir -p $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES ; \
- 		install -m 644 $$f $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES/$(PACKAGE).mo ; \
- 	done
-+endif
- 
- uninstall:
- 	for f in $(FILES_MO) ; do \
diff --git a/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild b/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild
deleted file mode 100644
index 64e36c7c268f..000000000000
--- a/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Periodic table application for Linux"
-HOMEPAGE="https://sourceforge.net/projects/gperiodic/"
-SRC_URI="http://www.frantz.fi/software/${P}.tar.gz"
-
-KEYWORDS="amd64 x86"
-SLOT="0"
-LICENSE="GPL-2"
-IUSE="nls"
-
-RDEPEND="
-	sys-libs/ncurses:0
-	x11-libs/gtk+:2
-	x11-libs/cairo[X]
-	nls? ( sys-devel/gettext )"
-
-DEPEND="${RDEPEND}
-		virtual/pkgconfig"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-makefile.patch \
-		"${FILESDIR}"/${P}-nls.patch
-	sed \
-		-e '/Encoding/d' \
-		-i ${PN}.desktop || die
-}
-
-src_compile() {
-	local myopts
-	use nls && myopts="enable_nls=1" || myopts="enable_nls=0"
-	emake CC=$(tc-getCC) ${myopts}
-}
-
-src_install() {
-	local myopts
-	use nls && myopts="enable_nls=1" || myopts="enable_nls=0"
-	emake DESTDIR="${D}" ${myopts} install
-	dodoc AUTHORS ChangeLog README NEWS
-	newdoc po/README README.translation
-}
diff --git a/sci-chemistry/gperiodic/gperiodic-3.0.1.ebuild b/sci-chemistry/gperiodic/gperiodic-3.0.1.ebuild
deleted file mode 100644
index 511cfe2ba428..000000000000
--- a/sci-chemistry/gperiodic/gperiodic-3.0.1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Periodic table application for Linux"
-HOMEPAGE="https://sourceforge.net/projects/gperiodic/"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
-
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-LICENSE="GPL-2"
-IUSE="nls"
-MY_AVAILABLE_LINGUAS=" be bg cs da de es fi fr gl id is it lt ms nl pl pt_BR pt ru sv tr uk"
-
-RDEPEND="
-	sys-libs/ncurses:0
-	x11-libs/gtk+:2
-	x11-libs/cairo[X]
-	nls? ( sys-devel/gettext )"
-DEPEND="${RDEPEND}
-		virtual/pkgconfig"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-makefile.patch \
-		"${FILESDIR}"/${P}-nls.patch
-	for lang in ${MY_AVAILABLE_LINGUAS}; do
-		if ! has ${lang} ${LINGUAS-${lang}}; then
-			einfo "Cleaning translation for ${lang}"
-			rm po/${lang}.po || die
-		fi
-	done
-}
-
-src_compile() {
-	local myopts
-	use nls && myopts="enable_nls=1" || myopts="enable_nls=0"
-	emake \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		CC=$(tc-getCC) ${myopts}
-}
-
-src_install() {
-	local myopts
-	use nls && myopts="enable_nls=1" || myopts="enable_nls=0"
-	emake DESTDIR="${D}" ${myopts} install
-	dodoc AUTHORS ChangeLog README
-	newdoc po/README README.translation
-}
diff --git a/sci-chemistry/gperiodic/gperiodic-3.0.3.ebuild b/sci-chemistry/gperiodic/gperiodic-3.0.3.ebuild
index 5f92d367c216..2ffd7a303310 100644
--- a/sci-chemistry/gperiodic/gperiodic-3.0.3.ebuild
+++ b/sci-chemistry/gperiodic/gperiodic-3.0.3.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="amd64 ~x86"
+KEYWORDS="amd64 x86"
 IUSE="nls"
 
 BDEPEND="
diff --git a/sci-chemistry/hollow/Manifest b/sci-chemistry/hollow/Manifest
deleted file mode 100644
