gentoo resync : 25.08.2020

author: V3n3RiX <venerix@redcorelinux.org> 2020-08-25 10:45:55 +0100
committer: V3n3RiX <venerix@redcorelinux.org> 2020-08-25 10:45:55 +0100
commit: 3cf7c3ef441822c889356fd1812ebf2944a59851 (patch)
tree: c513fe68548b40365c1c2ebfe35c58ad431cdd77 /sci-chemistry
parent: 05b8b0e0af1d72e51a3ee61522941bf7605cd01c (diff)
99 files changed, 614 insertions, 3724 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 08f6a519da1d..a1bf0e481100 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
deleted file mode 100644
index f00e4eaa7c6d..000000000000
--- a/sci-chemistry/apbs/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab57cfc8dd6e5cff358e27e2ac71b1e786bf9a4e3d96dfb4eea3596305beb5078746324769b582abf8a702a1c5 SHA512 70679623621fb56eeffc79166aa6fd35b5fa2fec828f6800a27b795a4e94c9eee673a7ba5f872c3266c9e78af8935d684fb5c4679b57da6a969189ce45e31468
-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 3033 BLAKE2B c5373211c86c086bd7fd1898ba2437496c4a9fb8971a7847625b5a5a438ae21b10a2c733d323c692b5a6f1a8c94c78b4630a326c7af84bb90b3200f8970a197c SHA512 7fba09a563be088193ab58b57c5f45288497f222058ab2189decc755f6a761ec15ceacf5fe5a8619224c75603e80db86d427c77f37ec4edb163f6d75d63747ef
-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
deleted file mode 100644
index 4ea1cfcd1fad..000000000000
--- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
+++ /dev/null
@@ -1,129 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_SINGLE_IMPL=true
-COMMIT="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
-inherit cmake-utils distutils-r1 flag-o-matic toolchain-funcs
-
-DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="https://www.poissonboltzmann.org/apbs/"
-#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
-SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${COMMIT}.zip -> ${P}.zip"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples fast +fetk iapbs mpi openmp python tools"
-
-REQUIRED_USE="
-	iapbs? ( fetk )
-	mpi? ( !python )
-	python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/maloc[mpi=]
-	sys-libs/readline
-	virtual/blas
-	fetk? (
-		sci-libs/amd
-		sci-libs/fetk
-		sci-libs/superlu
-		sci-libs/umfpack
-	)
-	mpi? ( virtual/mpi )
-	python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )
-"
-
-S="${WORKDIR}"/${PN}-pdb2pqr-${COMMIT}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-multilib.patch
-	"${FILESDIR}"/${P}-manip.patch
-	"${FILESDIR}"/${P}-python.patch
-)
-
-src_prepare() {
-	cmake-utils_src_prepare
-	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
-
-	sed \
-		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
-		-e "/TOOLS_PATH/d" \
-		-i CMakeLists.txt || die
-	use doc && MAKEOPTS+=" -j1"
-	if use python; then
-		unset PATCHES || die
-		cd tools/python || die
-		distutils-r1_src_prepare
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_SKIP_RPATH=ON
-		-DTOOLS_PATH="${ED%/}"/usr
-		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
-		-DLIBRARY_INSTALL_PATH=$(get_libdir)
-		-DFETK_PATH="${EPREFIX}"/usr/
-		-DBUILD_SHARED_LIBS=ON
-		-DENABLE_QUIT=OFF
-		-DBUILD_DOC=$(usex doc)
-		-DBUILD_TOOLS=$(usex tools)
-		-DENABLE_BEM=OFF
-# ENABLE_BEM: Boundary element method using TABIPB
-		-DENABLE_DEBUG=$(usex debug)
-		-DENABLE_VERBOSE_DEBUG=$(usex debug)
-		-DENABLE_FAST=$(usex fast)
-		-DENABLE_FETK=$(usex fetk)
-		-DENABLE_MPI=$(usex mpi)
-		-DENABLE_PYTHON=$(usex python)
-# ENABLE_TINKER: Enable TINKER support
-		-DENABLE_iAPBS=$(usex iapbs)
-# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
-	)
-	cmake-utils_src_configure
-	if use python; then
-		cd tools/python || die
-		distutils-r1_src_configure
-	fi
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use python; then
-		append-ldflags -L"${S}"/lib
-		cd tools/python || die
-		distutils-r1_src_compile
-	fi
-}
-
-src_test() {
-	python_setup
-	cd tests || die
-	LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die
-	grep -q 'FAILED' log && die "Tests failed"
-}
-
-src_install() {
-	dodir /usr/bin
-	cmake-utils_src_install
-	local i
-	for i in "${ED}"/usr/bin/*; do
-		if [[ ! "${i}" =~ .*apbs$ ]]; then
-			mv "${i}" "${i}-apbs" || die
-		fi
-	done
-	if use python; then
-		cd tools/python || die
-		distutils-r1_src_install
-		rm -rf "${ED}"/usr/share/apbs/tools/python || die
-	fi
-}
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
deleted file mode 100644
index 090a27d8a5a6..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
+++ /dev/null
@@ -1,50 +0,0 @@
- apbs/CMakeLists.txt             | 2 +-
- apbs/tools/CMakeLists.txt       | 4 ----
- apbs/tools/mesh/CMakeLists.txt  | 4 ++--
- 4 files changed, 5 insertions(+), 9 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 8917fc4..5152008 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF)
- 
- if(ENABLE_FETK)
-     message(STATUS "Checking for fetk components")
--    set(FETK_ENALBED 1)
-+    set(FETK_ENABLED 1)
- 
-     list(APPEND APBS_LIBS "-lstdc++")
-     list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-diff --git a/tools/manip/CMakeLists.txt b/tools/manip/CMakeLists.txt
-index 937dac7..5768cc5 100644
---- a/tools/manip/CMakeLists.txt
-+++ b/tools/manip/CMakeLists.txt
-@@ -4,9 +4,9 @@ set(LIBS "")
- list(APPEND LIBS "apbs_generic")
- list(APPEND LIBS "apbs_mg")
- list(APPEND LIBS "apbs_pmgc")
--if(FETK_ENALBED)
-+if(FETK_ENABLED)
-     list(APPEND LIBS "apbs_fem")
--endif(FETK_ENALBED)
-+endif(FETK_ENABLED)
- 
- message(STATUS "libraries: ${LIBS}")
- 
-diff --git a/tools/mesh/CMakeLists.txt b/tools/mesh/CMakeLists.txt
-index 1406377..6e6dfb9 100644
---- a/tools/mesh/CMakeLists.txt
-+++ b/tools/mesh/CMakeLists.txt
-@@ -4,9 +4,9 @@ set(LIBS "")
- list(APPEND LIBS "apbs_generic")
- list(APPEND LIBS "apbs_mg")
- list(APPEND LIBS "apbs_pmgc")
--if(FETK_ENALBED)
-+if(FETK_ENABLED)
-     list(APPEND LIBS "apbs_fem")
--endif(FETK_ENALBED)
-+endif(FETK_ENABLED)
- 
- message(STATUS "libraries: ${LIBS}")
- 
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
deleted file mode 100644
index a4e2d1761cf4..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
+++ /dev/null
@@ -1,92 +0,0 @@
- CMakeLists.txt          | 18 +++++++++---------
- src/CMakeLists.txt      |  1 -
- src/fem/CMakeLists.txt  |  2 +-
- src/pmgc/CMakeLists.txt |  2 +-
- 4 files changed, 11 insertions(+), 12 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 75ddbdd..c46f5e7 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib)
- set(TOOLS_PATH ${APBS_ROOT}/tools)
- set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
- 
--set(LIBRARY_INSTALL_PATH lib)
-+set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR})
- set(HEADER_INSTALL_PATH include/apbs)
- set(EXECUTABLE_INSTALL_PATH bin)
- set(SHARE_INSTALL_PATH share/apbs)
-@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
- list(APPEND CMAKE_INCLUDE_PATH /usr/include)
- list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
- 
--set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow")
--
- ################################################################################
- # Enable ansi pedantic compiling                                               #
- ################################################################################
-@@ -193,9 +191,11 @@ if(ENABLE_BEM)
-     else()
-         set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX})
-     endif()
--    
-+
-+    file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod)
-+
-     install(
--        FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod
-+        FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS}
-         DESTINATION ${LIBRARY_INSTALL_PATH}
-     )
-     set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME})
-@@ -210,7 +210,7 @@ if(ENABLE_BEM)
-     endif()
-     get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH)
-     find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH})
--    list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
-+    list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
- endif() # ENABLE_BEM
- 
- find_file( # this should be find path...
-@@ -228,7 +228,7 @@ endif()
- 
- 
- find_library(MALOC_LIBRARY  "maloc"
--    PATHS ${FETK_PATH}/lib ${CONTRIB_PATH}
-+    PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH}
-     DOC   "The fetk/maloc library"
- )
- if(MALOC_LIBRARY)
-@@ -296,9 +296,9 @@ if(ENABLE_FETK)
-     set(FETK_ENALBED 1)
- 
-     list(APPEND APBS_LIBS "-lstdc++")
--    list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-+    list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}")
-     list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack
---lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline )
-+-lblas -lvf2c -ltetgen -ltriangle -lreadline )
-     
-     SET(HAVE_MC_H YES)
- endif()
-diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt
-index 5a950c2..dc37f48 100644
---- a/src/fem/CMakeLists.txt
-+++ b/src/fem/CMakeLists.txt
-@@ -12,4 +12,4 @@ add_items(
-     vpee.h
- )
- 
--add_sublibrary(fem)
-+add_sublibrary(fem apbs_geoflow)
-diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt
-index 85b0c1e..97c95f0 100644
---- a/src/pmgc/CMakeLists.txt
-+++ b/src/pmgc/CMakeLists.txt
-@@ -42,4 +42,4 @@ add_items(
-     mgfasd.h
- )
- 
--add_sublibrary(pmgc)
-+add_sublibrary(pmgc apbs_geoflow)
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
deleted file mode 100644
index 5ad6613615f2..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
+++ /dev/null
@@ -1,122 +0,0 @@
- apbs/contrib/iapbs/src/apbs_driver.c |  6 +++---
- apbs/src/CMakeLists.txt              |  1 +
- apbs/tools/CMakeLists.txt            |  2 +-
- apbs/tools/python/CMakeLists.txt     |  1 +
- apbs/tools/python/apbslib.c          |  4 ++--
- apbs/tools/python/apbslib.i          |  4 ++--
- apbs/tools/python/setup.py           | 16 ++++++++++++++++
- 7 files changed, 26 insertions(+), 8 deletions(-)
-
-diff --git a/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c
-index c9e443b..e1ad67f 100644
---- a/contrib/iapbs/src/apbs_driver.c
-+++ b/contrib/iapbs/src/apbs_driver.c
-@@ -595,7 +595,7 @@ int apbsdrv_(
- 		printPBEPARM(pbeparm);
- 
- 		/* Refine mesh */
--		if (!preRefineFE(i, nosh, feparm, fetk)) {
-+		if (!preRefineFE(i, feparm, fetk)) {
- 		    Vnm_tprint( 2, "Error pre-refining mesh!\n");
- 		    VJMPERR1(0);
- 		}
-@@ -609,7 +609,7 @@ int apbsdrv_(
- 		Vnm_tprint(1, "  Beginning solve-estimate-refine cycle:\n");
- 		for (isolve=0; isolve<feparm->maxsolve; isolve++) {
- 		    Vnm_tprint(1, "    Solve #%d...\n", isolve);
--		    if (!solveFE(i, nosh, pbeparm, feparm, fetk)) {
-+		    if (!solveFE(i, pbeparm, feparm, fetk)) {
- 			Vnm_tprint(2, "ERROR SOLVING EQUATION!\n");
- 			VJMPERR1(0);
- 		    }
-@@ -622,7 +622,7 @@ int apbsdrv_(
- 		    /* We're not going to refine if we've hit the max number
- 		     * of solves */
- 		    if (isolve < (feparm->maxsolve)-1) {
--			if (!postRefineFE(i, nosh, feparm, fetk)) break;
-+			if (!postRefineFE(i, feparm, fetk)) break;
- 		    }
- 		    bytesTotal = Vmem_bytesTotal();
- 		    highWater = Vmem_highWaterTotal();
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 44d20fa..2577343 100644
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -68,6 +68,7 @@ configure_file(
- 
- if(ENABLE_iAPBS)
-     ADD_LIBRARY(apbs_routines routines.c routines.h)
-+    target_link_libraries(apbs_routines apbs_mg apbs_fem)
-     INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH})
-     INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH})
- endif()
-diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
-index 1982a3c..4acbe68 100644
---- a/tools/CMakeLists.txt
-+++ b/tools/CMakeLists.txt
-@@ -4,5 +4,5 @@ add_subdirectory(mesh)
- add_subdirectory(manip)
- 
- if(ENABLE_PYTHON)
--    add_subdirectory(manip)
-+    add_subdirectory(python)
- endif(ENABLE_PYTHON)
-diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
-new file mode 100644
-index 0000000..8b13789
---- /dev/null
-+++ b/tools/python/CMakeLists.txt
-@@ -0,0 +1 @@
-+
-diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
-index fef5cc8..feaaa2c 100644
---- a/tools/python/apbslib.c
-+++ b/tools/python/apbslib.c
-@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0};
- #include "maloc/maloc.h"
- #include "apbscfg.h" 
- #include "routines.h"
--#include "apbs/valist.h"
--#include "apbs/vatom.h"
-+#include "generic/valist.h"
-+#include "generic/vatom.h"
- 
- 
- #include <limits.h>
-diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i
-index 17fe521..44d05ea 100644
---- a/tools/python/apbslib.i
-+++ b/tools/python/apbslib.i
-@@ -15,8 +15,8 @@ Header files:
- #include "maloc/maloc.h"
- #include "apbscfg.h" 
- #include "routines.h"
--#include "apbs/valist.h"
--#include "apbs/vatom.h"
-+#include "generic/valist.h"
-+#include "generic/vatom.h"
- %} 
- 
- /* 
-diff --git a/tools/python/setup.py b/tools/python/setup.py
-new file mode 100644
-index 0000000..4a20198
---- /dev/null
-+++ b/tools/python/setup.py
-@@ -0,0 +1,16 @@
-+from distutils.core import setup, Extension
-+setup(name='apbs',
-+    version='1.4.1',
-+    package_dir={'apbs': '', 'vgrid': 'vgrid'},
-+    packages=['apbs', 'vgrid'],
-+    py_modules=['apbslib', 'main', 'noinput'],
-+    ext_modules=[
-+        Extension(
-+            '_apbslib',
-+            ['apbslib.i'],
-+            swig_opts=['-module', 'apbslib', '-I../include'],
-+            include_dirs=["../../src"],
-+            libraries=["apbs_generic", "apbs_routines"]
-+            )
-+        ],
-+    )
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
deleted file mode 100644
index a33a5468d19c..000000000000
--- a/sci-chemistry/apbs/metadata.xml
+++ /dev/null
@@ -1,25 +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="fetk">Include support for FeTK</flag>
-    <flag name="fast">APBS fast mode (experimental)</flag>
-    <flag name="iapbs">C/C++/Fortran interface</flag>
-    <flag name="tools">Install optional tools</flag>
-  </use>
-  <longdescription>
-APBS is a software package for modeling biomolecular solvation through solution 
-of the Poisson-Boltzmann equation (PBE), one of the most popular continuum 
-models for describing electrostatic interactions between molecular solutes in 
-salty, aqueous media. Continuum electrostatics plays an important role in 
-several areas of biomolecular simulation
-  </longdescription>
-  <upstream>
-    <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id>
-    <remote-id type="sourceforge">apbs</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/bkchem/Manifest b/sci-chemistry/bkchem/Manifest
deleted file mode 100644
index db9b3239f21c..000000000000
--- a/sci-chemistry/bkchem/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX bkchem-0.14.0_pre2-nolauncher.patch 2967 BLAKE2B 0953c3c969bb2955f13de81db84eef2f24d6a3999b1f9e8d3ed837cf04718386eb44a2141f55f1775339856698d1c5242564177e998203110776128b7bfde87b SHA512 dbd7b8eef583c3b64dfc1755a3b5eae5eb8ab222454936636147de64e021166e29f915655f1acf2d7252983bf4873dc8f2fb69ca58b56955ab1ce07e8ec82789
-DIST bkchem-0.14.0-pre2.tar.gz 998916 BLAKE2B 07c01abb31325c3721cc478438c1b34f156bc589a186eeedd62b6ac058f8ec64b1ea86a3c25bb6ab8045e0aaa838f10c5d16b68516fdea5607795b64fb4c39bb SHA512 7fc3bbd7bfe27bc91cf69a98c347a3fb92f4ea25b45a13debd0646a6b02d7a40c5729ae1b2a9ac33c1049d6b90e38355c3cd80e06660a0a2fcc5dafb3514ef20
-EBUILD bkchem-0.14.0_pre2-r2.ebuild 888 BLAKE2B 68092928e3c841dcb59ffa485c0ab356116f69d24ffdb58d0e11140e3eaff2034dcf79981f386f08e73dd6e074c2789c75ce08899dad3caa81f4005dc726ddb3 SHA512 f6505dde2dee31398bfc5be9999e8f47313ac7fa2f477ec0dc8f425d25ee2fb0f8998f350f42d511cb6dcc16545c3e8030e164b9c1046d25c31080dba2413bf2
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r2.ebuild b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r2.ebuild
deleted file mode 100644
index d6162080214b..000000000000
--- a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r2.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils versionator
-
-MY_P="${PN}-$(replace_version_separator 3 -)"
-
-DESCRIPTION="Chemical drawing program"
-HOMEPAGE="http://bkchem.zirael.org/"
-SRC_URI="http://bkchem.zirael.org/download/${MY_P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-LICENSE="GPL-2"
-IUSE="cairo"
-
-DEPEND="cairo? ( dev-python/pycairo[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-nolauncher.patch
-)
-
-python_install() {
-	distutils-r1_python_install "--strip=${ED}/_${EPYTHON}"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-	python_foreach_impl python_newscript ${PN}/${PN}.py ${PN}
-	make_desktop_entry bkchem BKChem "${EPREFIX}"/usr/share/${PN}/images/${PN}.png Science
-}
diff --git a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch
deleted file mode 100644
index 202c47a9c74f..000000000000
--- a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch
+++ /dev/null
@@ -1,106 +0,0 @@
- bkchem/bkchem.py | 24 +++++++++++++-----------
- setup.py         | 23 -----------------------
- 2 files changed, 13 insertions(+), 34 deletions(-)
-
-diff --git a/bkchem/bkchem.py b/bkchem/bkchem.py
-index b336b9c..bcb68b0 100644
---- a/bkchem/bkchem.py
-+++ b/bkchem/bkchem.py
-@@ -1,3 +1,4 @@
-+#!/usr/bin/env python2
- #--------------------------------------------------------------------------
- #     This file is part of BKChem - a chemical drawing program
- #     Copyright (C) 2002-2009 Beda Kosata <beda@zirael.org>
-@@ -18,18 +19,19 @@
- #--------------------------------------------------------------------------
- 
- 
--"""this is just a starter of the application"""
-+#"""this is just a starter of the application"""
- 
- ## support for loading from outside of bkchem dir
- 
--import os_support, sys
-+from bkchem import os_support
-+import sys
- sys.path.insert( 1, os_support.get_module_path())
- 
- 
- ### now starting for real
- 
--from singleton_store import Store
--import pref_manager
-+from bkchem.singleton_store import Store
-+from bkchem import pref_manager
- 
- # at first preference manager
- Store.pm = pref_manager.pref_manager(
-@@ -78,13 +80,13 @@ else:
- 
- 
- 
--import config
-+from bkchem import config
- 
- if not config.debug:
-   # checking of important modules availability
-   # import modules
--  import import_checker
--  import messages
-+  from bkchem import import_checker
-+  from bkchem import messages
- 
-   # we need sets from the 2.3 version
-   if not import_checker.python_version_ok:
-@@ -103,16 +105,16 @@ if not config.debug:
- 
-   
- #import Tkinter
--from main import BKChem
--from splash import Splash
--from singleton_store import Store
-+from bkchem.main import BKChem
-+from bkchem.splash import Splash
-+from bkchem.singleton_store import Store
- 
- myapp = BKChem()
- myapp.withdraw()
- 
- if __name__ == '__main__':
- 
--  import messages
-+  from bkchem import messages
-   enc = sys.getfilesystemencoding()
-   if not enc:
-     enc = sys.getdefaultencoding()
-diff --git a/setup.py b/setup.py
-index d4b2a21..2319216 100755
---- a/setup.py
-+++ b/setup.py
-@@ -91,26 +91,3 @@ if len( sys.argv) > 1 and sys.argv[1] == 'install' and '--help' not in sys.argv:
-   print "file %s created" % config_name
- 
- 
--  # the executable
--  if not os.path.isdir( bin_dir):
--    try:
--      os.mkdir( bin_dir)
--    except:
--      print "ERROR: could not create directory %s" % bin_dir
--      sys.exit( 201)      
--  exec_name = os.path.join( bin_dir, 'bkchem')
--  try:
--    file = open( exec_name, 'w')
--  except:
--    print "ERROR: couldn't open the file %s for write" %  exec_name
--    sys.exit( 201)
--  file.write( "#!/bin/sh\n")
--  file.write( 'python %s "$@"\n' % strip_path( os.path.join( py_dir, "bkchem", "bkchem.py")))
--  file.close()
--  print "file %s created" % exec_name
--  try:
--    os.chmod( os.path.join( bin_dir, 'bkchem'), 5+5*8+7*8*8)
--  except:
--    print "ERROR: failed to make %s executable" % exec_name
--    sys.exit( 201)
--  print "file %s made executable" % exec_name
diff --git a/sci-chemistry/bkchem/metadata.xml b/sci-chemistry/bkchem/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/bkchem/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/chemex/Manifest b/sci-chemistry/chemex/Manifest
index e0cd183bc7e8..446ce0b434b9 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,8 +1,6 @@
 AUX chemex-2018.10.2-tests-package.patch 418 BLAKE2B 7547e44f73bba8f48dda46e1867cff75a4343b26732b59b011470a7a8143bc0b17c7a7f87d97672239b679406fc54662d68f04e2b1548adddd723ecced954205 SHA512 5e3c58ab4ba271672381308177c462e0813a2e43ced602090b527d99be3e3f38f53f822cfe62ed8f841a16f4c04a933f4ed08d2e71c04777745298e3354bfb4a
-DIST chemex-0.6.1.tar.gz 1449216 BLAKE2B 6b7f7597b09cd43b9bec89b6359d1f650fdd7d4f3a373e706da80dafaf438417458f34af6bc378442b5b4a84cb8222103ebc8026c85583e8dece3fad0dc77204 SHA512 40f538ef9c162759c7a6863886da8d46746ac362fc19154f0a5f3dd8703f7fea7397c3f34092c86dbce486c452e0d3b09a76e4c11ae119834d7ca4912e7f3fdf
 DIST chemex-2018.10.2.tar.gz 546575 BLAKE2B c36ae3bc152459844633276ab286b6f750ed5b2538c4289ceb75de9a081ad74fe346a79357fd6fc2f8972722b3520473262c4d623e46d6a4b30395962164a51f SHA512 f8ed017c0881ea9188e150456827e2c6302bdfe546c8058bd0261e43d941fbd1ac9e6abf1621d82107a4f6bd4e9aa4bc70c46e42dc98eabf2dba45a4fa78f77e