index bb1715828169..000000000000
--- a/sci-chemistry/hollow/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST hollow-1.2.zip 62554 BLAKE2B 825ebbd5b9085d47be3487331ecabf80a6af73eda4525e1d073eea05b5fb0c1892b115f669c8ce3227bfb573f266d1a0225c7aaeee844338496bceb55d88edd6 SHA512 e253680cc0fae286ec697b2dac822b9e165d509cc7eefb27bbcafae6ab2617c3edc8cd9c8beefcc9ef2eb920c9d839fd0bc25f79d22160d857b1705cefbc05ca
-EBUILD hollow-1.2-r1.ebuild 839 BLAKE2B 5285c191fca679bd25576c4867c3ce1ae838d68f438154e02b729bf2677bf34ae00153b9058760d05e5caf846c8941e456bba96aac7c1e1ff26a3c7b90f6a20b SHA512 18d6aca5be599a6b02028657bff79025e2c107c2a9a24414c7f09cce664e4f958d278050738b7b0de73574aafbd9ad05e3f05e55ad81e787731d0495c25df554
-MISC metadata.xml 351 BLAKE2B 6f5289088abeea03575568a03f685e513d2138670a057ad9d84e3ccc2b3a2cfcdf1885d8593101671b4b4c6df9204c1390a35f9fc3555e2935dce9c128dd6052 SHA512 977d69a6514595888b2a8c193a60dd2ae50ddde7bf9bbacc9051781aab58d50ff2543a911d270c1ed5e5bd152a23b8b2a3f03a186052c74d71c82939e30eeb27
diff --git a/sci-chemistry/hollow/hollow-1.2-r1.ebuild b/sci-chemistry/hollow/hollow-1.2-r1.ebuild
deleted file mode 100644
index d1db2c19db3f..000000000000
--- a/sci-chemistry/hollow/hollow-1.2-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1 vcs-clean
-
-DESCRIPTION="Production of surface images of proteins"
-HOMEPAGE="http://hollow.sourceforge.net/"
-#SRC_URI="mirror://sourceforge/${P}.zip"
-SRC_URI="http://hollow.sourceforge.net/${P}.zip"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-3"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-DEPEND="${PYTHON_DEPS}
-	app-arch/unzip"
-
-src_install() {
-	python_setup
-	esvn_clean
-	python_foreach_impl python_domodule pdbstruct
-	python_moduleinto ${PN}
-	python_foreach_impl python_domodule *.py hollow.txt
-
-	python_foreach_impl python_newscript ${PN}.py ${PN}
-
-	dodoc README
-	python_optimize
-}
diff --git a/sci-chemistry/hollow/metadata.xml b/sci-chemistry/hollow/metadata.xml
deleted file mode 100644
index 266ef9d56913..000000000000
--- a/sci-chemistry/hollow/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="sourceforge">hollow</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest
deleted file mode 100644
index d1e2ba30e3e7..000000000000
--- a/sci-chemistry/modeller/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST modeller-9.20.tar.gz 34909796 BLAKE2B d89c81823c4d7784a7b3d64fdb01158a973edc7d8b316c773e038ba8645797c543d5bc58c1bff5462ae5975a6c2796f4b2d500641d226c3b2281cf794cfeba8d SHA512 667edeeda0a9038258f6932b3cef22a1e9d0fe47f47bd2ac612e7bac7f23a863f5a65cfd93abfa405310e7fb7b305d53e71d6c6e930613b0dbd43b24dcd5919a
-DIST modeller-9.22.tar.gz 34953371 BLAKE2B 3bf8828b38f22955dea973cfe54cbd2f77bf021900bd5aa3c75f083b12e2a7199c3173de526acfeab005c0606816bac347b9bdfb6b62d5e3db9c9e18fed99ac4 SHA512 0056f09a07d6e2b565c8f4accca48ad176c9d32634b75bc4db60a187d56f22ef1710296dfd31bf27f496c5ed100146420be7cfdb135ca8b2b0fac7d7f5fa877f
-EBUILD modeller-9.20.ebuild 3694 BLAKE2B 8547065d37bb0011ee88b5970984f6756a2194dcc6c256599d1ad78d8ca3e43b3ad08c30306993d8bf4404e7c407bf4162bcb7242427dbc105b66c14cb3cf26e SHA512 c89756d95e2990a2248794227771df67ca940a71e831a472252878ba027fcee95c8a00157cb3d3fa81591ab0f7c8984236c8235164669dc993d3ff0ae93850d4