 DIST chemex-2018.10.3.tar.gz 546696 BLAKE2B d283cfb94118686f1974780249641e0ea6f86cdb854c4a256897e361a300a94506813a5035ee2f300fca13263e8452b77e7a0817436cbd620ba16d801a541af7 SHA512 784bd03b354724d6aa52d663c6f661f865d4ef7ca345573bc8aae9ef63e5dbb3e65abba364de3ff441b78adfa588344c718809c5880b3fc70d8ed24be06a0826
-EBUILD chemex-0.6.1-r3.ebuild 1037 BLAKE2B 8d1d5ed8e4aea24247816a7db54644e421e720cc86e469abc62b3f0c61ad1b3178ecd6ab6318d0419f1e6d27796526f42c68f95574d65594c681142f64f71cd9 SHA512 5d0b85517336e7c47de49a0f5cc061c4eb46e6b6f02eff6d964e467cef78d19077635140d0150ad3cec698d5e98d1fae4abebcce834e1b31b485fe3b52efa75e
 EBUILD chemex-2018.10.2.ebuild 1155 BLAKE2B caf445596bf98c1b0fccaf1c894c23937fb2087d149254ff07bf1cd4d4c47acd4526f733f6c86739cb6206a73bf98b9b8f34fc074ed9d7d3f5ddb0551c34d8bc SHA512 c330644a70739efd68293d0cb9295bd3bae0635747fd402ab1b9ebd1d18e239f88eeadd95209e2cd660c0d1151e31c7d4bbfea9ed3493888360fcec57f287724
 EBUILD chemex-2018.10.3.ebuild 1051 BLAKE2B b021e1ccff297a6cee7aa940e45c64b8067c109ac2f9c2d03825ee9ce86a7f4d215111ad0c8a66877d13f224cd6bba7bb781caf86903d7dab27e6df3f8dce048 SHA512 7eb418b6d8443cada7146755fe011862d90e0c5d2085ed6b565dea1fba530bcff6464261e8e73eeeb5e09d354b84e41e717c40a81d84a18c7fa84fcd01a1a0e3
 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6
diff --git a/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild b/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild
deleted file mode 100644
index c6facbd71020..000000000000
--- a/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-DISTUTILS_SINGLE_IMPL="yes"
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
-HOMEPAGE="https://github.com/gbouvignies/chemex"
-SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	$(python_gen_cond_dep '
-		|| (
-			>=dev-python/matplotlib-python2-1.1[${PYTHON_MULTI_USEDEP}]
-			>=dev-python/matplotlib-1.1[${PYTHON_MULTI_USEDEP}]
-		)
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-		|| (
-			>=sci-libs/scipy-python2-0.11[${PYTHON_MULTI_USEDEP}]
-			>=sci-libs/scipy-0.11[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	# Fix quotes to detect the version properly
-	sed -i -e 's/matplotlib>=1.3.1/matplotlib>="1.3.1"/' setup.py || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/eden/Manifest b/sci-chemistry/eden/Manifest
deleted file mode 100644
index 18b6162cbafa..000000000000
--- a/sci-chemistry/eden/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX 5.3-makefile-fixes.patch 1647 BLAKE2B ead9023a9ae4c2a94a22de4ff5ef97f89b7602e914ebcc0a3295eb53a3cdf25639d9c8d74b14b9f75f2c5009812b8a23afd51432accfa2daec80484e4b5c4a49 SHA512 3ec4f8ba8d3b600b729bfb32cef3fb1f82a1f51a485ebab143e01052ea1487a78c3395c902079fe0e5d5c3df8a2a83b2ce4d37d823e1d89426087874ec47391d
-AUX eden-5.3-format-security.patch 3202 BLAKE2B a548dbb384d497a07806bcf9e25141d07a75a0381802b080eec02f14b6018e66c7d5b2a4c0caefc679d43736e15c4b00e460a82e3d40e65188a364d28469bde3 SHA512 01e100fe5481a73de2efa6652fe38c19337eae0dc13557ef0ad3e3a4f186becbfb8831aece0a619c08541e1a667e999c47b28438ec431f056c44f12849662c12
-AUX eden-5.3-impl-dec.patch 899 BLAKE2B 667a43677ff28192277ad3e259aa093ca03a05aa55bde0a175885823d2e48ddc64989c72e2c47884ff22c840addd87df9ea5925eeb6f20397be403f0e92cf44e SHA512 e89f1e0c028099e305a79befa558a86bc47d050c1e30394178999c7a1568bae9c3e525953bf152888690e0e1607dd72c522d2995f45b1eccfb9f7bf75e7866c2
-AUX makefile-fixes.patch 837 BLAKE2B fc20ba8c98e333b90bc3e028d572810fabe6305ec929a52aab5c4491b80fd370a604729ae29b22d078e872693fcab3e7d84f82524f29c09be74c8b41c128ec2f SHA512 818fe1d23fa940cb533afcb9e84bdc5c719651005136304ca66d368fc21cf4d7a1facb0a383c9689ab1658632cec30969322fdffccadae941a754900542237e7
-DIST eden_V5.3.tar.gz 1139981 BLAKE2B 237f054accbba72fcde3a43716915a8037412a26aee861839c4a6e404276126a3955e6e0a3c76078b2253658f3ab9bcf8ad628bba059421c5171d0394c41052b SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5
-EBUILD eden-5.3-r2.ebuild 1845 BLAKE2B c6b996398a511372ca4f8cec15d923056997747fc8c0bb37c1b88c57dc794d4aa304eca0bbfafc1d3d740d9f7534202da9113871c32f8d9a2adfe1f444971819 SHA512 5de7c7da62d7819ee74c8983ba5f222853995d9fae865a7a0802c7ee583f3406d6dbbdc335b3ad60c138d5642d6eb3df683c7a6f26ab91afd39707b63b1579a0
-MISC metadata.xml 383 BLAKE2B daa13ce13128bd1cd96fd95b063788d796bab9a455b7e552abfb76f2ce62369a3eaced99a7b53f248d99289774cfb8ff45b0848e759f3a2e6f89122f1e214141 SHA512 e23cc36f53622230ac9c70cb886cd9812e4bfefba8c0912059b3f072e063c235ba52cce893ea3b49ba05dda047097ba505c4ce5c53248d5acf720f16e123be84
diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild
deleted file mode 100644
index 8bf667224ba8..000000000000
--- a/sci-chemistry/eden/eden-5.3-r2.ebuild
+++ /dev/null
@@ -1,88 +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 multilib python-r1 toolchain-funcs
-
-MY_P="${PN}_V${PV}"
-
-DESCRIPTION="A crystallographic real-space electron-density refinement & optimization program"
-HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/"
-SRC_URI="mirror://gentoo/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="double-precision"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	sci-libs/fftw:2.1
-	sci-libs/gsl
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-SRC="${S}/source"
-
-pkg_setup() {
-	export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}"
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-makefile-fixes.patch \
-		"${FILESDIR}"/${P}-impl-dec.patch \
-		"${FILESDIR}"/${P}-format-security.patch
-
-	sed -i \
-		-e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \
-		-e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \
-		-e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \
-		-e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \
-		${SRC}/Makefile || die
-
-	if ! use double-precision; then
-		sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die
-		EDEN_EXE="s${PN}"
-	else
-		EDEN_EXE="d${PN}"
-	fi
-}
-
-src_compile() {
-	emake CC=$(tc-getCC) -C ${SRC}
-}
-
-src_install() {
-	emake -C ${SRC} install
-
-	python_foreach_impl python_newscript python/${PN}.py i${PN}
-	python_foreach_impl python_domodule python/FileListDialog.py
-
-	rm python/*py || die
-	insinto ${EDENHOME}/python
-	doins python/*
-
-	insinto ${EDENHOME}/help
-	doins help/*
-
-	insinto ${EDENHOME}/tools
-	doins tools/*
-
-	dodoc manual/UserManual.pdf
-
-	cat >> "${T}"/60${PN} <<- EOF
-	EDENHOME="${EDENHOME}"
-	EOF
-
-	doenvd "${T}"/60${PN}
-
-	dosym ${EDEN_EXE} /usr/bin/${PN}
-}
diff --git a/sci-chemistry/eden/files/5.3-makefile-fixes.patch b/sci-chemistry/eden/files/5.3-makefile-fixes.patch
deleted file mode 100644
index 632358341784..000000000000
--- a/sci-chemistry/eden/files/5.3-makefile-fixes.patch
+++ /dev/null
@@ -1,60 +0,0 @@
- source/Makefile |   17 ++++++++++-------
- 1 files changed, 10 insertions(+), 7 deletions(-)
-
-diff --git a/source/Makefile b/source/Makefile
-index 46d89cc..aa751c7 100644
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -78,8 +78,10 @@ CFLAGS		=   -Wall -pipe -g3
- #CFLAGS		=   -Wall -pipe -marchi686 -pedantic  -gdwarf-2 -g3
- #CFLAGS		=   -Wall -O3 -march=i686 
- ifneq ($(FFTW),/usr/local)
-+ifneq ($(FFTW),/usr)
- CFLAGS		+= -I$(INC)
- endif
-+endif
- 
- #			NOTE:
- # DOUBLESWITCH = ON	for double precision;
-@@ -91,15 +93,15 @@ endif
- DOUBLESWITCH 	= ON
- 
- ifeq ($(DOUBLESWITCH),ON)
--LDFLAGS	 = -L$(LIB) -ldfftw -lm  
-+LIBS	 = -L$(LIB) -ldfftw -lm  
- CFLAGS	+= -DDOUBLE 
- TARGET	 = deden
- else
--LDFLAGS	 = -L$(LIB) -lsfftw -lm  
-+LIBS	 = -L$(LIB) -lsfftw -lm  
- TARGET	 = seden
- endif
- 
--LDFLAGS += -g -lgsl -lgslcblas 
-+LIBS += -lgsl -lgslcblas 
- 
- # GSL_PREFIX:= /sw/lib
- # LDFLAGS += -l$(GSL_PREFIX)/libgsl.a -l$(GSL_PREFIX)/libgslcblas.a 
-@@ -120,17 +122,18 @@ OBJ	= 	addmaps.o   apodfc.o   apodfo.o     back.o     cadhkl.o  \
- all:		eden	fbyteswap 
- 
- eden:  		eden.o   $(OBJ)
--		$(CC)  $^ $(LDFLAGS) -o $@
-+		$(CC)  $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- fbyteswap:	fbyteswap.c		
--		$(CC) -o $@ $^
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- install:	all
-+		mkdir -p $(BIN)
- 		mv fbyteswap $(BIN)
- 		mv eden $(BIN)/$(TARGET)
- 		chmod 751 $(BIN)/$(TARGET)
--		chmod +x mkeden.csh
--		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
-+#		chmod +x mkeden.csh
-+#		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
- 
- dist:		clean
- 		cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar
diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch
deleted file mode 100644
index 04b5ecfddebb..000000000000
--- a/sci-chemistry/eden/files/eden-5.3-format-security.patch
+++ /dev/null
@@ -1,96 +0,0 @@
- source/back.c     | 2 +-
- source/concosts.c | 4 ++--
- source/count.c    | 4 ++--
- source/eden.c     | 2 +-
- source/util.c     | 4 ++--
- 5 files changed, 8 insertions(+), 8 deletions(-)
-
-diff --git a/source/back.c b/source/back.c
-index fd517b9..185a02b 100644
---- a/source/back.c
-+++ b/source/back.c
-@@ -112,7 +112,7 @@ void	back_main(int argc, char *argv[])
-           ballpark(caller) ;
- 
-      if (argc > optind+2)
--	  sprintf(sf_filename, argv[optind+2]) ;
-+	  sprintf(sf_filename, "%s", argv[optind+2]) ;
- 
-   /*********************************************
-   Pull off prefix defining whereabouts of input 
-diff --git a/source/concosts.c b/source/concosts.c
-index d62d2e3..590f073 100644
---- a/source/concosts.c
-+++ b/source/concosts.c
-@@ -452,7 +452,7 @@ void	prepare_singlets(char *filename)
-                       sprintf(message, 
- 		      "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", 
-                       s, p, n, phase, *(checks+n), phase-*(checks+n)) ;
--                      fprintf(fp_log, message) ;
-+                      fprintf(fp_log, "%s", message) ;
-                  }
-               } 
- 		/***********************************************
-@@ -556,7 +556,7 @@ void	prepare_triplets(char *filename)
- 		 sprintf(message, 
- "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n",
- 		   newh, newk, newl, t_h[q], t_k[q], t_l[q]) ;
--		 fprintf(fp_log, message) ;
-+		 fprintf(fp_log, "%s", message) ;
- 		 legal_triplet = FALSE ;
-               }
-            }
-diff --git a/source/count.c b/source/count.c
-index c3bc390..ca13008 100644
---- a/source/count.c
-+++ b/source/count.c
-@@ -460,12 +460,12 @@ void	print_el_count(char *filename,
-      }
- 
-      sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ;
--     fprintf(fp, message) ;
-+     fprintf(fp, "%s", message) ;
-      printTwice(message) ;
- 
-      sprintf(message, "Count of all remaining electrons: %g %g %g\n", 
-      remainder0*volvox, remainder1*volvox, remainder2*volvox) ;
--     fprintf(fp, message) ;