-EBUILD modeller-9.22.ebuild 3682 BLAKE2B 0834fd52f447c66e9518bd9068669c21b7aaa4731b608b29bed47de48c87e2f45c825997760d07a05fcb88e4255f82cf9d09cd5a410fc337a057532c3d121cce SHA512 02458a89515ef1b14ea59789d7d32c82c52a7e84b86140eb3f866a65be8ca134bc825c5e03785bffeb056a405bb822dfe3b33394ee52a4fe3166b86770228162
-MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml
deleted file mode 100644
index da36ecbfcd6a..000000000000
--- a/sci-chemistry/modeller/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/modeller/modeller-9.20.ebuild b/sci-chemistry/modeller/modeller-9.20.ebuild
deleted file mode 100644
index 641395067b0d..000000000000
--- a/sci-chemistry/modeller/modeller-9.20.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib versionator
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="https://salilab.org/modeller/"
-SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all() {
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all() {
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/modeller/modeller-9.22.ebuild b/sci-chemistry/modeller/modeller-9.22.ebuild
deleted file mode 100644
index 2bc08bd43d4e..000000000000
--- a/sci-chemistry/modeller/modeller-9.22.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="https://salilab.org/modeller/"
-SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all() {
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all() {
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest
index 22008bf7cef6..c84a62817835 100644
--- a/sci-chemistry/propka/Manifest
+++ b/sci-chemistry/propka/Manifest
@@ -1,3 +1,3 @@
-DIST propka-3.1_p140511.tar.xz 151284 BLAKE2B 16b3528fb9ac224632f99c665c98b2349e49af92479a0b1ec411a08196724c14ba35199c69280d9f1c7e6126a347eede70e229ebd76392d887fe8bef7aad9283 SHA512 c2938af41ed386e267cd045b14e34779889b3c206016d747b68c400f2c8b37bd50cc3b74d055d931476065ac6817a2dd2cb87d68de9911adfff1c8e34a667fc3
-EBUILD propka-3.1_p140511.ebuild 809 BLAKE2B a16f0aecb2e419afff73e4162c82ad0ece517e767cc26d40ef9c2466be00e29bf2a62f0405c6a3f632415e2436c615fb7a625d9a7cf3b245655c640d0a892f35 SHA512 594f0b00d9ef1782e881e522b6ffdaf5941adde282901a616d9ce548a322812079914fe9b830a5eb498c74f878a4917bc0b1c8af9eccd77087f3ac3d62e72640
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
+DIST propka-3.2.0.tar.gz 73746 BLAKE2B f79e493d5a195b81dc5d11cc21b9ab16c8d1fa48f15f7e23e2b2936dfb8634fdb00c7838b8dbdb4a68726dab0f16e54522ad71d71b3273ac93c03a737ae06f04 SHA512 98f2240b28b33bab94cdbe9392062bb7f6b87e75b94c2af91e178f874a74d210601161ebc835c4d751b89d37b32348fdfb096e28cbf8e9237b3f472d3fb6b4fc
+EBUILD propka-3.2.0.ebuild 848 BLAKE2B 3f48d2b0f6b17916f2a9b9baf2d11b0d40beb24498190408320b2e11226aacc81a45a0600506905d03b8f99d33663d461e7eeaaf6f4d2bf5e66f724fde910125 SHA512 5b84c1a85d41570d6704bf87b04f465d50a7e8b4f43fc450c37c4bd558b188d85b56b3073c2bdc750ea8607a2946cb3210ba8bbed8e8bde83db19d0b3109d7a6
+MISC metadata.xml 392 BLAKE2B 0fdf293dc124a506ef9ee8e62b130819cc507b3c993d011914b6d691d823f00df82633e7499c3d22d18c3b927863ed654f924fb44731cad20178ede798bf9c52 SHA512 7aa53fe4d5b5b672748833e0e2afa7a6fe367289325ae6673db71d0d964b4e5d1df35b5ff7557e10e87599e8744d51892a8bff73f9ffe2cea57b6e11ad2d61fb