-+     fprintf(fp, "%s", message) ;
-      printTwice(message) ;
- 
-      fclose(fp) ;
-diff --git a/source/eden.c b/source/eden.c
-index dea3246..5a9b389 100644
---- a/source/eden.c
-+++ b/source/eden.c
-@@ -319,7 +319,7 @@ int	main(int argc, char *argv[])
- 
-      get_unique_logname() ;
- 
--     sprintf(command_line, argv[0]) ;
-+     sprintf(command_line, "%s", argv[0]) ;
- 
-      for (k = 1; k < argc; k++) { 
-          strcat(command_line, " ") ;
-diff --git a/source/util.c b/source/util.c
-index 6fff179..41c624c 100644
---- a/source/util.c
-+++ b/source/util.c
-@@ -266,7 +266,7 @@ void	printTwice(char *mess)	/* send info to terminal (stdout) and to log */
-  
- void	prompt(char *mess)	/* Send message to user, await reply */
- {
--    fprintf(stdout, mess) ;
-+    fprintf(stdout, "%s", mess) ;
- 
-     while (fgets(terminp, MAXSTRING, stdin) != NULL)  {
- 	if ((int)strlen(terminp) > 0) 
-@@ -722,7 +722,7 @@ void	start_record()
-      int	k ;
- 
-      rec_length = k = sprintf(record, "\n") ;
--     rec_length += sprintf(record+k, timestamp()) ;
-+     rec_length += sprintf(record+k, "%s", timestamp()) ;
-      k = rec_length ;
- 
-      if ((cwd = getcwd(NULL, 120)) == NULL) 
diff --git a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch
deleted file mode 100644
index af67508d090e..000000000000
--- a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- source/fbyteswap.c |    1 +
- source/util.c      |    1 +
- 2 files changed, 2 insertions(+), 0 deletions(-)
-
-diff --git a/source/fbyteswap.c b/source/fbyteswap.c
-index 83015b9..c9033c3 100644
---- a/source/fbyteswap.c
-+++ b/source/fbyteswap.c
-@@ -39,6 +39,7 @@ and shall not be used for advertising or product endorsement purposes.
- 
- #include <stdio.h>
- #include <fcntl.h>
-+#include <unistd.h>
- #include <sys/stat.h>
- #include <sys/types.h>
- void byteswap();
-diff --git a/source/util.c b/source/util.c
-index 6fff179..ca7a957 100644
---- a/source/util.c
-+++ b/source/util.c
-@@ -89,6 +89,7 @@ and shall not be used for advertising or product endorsement purposes.
- 
- *******************************************************************************/
- #include  <sys/time.h>	/* ... for picking up date & time	*/
-+#include <time.h>
- #include  <signal.h>	/* ... for capturing kill		*/
- #include  "util.h"
- 
diff --git a/sci-chemistry/eden/files/makefile-fixes.patch b/sci-chemistry/eden/files/makefile-fixes.patch
deleted file mode 100644
index 4cfff3f515df..000000000000
--- a/sci-chemistry/eden/files/makefile-fixes.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff -ur eden.orig/source/Makefile eden/source/Makefile
---- eden.orig/source/Makefile	2004-10-18 10:40:03.000000000 -0700
-+++ eden/source/Makefile	2005-12-15 22:32:45.000000000 -0800
-@@ -78,8 +78,10 @@
- #CFLAGS		=   -Wall -pipe -marchi686 -pedantic  -gdwarf-2 -g3
- #CFLAGS		=   -Wall -O3 -march=i686 
- ifneq ($(FFTW),/usr/local)
-+ifneq ($(FFTW),/usr)
- CFLAGS		+= -I$(INC)
- endif
-+endif
- 
- #			NOTE:
- # DOUBLESWITCH = ON	for double precision;
-@@ -129,8 +131,8 @@
- 		mv fbyteswap $(BIN)
- 		mv eden $(BIN)/$(TARGET)
- 		chmod 751 $(BIN)/$(TARGET)
--		chmod +x mkeden.csh
--		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
-+#		chmod +x mkeden.csh
-+#		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
- 
- dist:		clean
- 		cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar
diff --git a/sci-chemistry/eden/metadata.xml b/sci-chemistry/eden/metadata.xml
deleted file mode 100644
index 6113635247f3..000000000000
--- a/sci-chemistry/eden/metadata.xml
+++ /dev/null
@@ -1,12 +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="double-precision">More precise calculations at the expense of
-    speed</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 54979d004776..015a4eab9de9 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,6 +4,7 @@ DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b
 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
 DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
 DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c
+DIST gromacs-2020.3.tar.gz 29143950 BLAKE2B ea88fcacc3958f1123c1fe4852f7160a04e4daff15dd2eb87c23197bff2e6379f396df0747b078dc86e7bb909ecbb4b6d98530a34234c989a636dbdb2327562d SHA512 8dbd13f8c6dd9ac337e0bea683aeff38010ee9b4ef438de230beb76e5a54884a5c1eda72f20294b7920758978e247900ac3db32b95c7452350fc1f5ef0a4bcc8
 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
 DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605
 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
@@ -12,11 +13,13 @@ DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f
 DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
 DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8
 DIST regressiontests-2020.2.tar.gz 48539492 BLAKE2B 08222ec18e70f551194fc0a060facda394c0d9999e162dace06029aa5f36e7237aeb2468a80d1198257a45fb076f8f633a7279a85976484900bf4154176aa070 SHA512 3066d92a59dafade78807612681d82a7b8a0bd9b74fa7e8784063a908418c55b4427482dc7feb261ff6981fabb2d64a800d3e90ed647ab45e201f4847347bac7
-EBUILD gromacs-2018.8.ebuild 7012 BLAKE2B c54d0bce4d4ffca3365f6f574313ebdf9b0a7e71a8bd7e10c3ffe10f7bddce9854cc4707d1c9f0611e3a0d353fe4ec215d3ee385459748d5266d98f1b5e861a6 SHA512 1de3a0dbba1c03730f7709013515d2282951e0e87e962dce8c46f227bf0e9ddc2034b28ac797c3c2feb81a1c27f1fa10136ea60c861d266ca708e3aac687b8df
-EBUILD gromacs-2019.5-r1.ebuild 7334 BLAKE2B 1f53f81589e531a292a8bf191064b446ea7b021c73df2645e1f8a2d793d7b7020f6908c7b90066f3e328eb78ed42eed91fb40ec98a08254c7538b29c31f9bdf3 SHA512 f57ebd19ee8f5653b7ec80e6981fced22014b8dc7f54be0a438ffe5db0de94f8b1db13b8698cce616544d04b65672465402a4057ee47924478a4d5dd59901c0f
-EBUILD gromacs-2019.6.ebuild 7337 BLAKE2B c12b7eb0e5a53c8b215fc1862b229c75d723865340d0eabd5b660feb613a9dec1482632a975a3f3689c90ada28096a04b819ebd8616f1de35fb1224b92ef85ea SHA512 4bee46c3a389251149573e391214cf3a8a394cca0ccd1c29f5bf827106580007f7e6dbad319a39fe637db5d7a96f4c9883bb81f0975dc214f8af89f0f1d50930
-EBUILD gromacs-2020.1-r1.ebuild 9916 BLAKE2B 1bface90982f6c78c024e92d9741b97a4658f037e73b9126a9cca33ee0169baec055ecbe21d307e3b79488241cd98b2d0a3df644fb330ffdc2819d360ddc981c SHA512 a41b93992725a08eea05125c4685b0c726fa0f1e284879d5ae6c20327ff19d681c135f736829fd546d122dd50587f9fff387220dc685f5989ceca1b45b2c4eba
-EBUILD gromacs-2020.2.ebuild 9916 BLAKE2B 1bface90982f6c78c024e92d9741b97a4658f037e73b9126a9cca33ee0169baec055ecbe21d307e3b79488241cd98b2d0a3df644fb330ffdc2819d360ddc981c SHA512 a41b93992725a08eea05125c4685b0c726fa0f1e284879d5ae6c20327ff19d681c135f736829fd546d122dd50587f9fff387220dc685f5989ceca1b45b2c4eba
-EBUILD gromacs-2020.9999.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
-EBUILD gromacs-9999.ebuild 9827 BLAKE2B 20a6e2e5b0d70a1c0ada0cafcb12eb170b99ebb37778f467dda1800cabb05d6a34d0dfef9bfaa04b5e6f3b781ed2e5eb97a1f61044e54e526559a9f9093be648 SHA512 19c73f34eda0ed83e58b67c7feb87e6540fb441806c27ae3b6b7d0e59c33cd220d87873fa3b3b9b5c72e8f9f73b778d41d69f21a3fded51a030d1ac6854bc2a2
+DIST regressiontests-2020.3.tar.gz 48541439 BLAKE2B c8b3840b76b7974e5efd518d02da2be3c8e685a420462962cf4ffb7b234bd5ffec0fb83adc962e4ce4716098667e1431f7bc46911bf5400f369881c697c1d0cb SHA512 84848210b2c4c0387c3f347237d58a114bd28c2d248f359e40a4a5b3557fca7763c431d1e03f167dcf22296a48dd47413a644238d72edc1414e3f830dd732416
+EBUILD gromacs-2018.8.ebuild 6958 BLAKE2B 17452127d480265b57b435d84de5860729860e72a47f89ced75cfa18e9efc1b6dc478785545a86313e9fc6a93647d1ae9f4b78167654acc0a95288215df3d35a SHA512 a2c23b418af81162c22b06d4b5fe2114d09288f314dacb6ca7a5b0fecd50a3bf0069237ec036da8c420b133daaf1eef43d40d1b13c525df8f362f9a0a7b9ec51
+EBUILD gromacs-2019.5-r1.ebuild 7280 BLAKE2B 9d26c304b6e67d00a69d6919daf2bde5b542c9e1c5e1e2f44a2fb1350986a1175737bc9f7325c71cca8479a3e90fca63a0debb01eff5bb94113533a0be364839 SHA512 c991901aed3149fa7872f02647aaff424bd93508157c0f734cc0b14b9f81fe55ff996d8a5a7fb7ba1514cf737047cfbd389a54804d2b5659d728df6f004a847e
+EBUILD gromacs-2019.6.ebuild 7283 BLAKE2B 00055c4ba5cf660237d73232aa7a76857bc141eaa79fdbf81985d337c134123ad7fd92b69d017425ec3f11eb2f367a25e8c4168b948f1092b2a1e538cb991886 SHA512 c307ea57a5b7c468ddd454ee97743643363121757c50cda948398090fa9368dc7b52255e6c3a261565894edd77f91d62c221841c1aca3644691c7fb9a0a8d5ef
+EBUILD gromacs-2020.1-r1.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
+EBUILD gromacs-2020.2.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
+EBUILD gromacs-2020.3.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
+EBUILD gromacs-2020.9999.ebuild 9759 BLAKE2B bf1d5b859c466f05b4909113c90faaed916512809ec9563c474461906d49261baeca9b8f7e5bdf85a3fffd32b1b84b4ec47d4523105bba3ed32ce73491d6e7d1 SHA512 cac942e6effce1c0c7ff99ac56c88d9422a89b1b275d3555c5a15a00640c253bd3a98301b9509daf14b3e4d3f1577a8fe6647aab10bf645645ccf35b57470208
+EBUILD gromacs-9999.ebuild 9755 BLAKE2B ee04718fea528c500f797f0ee1ebfb2307772ff5ab4cfc3293f3bf6f93a25ee6155c0b888a4d25371c6a9c4fb022d9e79da9a9df85d7fc82a97442755314ff28 SHA512 5338d8d45908e0b618c21908162e16fff4fba74d671a756229f1f05bce9fd578e923d6289609344cd4a28a78995e2609908de0598cc5d60d45a029ac97b7bba4
 MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77
diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
index feaa75c10bff..f124a0eac166 100644
--- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
@@ -68,7 +68,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -158,7 +158,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -176,7 +176,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -186,31 +186,31 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use doc; then
 			newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
index d5258ab6f232..7ea93b91af9f 100644
--- a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
@@ -71,7 +71,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -170,7 +170,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -189,7 +189,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -199,31 +199,31 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use doc; then
 			newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
index e8541e9964ed..85004d2644a2 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
@@ -71,7 +71,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -170,7 +170,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -189,7 +189,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -199,31 +199,31 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use doc; then
 			newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
index 9d71d0f73354..ba456196edd8 100644
--- a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7,8} )
 
 DISTUTILS_SINGLE_IMPL=1
 
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -244,7 +244,7 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -263,7 +263,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -273,46 +273,46 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile	python_packaging/all
+				cmake_src_compile	python_packaging/all
 			BUILD_DIR="${WORKDIR}/${P}" \
 				distutils-r1_src_compile
 		fi
 		# not 100% necessary for rel ebuilds as available from website
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
+				cmake_src_compile manual
 		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake-utils_src_install	python_packaging/install
+				cmake_src_install	python_packaging/install
 		fi
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2020.2.ebuild b/sci-chemistry/gromacs/gromacs-2020.2.ebuild
index 9d71d0f73354..ba456196edd8 100644
--- a/sci-chemistry/gromacs/gromacs-2020.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.2.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7,8} )
 
 DISTUTILS_SINGLE_IMPL=1
 
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -244,7 +244,7 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -263,7 +263,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -273,46 +273,46 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile	python_packaging/all
+				cmake_src_compile	python_packaging/all
 			BUILD_DIR="${WORKDIR}/${P}" \
 				distutils-r1_src_compile
 		fi
 		# not 100% necessary for rel ebuilds as available from website
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
+				cmake_src_compile manual
 		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake-utils_src_install	python_packaging/install
+				cmake_src_install	python_packaging/install
 		fi
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2020.3.ebuild b/sci-chemistry/gromacs/gromacs-2020.3.ebuild
new file mode 100644
index 000000000000..ba456196edd8
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2020.3.ebuild
@@ -0,0 +1,341 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{6,7,8} )
+
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		https://github.com/gromacs/gromacs.git
+		https://repo.or.cz/r/gromacs.git"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+	inherit git-r3
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+	opencl? ( virtual/opencl )
+	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
+	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	${PYTHON_DEPS}
+	!sci-chemistry/gmxapi
+	"
+BDEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
+		media-gfx/mscgen
+		media-gfx/graphviz
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	cuda? ( !opencl )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	xdg_environment_reset #591952
+
+	cmake_src_prepare
+
+	use cuda && cuda_src_prepare
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
+
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+
+	# try to create policy for imagemagik
+	mkdir -p ${HOME}/.config/ImageMagick
+	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+	<?xml version="1.0" encoding="UTF-8"?>
+	<!DOCTYPE policymap [
+	<!ELEMENT policymap (policy)+>
+	!ATTLIST policymap xmlns CDATA #FIXED ''>
+	<!ELEMENT policy EMPTY>
+	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+	]>
+	<policymap>
+		<policy domain="coder" rights="read | write" pattern="PS" />
+		<policy domain="coder" rights="read | write" pattern="PS2" />
+		<policy domain="coder" rights="read | write" pattern="PS3" />
+		<policy domain="coder" rights="read | write" pattern="EPS" />
+		<policy domain="coder" rights="read | write" pattern="PDF" />
+		<policy domain="coder" rights="read | write" pattern="XPS" />
+	</policymap>
+	EOF
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		local acce="None"
+		use cpu_flags_x86_sse2 && acce="SSE2"
+		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+		use cpu_flags_x86_avx && acce="AVX_256"
+		use cpu_flags_x86_avx2 && acce="AVX2_256"
+	else
+		strip-flags
+	fi
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	if use lmfit; then
+		local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
+	else
+		local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${x} = "double" ]] && suffix="_d"
+		local p
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			cuda=( "-DGMX_GPU=ON" )
+		local opencl=( "-DGMX_USE_OPENCL=OFF" )
+		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+			"${opencl[@]}"
+			"${cuda[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			-DGMX_PYTHON_PACKAGE=$(usex python)
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON
+			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile	python_packaging/all
+			BUILD_DIR="${WORKDIR}/${P}" \
+				distutils-r1_src_compile
+		fi
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile manual
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake_src_compile
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_make check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake_src_install
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}" \
+				cmake_src_install	python_packaging/install
+		fi
+		if use doc; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake_src_install
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${ED}"/usr/bin/GMXRC* || die
+	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
+		local n=${x##*/gmx-completion-}
+		n="${n%.bash}"
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+		newbashcomp "${T}"/"${n}" "${n}"
+	done
+	rm "${ED}"/usr/bin/gmx-completion*.bash || die
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "https://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index a2dcda755c8b..92600477ee91 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7} )
 
 DISTUTILS_SINGLE_IMPL=1
 
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -240,7 +240,7 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -259,7 +259,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -269,46 +269,46 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile	python_packaging/all
+				cmake_src_compile	python_packaging/all
 			BUILD_DIR="${WORKDIR}/${P}" \
 				distutils-r1_src_compile
 		fi
 		# not 100% necessary for rel ebuilds as available from website
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
+				cmake_src_compile manual
 		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake-utils_src_install	python_packaging/install
+				cmake_src_install	python_packaging/install
 		fi
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 11c545362c66..203a0f716f57 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7} )
 
 DISTUTILS_SINGLE_IMPL=1
 
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
 
 	xdg_environment_reset #591952
 
-	cmake-utils_src_prepare
+	cmake_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -240,7 +240,7 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
@@ -259,7 +259,7 @@ src_configure() {
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
@@ -269,46 +269,46 @@ src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
+			cmake_src_compile
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile	python_packaging/all
+				cmake_src_compile	python_packaging/all
 			BUILD_DIR="${WORKDIR}/${P}" \
 				distutils-r1_src_compile
 		fi
 		# not 100% necessary for rel ebuilds as available from website
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
+				cmake_src_compile manual
 		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
+			cmake_src_compile
 	done
 }
 
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
+			cmake_src_make check
 	done
 }
 
 src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
+			cmake_src_install
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake-utils_src_install	python_packaging/install
+				cmake_src_install	python_packaging/install
 		fi
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
+			cmake_src_install
 	done
 
 	if use tng; then
diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest
index 5ded7d1cda4a..cc936a87477e 100644
--- a/sci-chemistry/openbabel-python/Manifest
+++ b/sci-chemistry/openbabel-python/Manifest
@@ -1,4 +1,4 @@
 AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 637 BLAKE2B e913c1d1bc93fd8443faa20fc9d7b28b89b276f7561d4208a42abd379111d19ff26179b2fbdca946a9df38e42d31f32b68423be073611e79615dcd6ae20d8f0d SHA512 0108f7bc83e046e29b2ae0b822787f58c6930de775dc94df89ba741f41cb3873a3bd2b677c11ccad4c32172e486b8331c25492127c83e4ab8d066bd129aa5538
 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
-EBUILD openbabel-python-2.4.1-r1.ebuild 2166 BLAKE2B 45ed425ebe47014c04d8f71661d0e29259d7b3d598695de0c7f0c7027b1488e70855ab4acb74b3d901f706bd58a8cb43ef7f4b1d5f927f8a16220f0cf7ffba41 SHA512 03bfaad27c45362252ebd719d7b526e977b1330e02251e8c82e0568c9f8a8759a5796dd2a22f22419d0f3465fe325d45c4f41a40b9a85edb14cd0a8ad4bed1b7
+EBUILD openbabel-python-2.4.1-r1.ebuild 2156 BLAKE2B 5d6def900a348c7d090e2caa177ca7b4a5c2dc08ed6e77bec76801b36d3bdc092a0fa31bc4ae18d4152c6391feaf35e8856cda50e4889d5c0643e25528fd53ed SHA512 df4c7d34a91ab093a39d99b342b36c9c9984e8bc9e7e18f31641873da86baef4f1141bef20cb2493287bd38e1099b48b6b212fae2e0d21eaf5b04a30943cf281
 MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e
diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild
index 270018c23410..fe6933bd9868 100644
--- a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild
+++ b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_6 )
+PYTHON_COMPAT=( python3_6 )
 