diff --git a/sci-chemistry/propka/metadata.xml b/sci-chemistry/propka/metadata.xml
index 8937bad0b175..6bfad85b4001 100644
--- a/sci-chemistry/propka/metadata.xml
+++ b/sci-chemistry/propka/metadata.xml
@@ -1,8 +1,12 @@
 <?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>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">propka</remote-id>
+		<remote-id type="github">jensengroup/propka</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-chemistry/propka/propka-3.1_p140511.ebuild b/sci-chemistry/propka/propka-3.2.0.ebuild
index 4b90e9aeab97..b5dadd1825d2 100644
--- a/sci-chemistry/propka/propka-3.1_p140511.ebuild
+++ b/sci-chemistry/propka/propka-3.2.0.ebuild
@@ -1,24 +1,28 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8} )
 
 inherit distutils-r1
 
 DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes"
-HOMEPAGE="http://propka.ki.ku.dk/"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+HOMEPAGE="https://github.com/jensengroup/propka"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 SLOT="0"
-LICENSE="all-rights-reserved"
+LICENSE="LGPL-2.1"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
+IUSE="test"
 
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
+RESTRICT="!test? ( test )"
 
-RESTRICT="mirror bindist"
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="test? (
+			${RDEPEND}
+			dev-python/pandas[${PYTHON_USEDEP}]
+)"
 
 python_prepare_all() {
 	sed -e "/exclude/s:scripts:\', \'Tests:g" \
@@ -32,6 +36,5 @@ python_test() {
 }
 
 python_install_all() {
-	dosym ${PN}31 /usr/bin/${PN}
 	distutils-r1_python_install_all
 }
diff --git a/sci-chemistry/pymol-plugins-msms/Manifest b/sci-chemistry/pymol-plugins-msms/Manifest
deleted file mode 100644
index ddc05c719169..000000000000
--- a/sci-chemistry/pymol-plugins-msms/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX 100415-msms.patch 1687 BLAKE2B ad00adc0dc028b44296d22dd0f807fc2c3b936e508e56049ff870b437ca0f86a7bc90aaa8dd3fc5dc792d3611541722c2d1cef2cb775a59ea80c464373ab643a SHA512 52410d467c314578cd22e777ae45a0012203fd21d2afa6ff329fa67db6d7ee2cb381558ce6aef48a1305a572f9218cf962ab1fc552ebe1873f94a4d6d2db1bcf
-DIST pymol-plugins-msms-100415.py 62320 BLAKE2B 2778221bd0138764b9f0b75202de8bc46d71005b26d0e23faba582d5f49fc0c3edca04d0ffcddf8f3be541a2142b739afe8a2904912a29d2443d9e6974f453a5 SHA512 924d89836f92d0be52d7534cbe6dc9338dac1c2263a51900ab62dbe96e4f54f565dbaa6bdf51236d8ea8e9042aa09283a117f5285561b252177a5a32f3876489
-EBUILD pymol-plugins-msms-100415-r1.ebuild 1045 BLAKE2B 63743b1514b174576970ef4b19d7a6d6546bf018c005bd9cbf93ad4f0898597cb372923732049a4a05f240fff751977609fc1cb889c48999e24e1fcc319bba50 SHA512 20799591eee520158f5872748c58b5280ec2fa0c0292fc1f069f823b20b6c4134a5b82ac57f884ecd2f8da3add00034ecc961463eada3e503a07246b823c084b
-MISC metadata.xml 705 BLAKE2B a756b9ab6e253b5f6fac0ff6ff637df4952389dfe9aa9391cb6ea0b926c06f9a361bd89340d5cd74047790cdd414232016c85ad9735a12d84f60bd0c8fb6d6eb SHA512 e33e7c380ff1f99f62fc75871dd3f3d0bc98bd3629a5e46c9dcae83ad039f88450d83b46379a6da88636795fb8e7c73c72480c4054a64dedd9c6bb0b501cf210
diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
deleted file mode 100644
index 0d26fb31c5f1..000000000000
--- a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
+++ /dev/null