 inherit cmake-utils python-r1
 
diff --git a/sci-chemistry/p3d/Manifest b/sci-chemistry/p3d/Manifest
deleted file mode 100644
index 8edb957e6d33..000000000000
--- a/sci-chemistry/p3d/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-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 521 BLAKE2B 4d493463768caa477059286c3d14584d5ba779e7b88dd98125db6e96c0ef658cc3ca4aeae67103f9366a80e055dcfdfed1764d1281777b3e2922916c30a21002 SHA512 0484f573edd3b3df049d884f387e9d062bc6590a228ec70c88c99c70e72f24d94d29d53c5f5cfd0a71e1669590c3c1810eda4a5e9a62c218e1df808c863d2d9a
-MISC metadata.xml 1151 BLAKE2B db264a2a0e24aedec15301bb5a6bfe6b83d815e5dc146ccdbcc427d97c0b78ba98050bbc06d230988e1643be858a56469271b92b118bea373a7e284a54f18fb0 SHA512 322b35766a1e71129165a8559fe3caac109dfa85be2b0fa630fa249b28cf603e86f152c47835020ff1f5f0d12b7cbbff8758c08248522a7d2b1188812ec99722
diff --git a/sci-chemistry/p3d/metadata.xml b/sci-chemistry/p3d/metadata.xml
deleted file mode 100644
index bd505aa96a4e..000000000000
--- a/sci-chemistry/p3d/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>
-	<longdescription>
-p3d was developed in order to offer a Python module that is powerful and fast,
-yet intuitive to use. The simplicity of p3d is due to the usage of object 
-oriented programming (i.e. atoms are treated as vectors), the implementation 
-of a query parser that translates queries readable by humans into a combination
-of algebra set operations the fact that no additional Python packages are 
-necessary. The speed is due to the usage of a binary space partitioning (BSP)
-tree which allows very fast queries in 3D (Henry et al. 1980). The additional 
-synergy is obtained by the flexible combination of both speed and complexity in
-the queries to the structural data. The combination of these factors makes p3d
-the optimal module to rapidly develop new and powerful bioinformatic tools that
-follow the Python philosophy of making the source code readable.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild b/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild
deleted file mode 100644
index 04d5f49cf7b2..000000000000
--- a/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 vcs-snapshot versionator
-
-MY_P="${PN}-$(replace_version_separator 3 -)"
-GITHUB_ID="gb8b9a75"
-
-DESCRIPTION="Python module for structural bioinformatics"
-HOMEPAGE="http://p3d.fufezan.net/"
-SRC_URI="https://nodeload.github.com/fu/${PN}/tarball/${PV} -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-3"
-IUSE="examples"
-
-src_install() {
-	distutils-r1_src_install
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r pdbs exampleScripts
-	fi
-}
diff --git a/sci-chemistry/p3d/p3d-9999.ebuild b/sci-chemistry/p3d/p3d-9999.ebuild
deleted file mode 100644
index 5dd3fdc9a942..000000000000
--- a/sci-chemistry/p3d/p3d-9999.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3 versionator
-
-DESCRIPTION="Python module for structural bioinformatics"
-HOMEPAGE="http://p3d.fufezan.net/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/fu/p3d.git"
-
-SLOT="0"
-KEYWORDS=""
-LICENSE="GPL-3"
-IUSE="examples"
-
-src_install() {
-	distutils-r1_src_install
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r pdbs exampleScripts
-	fi
-}
diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest
deleted file mode 100644
index 351e29ce5d76..000000000000
--- a/sci-chemistry/pdb-tools/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST pdbTools_0.2.1.tar.gz 103835 BLAKE2B ad4b5c8d6eb000c79a6d2797519b99027350fa34f6d543f6302f1a9edbe3497afe1a7b5c5c0e7243081cc709d9f1c37da5fc31605a0a225413851ce7288f64c9 SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724
-EBUILD pdb-tools-0.2.1-r1.ebuild 1661 BLAKE2B c4e0dde9acb97813824bb8992c747fd850c47e6cd346d921e37cd39a4e1c0e18ee883ecdd90edec1eb8aa5e81afa90ad3d5719b4038a652244ed678e20a267fc SHA512 744eaff99bf693c803b20546a6a9d4b8a1083d7278fa363ba50ae709d6ab1c6e9bd3100ad992b3bce419ef5dd16036e6397465fb6b2a413764e73f10d2818721
-EBUILD pdb-tools-0.2.1-r2.ebuild 1734 BLAKE2B f1b28c6b9c60c5573c9bf6ab092c32f3e4aa6df7bc484dca74aeda8c12f78dafcd94db9f1976932264be4be24c01f29a38750cfe1081058fe0e964345bfe9565 SHA512 dd9a534af4c275a3fba95ce88e4a9e22e5f182c63210717fb66ab62afd67e179541e58d6d1a3af03a550f5718166f9d0974f7d2f47b401adf670b27376f73cf8
-MISC metadata.xml 413 BLAKE2B f3fc199d95acf174f2d5cf9e0ea9c645e3b49e7241122bde730db90a095a0ef0f763dd3dcbcd5f14c1da520630c58bf9e7fe40828d267cb5a2ad5c796b72993e SHA512 74abf290517514aa17fadf8271d2af124fef766b473199502959a662d3bf7a8fed59746b43b3084b83bc14f8d5b9048b419f59d901dec100cbdd81975864cce2
diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml
deleted file mode 100644
index 25095bc4b42e..000000000000
--- a/sci-chemistry/pdb-tools/metadata.xml
+++ /dev/null
@@ -1,12 +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="google-code">pdb-tools</remote-id>
-    <remote-id type="github">harmslab/pdbtools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
deleted file mode 100644
index 090b7c041dfe..000000000000
--- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
+++ /dev/null
@@ -1,79 +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 fortran-2 python-single-r1 toolchain-funcs
-
-MY_PN="pdbTools"
-
-DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files"
-HOMEPAGE="https://github.com/harmslab/pdbtools"
-SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${MY_PN}_${PV}
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \
-		-i pdb_sasa.py || die
-	sed \
-		-e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \
-		-i pdb_satk.py || die
-	sed \
-		-e 's:> %:>%:g' \
-		-i pdb_seq.py || die
-}
-
-src_compile() {
-	mkdir bin
-	cd satk
-	for i in *.f; do
-		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
-		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
-		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
-		sed \
-			-e "s:${i/.f}.out:${i/.f}:g" \
-			-i ../pdb_satk.py || die
-	done
-}
-
-src_install() {
-	local script
-	insinto /usr/share/${PN}
-	doins -r pdb_data/peptides
-	rm -rf pdb_data/peptides || die
-
-	python_domodule helper pdb_data
-
-	python_moduleinto ${PN/-/_}
-	python_domodule *.py
-
-	for i in pdb_*.py; do
-		cat > ${i/.py} <<- EOF
-		#!${EPREFIX}/bin/bash
-		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
-		EOF
-		dobin ${i/.py}
-	done
-
-	dobin bin/*
-	dodoc README
-}
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
deleted file mode 100644
index a476a801611a..000000000000
--- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit fortran-2 python-single-r1 toolchain-funcs
-
-MY_PN="pdbTools"
-
-DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files"
-HOMEPAGE="https://github.com/harmslab/pdbtools"
-SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${MY_PN}_${PV}
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \
-		-i pdb_sasa.py || die
-	sed \
-		-e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \
-		-i pdb_satk.py || die
-	sed \
-		-e 's:> %:>%:g' \
-		-i pdb_seq.py || die
-
-	sed \
-		-e "/import/s:helper:${PN/-/_}.helper:g" \
-		-i *.py || die
-}
-
-src_compile() {
-	mkdir bin
-	cd satk
-	for i in *.f; do
-		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
-		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
-		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
-		sed \
-			-e "s:${i/.f}.out:${i/.f}:g" \
-			-i ../pdb_satk.py || die
-	done
-}
-
-src_install() {
-	local script
-	insinto /usr/share/${PN}
-	doins -r pdb_data/peptides
-	rm -rf pdb_data/peptides || die
-
-	python_domodule pdb_data
-
-	python_moduleinto ${PN/-/_}
-	python_domodule helper *.py
-
-	for i in pdb_*.py; do
-		cat > ${i/.py} <<- EOF
-		#!${EPREFIX}/bin/bash
-		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
-		EOF
-		dobin ${i/.py}
-	done
-
-	dobin bin/*
-	dodoc README
-}
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
deleted file mode 100644
index d057f25d651e..000000000000
--- a/sci-chemistry/pdb2pqr/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX pdb2pka 270 BLAKE2B c4b063cc22f416e5847ceec3377b43f2a7ddda7d204dd07c2870f499483d2ff9edada0632629336b268df904e960d4cb1dad92075ddf42b73d052e7214b20c45 SHA512 c6e66fa73a3119ea84a9bf304c9c8701a6eaf32870ba8c1755bfd8f2055e20af2f2ebc01fd2bf6a663e5873f3d6da7387a439efac3dcb7d4a415c176cb2f761b
-AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b28950961eeffac1c9e4c67102924ecaad002fc5c3d9f2a6955f66eb0699139486caa5372 SHA512 5f8c963fc5addf782579b9312f601ec4547573c7ab88df5a6e38c71c9e31e7b7eea3cde99bdac8f8270f3646d933a0b510a94046e3a30736f75953af5d160b8d
-AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b
-AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2
-DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f
-EBUILD pdb2pqr-1.9.0-r3.ebuild 2679 BLAKE2B 882e244c9764c317df96195e4c9049a8a23872c458487ed4e897263cc99b5e1fa8bb7a3a70bf34fda447d71767ee4eb59fa49c4beecbd04fd2577438bb8aaf8e SHA512 f5037488f9ecdc9be44fb1dcc15ec55db932fc4268b61db7d95375e0e22d9f54f0315a5c0eb4398919f8620c167adbdd5e632bcdb241724ebc77efb7e7442802
-MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka
deleted file mode 100644
index 2406b0c4773f..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pka
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-import subprocess
-import site
-import sys
-import os
-
-sitepackages = site.getsitepackages()[0]
-
-_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")]
-_cmd.extend(sys.argv[1:])
-
-subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr
deleted file mode 100644
index 8c0635aea94e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-import subprocess
-import site
-import sys
-import os
-
-sitepackages = site.getsitepackages()[0]
-
-_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")]
-_cmd.extend(sys.argv[1:])
-
-subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
deleted file mode 100644
index fac32b233e6b..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- pdb2pka/SConscript           | 9 ++++++++-
- pdb2pka/substruct/SConscript | 6 ++++++
- 2 files changed, 14 insertions(+), 1 deletion(-)
-
-diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript
-index 583cdc5..6c30011 100644
---- a/pdb2pka/SConscript
-+++ b/pdb2pka/SConscript
-@@ -1,4 +1,11 @@
- Import('env')
-+import os
-+
-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
-+env['CXX'] = os.environ['CXX']
-+env['LINK'] = os.environ['CXX']
-+
- 
- if env['REBUILD_SWIG']:
-     pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])
-@@ -9,4 +16,4 @@ Default(pyc)
-     
- algorithms_module = SConscript('substruct/SConscript')
- 
--Return('pyc algorithms_module')
-\ No newline at end of file
-+Return('pyc algorithms_module')
-diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript
-index 7dbcdb0..56fb577 100644
---- a/pdb2pka/substruct/SConscript
-+++ b/pdb2pka/substruct/SConscript
-@@ -1,7 +1,13 @@
- import distutils
- import numpy
-+import os
- Import('env')
- 
-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
-+env['CXX'] = os.environ['CXX']
-+env['LINK'] = os.environ['CXX']
-+
- env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
- 
- algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
deleted file mode 100644
index 2695b013c66a..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- SConscript-install.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/SConscript-install.py b/SConscript-install.py
-index e2f9f09..1fdf1a8 100644
---- a/SConscript-install.py
-+++ b/SConscript-install.py
-@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'):
- 		if GetOption("clean"):
- 			env.Default(result)
- 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))
-+		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
- 	else:
- 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
- 
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
deleted file mode 100644
index 36fd8c04ac52..000000000000
--- a/sci-chemistry/pdb2pqr/metadata.xml
+++ /dev/null
@@ -1,15 +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="opal">Add web interface via opal</flag>
-    <flag name="pdb2pka">Install experimental pdb2pka interface</flag>
-  </use>
-  <upstream>
-    <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
deleted file mode 100644
index 179e6448d605..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
+++ /dev/null
@@ -1,114 +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 scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-HOMEPAGE="https://www.poissonboltzmann.org/"
-SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-		sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}]
-		opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] )
-	')
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )"
-DEPEND="${RDEPEND}
-	dev-lang/swig:0"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-flags.patch
-	"${FILESDIR}"/${P}-install-py.patch
-)
-
-pkg_setup() {
-	if [[ -z ${MAXATOMS} ]]; then
-		einfo "If you like to have support for more then 10000 atoms,"
-		einfo "export MAXATOMS=\"your value\""
-		export MAXATOMS=10000
-	else
-		einfo "Allow usage of ${MAXATOMS} during calculations"
-	fi
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
-
-	export CXXFLAGS="${CXXFLAGS}"
-	export LDFLAGS="${LDFLAGS}"
-
-	epatch "${PATCHES[@]}"
-	tc-export CXX
-	rm -rf scons || die
-}
-
-src_configure() {
-	cat > build_config.py <<- EOF
-		PREFIX="${D}/$(python_get_sitedir)/${PN}"
-		#URL="http://<COMPUTER NAME>/pdb2pqr/"
-		APBS="${EPREFIX}/usr/bin/apbs"
-		#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
-		#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
-		MAX_ATOMS=${MAXATOMS}
-		BUILD_PDB2PKA=$(usex pdb2pka True False)
-		REBUILD_SWIG=True
-	EOF
-}
-
-src_compile() {
-	escons
-}
-
-src_test() {
-	local myesconsargs=( -j1 )
-	escons test
-	escons advtest
-	escons complete-test
-}
-
-src_install() {
-	dodir /usr/share/doc/${PF}/html
-	local lib
-
-	escons install
-
-	find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
-
-	python_doscript "${FILESDIR}"/{${PN},pdb2pka}
-
-	for lib in apbslib.py{,c,o}; do
-		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-	done
-	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
-	python_optimize
-
-	if use doc; then
-		pushd doc > /dev/null
-		docinto html
-		dodoc -r *.html images pydoc
-		popd > /dev/null
-	fi
-
-	use examples && \
-		insinto /usr/share/${PN}/ && \
-		doins -r examples
-
-	dodoc *md NEWS
-}
diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest
deleted file mode 100644
index 6a19b100ad23..000000000000
--- a/sci-chemistry/prodecomp/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d
-EBUILD prodecomp-3.0-r3.ebuild 1191 BLAKE2B 25903c84628554ea37a9d20ee8fc0b0315d30526ed2c7e41bc6697235c04e3f9682ebb64aed7358009fd45502fcfe1fb66355c3f7209e39aeee6a1064cb34a5d SHA512 692a231b2e180d4a4114ce2441eb178adafb9ab725fcc2b1a0bdbeb675134ee823fb694546d033832393d4562c948073f47715ee29daaad9a938ce5112dd5f1e
-MISC metadata.xml 825 BLAKE2B 6874942c301b7d68f9184de8eb7482b790d2bd51c3a853132da3ed7bb0eacf54f608f816965bbfb27b81b90fecc3eee77596d73a78f5ec67703c53ad2bc2556d SHA512 94e41d5648ac93257f11f305bf2aaf926cc103240beec884142cda42c3d4e4fae5629e26b43cd945c945af706d5b5172fcd2c30ec6cb9067b152a22cd09bddcf
diff --git a/sci-chemistry/prodecomp/metadata.xml b/sci-chemistry/prodecomp/metadata.xml
deleted file mode 100644
index 168ce755cbc8..000000000000
--- a/sci-chemistry/prodecomp/metadata.xml
+++ /dev/null
@@ -1,18 +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>
-		PRODECOMP (PROjection DECOMPosition) is a software tool for
-		decomposition of 2D projections of high-dimensional NMR spectra to a set
-		of components (defined in turn by one-dimensional "shapes").
-		Simultaneous analysis of projections from one or several
-		high-dimensional experiments provide unambigous chemical shifts for
-		large spin systems. The latter can be used for backbone and side-chain
-		assignments as well as structural studies of proteins
-		(Malmodin and Billeter 2005; 2006; Staykova et al. 2008a,b).
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild
deleted file mode 100644
index 65683c21b0fa..000000000000
--- a/sci-chemistry/prodecomp/prodecomp-3.0-r3.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
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit python-single-r1
-
-DESCRIPTION="Decomposition-based analysis of NMR projections"
-HOMEPAGE="http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${DEPEND}
-	$(python_gen_cond_dep '
-		|| (
-			sci-libs/scipy-python2[${PYTHON_MULTI_USEDEP}]
-			sci-libs/scipy[${PYTHON_MULTI_USEDEP}]
-		)
-	')"
-
-S="${WORKDIR}"/NMRProjAnalys
-
-src_install() {
-	python_export
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r ExampleData Results
-	fi
-
-	dodoc ProjTools/Manual.pdf
-	rm -rf ProjTools/Manual.pdf ProdecompOutput || die
-
-	python_moduleinto ${PN}
-	python_domodule ProjTools/.
-	python_optimize
-
-	cat >> "${T}"/${PN} <<- EOF
-	#!/bin/bash
-	${PYTHON} -O $(python_get_sitedir)/${PN}/ProjAnalys.py \$@
-	EOF
-	dobin "${T}"/${PN}
-
-	dosym ../../../../share/doc/${PF}/Manual.pdf "${PYTHON_SITEDIR##${EPREFIX}}"/${PN}/Manual.pdf
-}
diff --git a/sci-chemistry/pymol-plugins-bni-tools/Manifest b/sci-chemistry/pymol-plugins-bni-tools/Manifest
deleted file mode 100644
index 5cd55b7d9206..000000000000
--- a/sci-chemistry/pymol-plugins-bni-tools/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST bni-tools-027.zip 33753 BLAKE2B 3cf52b42709c0e08879b7f3174ab6e7fd6c052a2827a0ee6d102fa16f30a985d7ff766abc6dc27595973a1f6151f684e97b34da981196c411fdac178499f9a51 SHA512 9c0ef1ca5bbb3040192ab2668f354f947e93d42c91a0cfdde5d05be273e6ba9f29ec3c6ee86367f18d87316282b4e0141183b8d6259bd36d44010b7bbb7666e5
-EBUILD pymol-plugins-bni-tools-0.27.ebuild 912 BLAKE2B 8c99230d03b369b03a29496aecb82ea37b1968e87537a634c85c0373c2ea11ce3a9a42482127bdce82c902906ff6bb13dc0a3862b62ffe6298ae7a9ce58c983c SHA512 4e685c3c1c96849cf7f5144fa3ac6114c943e4feb2d66f2797f2b611150d06d1849a140ffc8a8ba50d20dd9ee032392c38c144ebc52576666229854ff21544dc
-MISC metadata.xml 354 BLAKE2B 569e0dfba864883bafd31bf469136f0f710f1f035b4056babf6de5046b7a2cb7146d3f3d95970e75c5025230056249392cc664323cf2d4bf445b3d674ee36675 SHA512 b5f667e6315a0841a28c45fcd7c218d0b5c5e0ad3cdd63870001f1fcd2e4adf598d2b1270a77aa71c1d5d2fe985ca1d98d4c3f88cd540740e67f3469709a94a8
diff --git a/sci-chemistry/pymol-plugins-bni-tools/metadata.xml b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml
deleted file mode 100644
index 0f732a212193..000000000000
--- a/sci-chemistry/pymol-plugins-bni-tools/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">bni-tools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild
deleted file mode 100644
index 1de68c64d64f..000000000000
--- a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild
+++ /dev/null
@@ -1,37 +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 python-r1 versionator
-
-MY_PN="${PN#pymol-plugins-}"
-MY_P="${MY_PN}-$(delete_version_separator 1)"
-MY_P_DOT="${MY_PN}-${PV}"
-
-DESCRIPTION="Gives Pymol additional functionalities and presets to the PyMOL GUI"
-HOMEPAGE="http://bni-tools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${MY_PN}/${MY_PN}/${MY_P_DOT}/${MY_P}.zip"
-
-LICENSE="CNRI"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-DEPEND="${PYTHON_DEPS}
-	app-arch/unzip"
-
-S="${WORKDIR}"
-
-src_install() {
-	python_moduleinto pmg_tk/startup
-	python_foreach_impl python_domodule bni-tools.py
-	python_foreach_impl python_optimize
-	dodoc readme.txt
-	dohtml ShortCommandDescription.html
-}
diff --git a/sci-chemistry/pymol-plugins-caver/Manifest b/sci-chemistry/pymol-plugins-caver/Manifest
deleted file mode 100644
index 9b6a67eb2228..000000000000
--- a/sci-chemistry/pymol-plugins-caver/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST Caver2_1_2_pymol_plugin.zip 5698331 BLAKE2B e1accfaea6faf1e8c545b88c965228ccb62710d4015ff681506971feba6bd18a4a8b0b6e6caf621c99830ba529a6ec17873cdd3d5e52ad6dc6f67d9457e4eb87 SHA512 9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c
-EBUILD pymol-plugins-caver-2.1.2.ebuild 1307 BLAKE2B 72eb31fe4fecbbe94d79c7aac5494e46f998746ebaa6d39f90f3355aab61587c893dd468f5a51a5f397f4991dd9814cbe7d6b3f4e1ae8690466aef1947c59c2c SHA512 0bdee2ba446432beed93bdd7625061edc50560b5b9947cf1a65c88531c42ddcba501d5580c1edc86ed62a3ec503510a59ca58b7b12a72e1e9b69026738b7c927
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/pymol-plugins-caver/metadata.xml b/sci-chemistry/pymol-plugins-caver/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/pymol-plugins-caver/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/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
deleted file mode 100644
index e189f885dcc5..000000000000
--- a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit multilib python-r1 eutils versionator java-utils-2
-
-MY_PV="$(replace_all_version_separators _)"
-MY_P="Caver${MY_PV}_pymol_plugin"
-
-DESCRIPTION="Calculation of pathways of proteins from buried cavities to outside solvent"
-HOMEPAGE="http://loschmidt.chemi.muni.cz/caver/"
-SRC_URI="${MY_P}.zip"
-
-LICENSE="CAVER"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	>=virtual/jre-1.6
-	sci-chemistry/pymol[${PYTHON_USEDEP}]
-	${PYTHON_DEPS}"
-DEPEND="app-arch/unzip
-	${PYTHON_DEPS}"
-
-RESTRICT="bindist fetch"
-
-S="${WORKDIR}/${MY_P}"/linux_mac
-
-pkg_nofetch() {
-	elog "Download ${A}"
-	elog "from ${HOMEPAGE}. This requires registration."
-	elog "Place tarballs into your DISTDIR directory."
-}
-
-src_install() {
-	java-pkg_dojar Caver${MY_PV}/*.jar
-
-	java-pkg_jarinto /usr/share/${PN}/lib/lib/
-	java-pkg_dojar Caver${MY_PV}/lib/*.jar
-
-	installation() {
-		sed \
-			-e "s:directory/where/jar/with/plugin/is/located:${EPREFIX}/usr/share/${PN}/lib/:g" \
-			-i Caver${MY_PV}.py || die
-
-		python_moduleinto pmg_tk/startup/
-		python_domodule Caver${MY_PV}.py
-		python_optimize
-	}
-	python_foreach_impl installation
-}
diff --git a/sci-chemistry/pymol-plugins-dssp/Manifest b/sci-chemistry/pymol-plugins-dssp/Manifest
deleted file mode 100644
index 3c9bf42c8721..000000000000
--- a/sci-chemistry/pymol-plugins-dssp/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST pymol-plugins-dssp-110430.py.xz 6836 BLAKE2B d8a58d1ad85aaa45acdcac40d022bac8035baf9c95c05e2cd6abb1dd82f1cd390515e04b4c65ff96902655a366ca2e4eab8e86060dffb27ea146298f827fbd7c SHA512 521e0a32ca6d2c8c21c690815b0654bb44303bd7fb9a1eb76227030b2ad7311fadb0d748e49b8bbc16cd5e69acba375b5353de7bffef1ff69686e62021fe64f4
-EBUILD pymol-plugins-dssp-110430-r1.ebuild 885 BLAKE2B db52dd99fc40b04a8a832a4c565e450f35d098120546dabbf53a5e307233664e619ad988eba51c4f7b9b8a06714be96742446b63e28014fdb3098db1f87133bb SHA512 617949f73a08f3b53ceecbce15669202e935c18e4b052092a810b644c9d11e9b5cbf0663c4c830895d0f19c55d34a55c2e1bcf405d3ec0d1e4ec29c8a56c642c
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/pymol-plugins-dssp/metadata.xml b/sci-chemistry/pymol-plugins-dssp/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/pymol-plugins-dssp/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/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild
deleted file mode 100644
index 11269a75591f..000000000000
--- a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild
+++ /dev/null
@@ -1,39 +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 python-r1
-
-DESCRIPTION="DSSP Plugin for PyMOL"
-HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.py.xz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD pymol"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${DEPEND}
-	sci-chemistry/dssp
-	sci-biology/stride
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	sed \
-		-e "s:GENTOO_DSSP:${EPREFIX}/usr/bin/dssp:g" \
-		-e "s:GENTOO_STRIDE:${EPREFIX}/usr/bin/stride:g" \
-		-i ${P}.py || die
-}
-
-src_install() {