@@ -1,33 +0,0 @@
- pymol-plugins-msms-100415.py |   18 ++++++++++--------
- 1 files changed, 10 insertions(+), 8 deletions(-)
-
-diff --git a/pymol-plugins-msms-100415.py b/pymol-plugins-msms-100415.py
-index 725934d..7ea00bf 100644
---- a/pymol-plugins-msms-100415.py
-+++ b/pymol-plugins-msms-100415.py
-@@ -99,15 +99,17 @@ class MSMSPlugin:
-         self.cleanup_saved_pymol_sel.set(True) # by default, clean up
- 
-         self.pdb_fn.set('')
--        if 'MSMS_BIN' in os.environ:
--            if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN']
--            self.msms_bin.set(os.environ['MSMS_BIN'])
--        else:
--            if VERBOSE: print 'MSMS_BIN not found in environmental variables.'
--            self.msms_bin.set('')
-+        self.msms_bin.set('GENTOOMSMS')
-+##        if 'MSMS_BIN' in os.environ:
-+##            if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN']
-+##            self.msms_bin.set(os.environ['MSMS_BIN'])
-+##        else:
-+##            if VERBOSE: print 'MSMS_BIN not found in environmental variables.'
-+##            self.msms_bin.set('')
- ##         self.pdb2xyzr_bin.set('')
--        if 'PDB2XYZRN' in os.environ:  self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN'])
--        else:                          self.pdb2xyzrn_bin.set('')
-+        self.pdb2xyzrn_bin.set('GENTOOXYZRN')
-+##        if 'PDB2XYZRN' in os.environ:  self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN'])
-+##        else:                          self.pdb2xyzrn_bin.set('')
-         self.tmp_dir.set('/tmp')
-         self.cleanup_msms_output = Tkinter.BooleanVar()
-         self.cleanup_msms_output.set(True) # by default, clean up msms output
diff --git a/sci-chemistry/pymol-plugins-msms/metadata.xml b/sci-chemistry/pymol-plugins-msms/metadata.xml
deleted file mode 100644
index 214696c4a1f7..000000000000
--- a/sci-chemistry/pymol-plugins-msms/metadata.xml
+++ /dev/null
@@ -1,17 +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>
-MSMS is an excellent tool for computing protein solvent excluded surface (SES).
-MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and 
-displaying its results in PyMOL. 
-
-1. Citation for this plugin: 
-    Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden.
-2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild
deleted file mode 100644
index 33c7dbf9be7d..000000000000
--- a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils python-r1
-
-DESCRIPTION="GUI for MSMS and displaying its results in PyMOL"
-HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html"
-SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD pymol"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	sci-chemistry/msms-bin
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-src_unpack() {
-	mkdir "${S}" || die
-	cp "${DISTDIR}"/${A} "${S}/" || die
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-msms.patch
-	sed \
-		-e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \
-		-e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \
-		-i ${A} || die
-}
-
-src_install() {
-	python_moduleinto pmg_tk/startup
-	python_foreach_impl python_domodule ${P}.py
-	python_foreach_impl python_optimize
-}