-	python_moduleinto pmg_tk/startup
-	python_foreach_impl python_domodule ${P}.py
-	python_foreach_impl python_optimize
-}
diff --git a/sci-chemistry/pymol-plugins-emovie/Manifest b/sci-chemistry/pymol-plugins-emovie/Manifest
deleted file mode 100644
index bc3bedfdd4e6..000000000000
--- a/sci-chemistry/pymol-plugins-emovie/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX 1.0.4-indent.patch 706 BLAKE2B f99a3554f0a00c5c075ba23179238d32ce7acddcace31e4c7cb0f995cf2c5a7a0ee4c5a0db4b2dc079a70d6e0ca34e52ac5276ffddcca441e49eb1746ba2962d SHA512 6788795d177db8c7597376a364eed79cc40a2423c6d86b837f4378308515d6f41a6c352df775de309d363ec284997a688285f2f851d5d84e891e78a771580b0e
-DIST eMovie_package.zip 22840 BLAKE2B 593548d5f940432cbf71580410fba01bcf54f884d6ac1a726a0ce65a7efa4d90c283985f81b5348eadaf54f497a32e1d478ca803cb0fbdacd7bfde30b939d864 SHA512 5d4af5f8bd6e7e0f24f33d769925bd0444389b1c0fbdd14776f4073fd3e1e818c4623791bcb0cff5496729dc55e0429c48c3c16cb5fdbb91c51f9c5445c7afe4
-EBUILD pymol-plugins-emovie-1.0.4.ebuild 767 BLAKE2B de65bfdc624e16c23026729e7853a8f44e861583684c92c1574c7a8cab6442a86b2d9874e3456065d780bebd55e5046472326bb2d1914b16d784c008892ab94b SHA512 d915784d50895f04230189d39b8d819cbdca7fcf620ce6cd688139fd5a687ee8fef1415fb63f54758b588774c06672b9712943fed126a7de6db436034588de5f
-MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch b/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch
deleted file mode 100644
index a9a77e5055dd..000000000000
--- a/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/eMovie.py b/eMovie.py
-index a865732..8b5b068 100644
---- a/eMovie.py
-+++ b/eMovie.py
-@@ -931,7 +931,7 @@ class Story(tkSimpleDialog.Dialog):
- 
-         	if self.parent is not None:
-             		self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50))
--			self.initial_focus.focus_set()
-+            		self.initial_focus.focus_set()
- 
-         	self.wait_window(self)
- 
-@@ -2041,7 +2041,7 @@ class AddMorph(tkSimpleDialog.Dialog):
- 
-         	if self.parent is not None:
-             		self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50))
--		self.initial_focus.focus_set()
-+        	self.initial_focus.focus_set()
- 
-         	self.wait_window(self)
- 
diff --git a/sci-chemistry/pymol-plugins-emovie/metadata.xml b/sci-chemistry/pymol-plugins-emovie/metadata.xml
deleted file mode 100644
index da36ecbfcd6a..000000000000
--- a/sci-chemistry/pymol-plugins-emovie/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/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild
deleted file mode 100644
index e7b2eb7d4771..000000000000
--- a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild
+++ /dev/null
@@ -1,35 +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 eutils python-r1
-
-DESCRIPTION="PyMOL plugin for convinient movie creation"
-SRC_URI="http://www.weizmann.ac.il/ISPC/eMovie_package.zip"
-HOMEPAGE="http://www.weizmann.ac.il/ISPC/eMovie.html"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	>sci-chemistry/pymol-0.99[${PYTHON_USEDEP}]"
-DEPEND="app-arch/unzip"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-indent.patch
-}
-
-src_install() {
-	python_moduleinto pmg_tk/startup
-	python_foreach_impl python_domodule eMovie.py
-	python_foreach_impl python_optimize
-}
diff --git a/sci-chemistry/pymol-plugins-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest
deleted file mode 100644
index 7a00b495997e..000000000000
--- a/sci-chemistry/pymol-plugins-promol/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST pymol-plugins-promol-3.0.2.zip 2219295 BLAKE2B 7e81de98ee20f6b22fabeca35b0825250c3b839b9ea51f6c0b51f15062c73810474bd377d0e39d3c2ac0d61f1b5cfb4174c53f1dfc67a11dfcd707eee417a7ed SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7
-EBUILD pymol-plugins-promol-3.0.2-r1.ebuild 1560 BLAKE2B c4f52140e4baa9f5a6beddfbace78ff111a3f78f8bdfd0fb220b0e17555175d48533079a798f98eda32b7880f23a37fdbacd0904a988871a1b8eb91f6e9a23fb SHA512 1b3962ba9471e9c2d6af5ebac500a317b44fe261ceeeb8ee8f156211d9aad39ce720e29be5d859a5867df5b87904b2084eb95d21d63806ba0452222ef96ac6cb
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/pymol-plugins-promol/metadata.xml b/sci-chemistry/pymol-plugins-promol/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/pymol-plugins-promol/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/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
deleted file mode 100644
index 6cd842f3703d..000000000000
--- a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
+++ /dev/null
@@ -1,60 +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
-
-DESCRIPTION="Fast and accurate regognition of active sites"
-HOMEPAGE="https://www.rit.edu/cos/ezviz/ProMOL_dl.html"
-SRC_URI="https://www.rit.edu/cos/ezviz/ProMOL.zip -> ${P}.zip"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-LICENSE="all-rights-reserved"
-IUSE=""
-
-RESTRICT="mirror bindist"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-python/pmw:py2[${PYTHON_USEDEP}]
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-DEPEND=""
-
-S="${WORKDIR}/ProMOL Folder"
-
-src_prepare() {
-	python_copy_sources
-	preparation() {
-		cd "${BUILD_DIR}" || die
-		sed \
-			-e "s:./modules/pmg_tk/startup:$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \
-			-i ProMOL_302.py || die
-	}
-	python_foreach_impl preparation
-}
-
-src_install() {
-	dodoc *doc
-	dohtml -r Thanks.html EDMHelp.htm Help
-
-	installation() {
-		cd "${BUILD_DIR}" || die
-		python_moduleinto pmg_tk/startup/ProMol
-		python_domodule PDB_List AminoPics Motifs *GIF pdb_entry_type.txt Master.txt Scripts
-		python_moduleinto pmg_tk/startup
-		python_domodule *.py
-		dosym ../../../../../../share/doc/${PF}/html/Help \
-			$(python_get_sitedir)/pmg_tk/startup/ProMol/Help
-		dosym ../../../../../../share/doc/${PF}/html/Thanks.html \
-			$(python_get_sitedir)/pmg_tk/startup/ProMol/Thanks.html
-		dosym ../../../../../../share/doc/${PF}/html/EDMHelp.htm \
-			$(python_get_sitedir)/pmg_tk/startup/ProMol/EDMHelp.htm
-	}
-	python_foreach_impl installation
-}
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index fcffc5ef7882..69bc84fa32a7 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,4 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
-EBUILD pymol-2.3.0-r2.ebuild 3189 BLAKE2B b696daab150edc9c5b69e330f68d0a79bb825d39d69e6b149a90be7f12a3956525b91373f330e528178b2732b84b86f6e9ae1624c8cad48eb1580e81b4bde38a SHA512 4c4c4e94c768325728584e6c424e7c7d87e4daab291c0f6bad2c6f527645056d0b9b4fefc822543542f27431f51a1f1a6cda1ab7fb9136d0f44a11c6129060be
 EBUILD pymol-2.3.0-r3.ebuild 3005 BLAKE2B 697c52ef412f18a8088c82c6f71ef7b10ffb28201aaaf5b651cfad512ce1f3340f74292dc54e9005e5c153d50bf8d3c9de1df1a71516c5258b4a6256fc9b9429 SHA512 9f248137b6cd1c4a0233c83738597e42b43b65f1331c6a19a841a36719328996fc9902f599848d791963f41e65dc9f7c76f967dae26286488a49b5cfd13572d1
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
deleted file mode 100644
index 5eadc9a8512d..000000000000
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ /dev/null
@@ -1,118 +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 desktop eutils flag-o-matic xdg-utils
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	"
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-	dev-libs/msgpack[cxx]
-	dev-libs/mmtf-cpp
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	dev-python/pmw:py2[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/glm
-	media-libs/libpng:0=
-	media-video/mpeg-tools
-	sys-libs/zlib
-	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}
-	sci-chemistry/chemical-mime-data
-"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-	sed \
-		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
-		-i setup.py || die
-
-	append-cxxflags -std=c++0x
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install \
-		--pymol-path="${EPREFIX}/usr/share/pymol"
-
-	sed \
-		-e '1d' \
-		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
-		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
-		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
-		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed \
-		-e '1i#!/usr/bin/env python' \
-		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
-
-	python_foreach_impl python_doscript "${T}"/${PN}
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
-	xdg_desktop_database_update
-	xdg_mimeinfo_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	xdg_desktop_database_update
-	xdg_mimeinfo_database_update
-}
diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest
deleted file mode 100644
index 56c32abe4254..000000000000
--- a/sci-chemistry/relax/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST relax-4.0.0.src.tar.bz2 105659752 BLAKE2B ce5fc9b7f31787f2189e75a543f8ba6fe3cd59ce7382c6c0f79c419b9f71b2d09bd16685e7fed3c9e3205be531efa2a8dc1cce707e77e2386d2a9f7a71b4b0c1 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e
-EBUILD relax-4.0.0-r4.ebuild 1883 BLAKE2B 83dbe09ddc6feb3b7ec4af472eeac4e49c2cda90c84d2f19f19bdcf9414b97f0e7221a9e048c68535e6d5239511013738f4d969b01233034212efcefd7dca3c8 SHA512 5f657c2798e1a83626056ff7849339d3bb05f014ea579a1697e022a7b9628256c7c14a37fa71869be9d66fb1a935bc4907329c45d9cb9af7c6270ba1690046ef
-MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e
diff --git a/sci-chemistry/relax/metadata.xml b/sci-chemistry/relax/metadata.xml
deleted file mode 100644
index 00870a633858..000000000000
--- a/sci-chemistry/relax/metadata.xml
+++ /dev/null
@@ -1,30 +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 program relax is a software package designed for the study of molecular
-		dynamics through the analysis of experimental NMR data. Organic molecules,
-		proteins, RNA, DNA, sugars, and other biomolecules are all supported. It
-		was originally written for the model-free analysis of protein dynamics,
-		though its scope has been significantly expanded.
-
-		relax is a community driven project created by NMR spectroscopists for
-		NMR spectroscopists. It supports a diverse range of analyses:
-
-		Model-free analysis - the Lipari and Szabo model-free analysis of NMR
-			relaxation data.
-		R1 and R2 - the exponential curve fitting for the calculation of the
-			Rx NMR relaxation rates.
-		NOE - the calculation of the steady-state NOE NMR relaxation data.
-		Consistency testing of multiple field NMR relaxation data.
-		RSDM - Reduced Spectral Density Mapping.
-		Frame order and N-state model - study of domain motions via the N-state
-			model and frame order dynamics theories using anisotropic
-			NMR parameters such as RDCs and PCSs.
-		Stereochemistry investigations.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/relax/relax-4.0.0-r4.ebuild b/sci-chemistry/relax/relax-4.0.0-r4.ebuild
deleted file mode 100644
index ba03dbad8454..000000000000
--- a/sci-chemistry/relax/relax-4.0.0-r4.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-WX_GTK_VER="3.0"
-
-inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx
-
-DESCRIPTION="Molecular dynamics by NMR data analysis"
-HOMEPAGE="https://www.nmr-relax.com/"
-SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	$(python_gen_cond_dep "
-		dev-python/Numdifftools[\${PYTHON_MULTI_USEDEP}]
-		|| (
-			dev-python/matplotlib-python2[\${PYTHON_MULTI_USEDEP}]
-			dev-python/matplotlib[\${PYTHON_MULTI_USEDEP}]
-		)
-		|| (
-			dev-python/numpy-python2[\${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[\${PYTHON_MULTI_USEDEP}]
-		)
-		dev-python/wxpython:${WX_GTK_VER}[\${PYTHON_MULTI_USEDEP}]
-		sci-chemistry/pymol[\${PYTHON_MULTI_USEDEP}]
-		>=sci-libs/bmrblib-1.0.3[\${PYTHON_MULTI_USEDEP}]
-		>=sci-libs/minfx-1.0.11[\${PYTHON_MULTI_USEDEP}]
-		|| (
-			sci-libs/scipy-python2[\${PYTHON_MULTI_USEDEP}]
-			sci-libs/scipy[\${PYTHON_MULTI_USEDEP}]
-		)
-	")
-	sci-chemistry/molmol
-	sci-chemistry/vmd
-	sci-visualization/grace
-	sci-visualization/opendx
-	x11-libs/wxGTK:${WX_GTK_VER}[X]"
-DEPEND="${RDEPEND}
-	media-gfx/pngcrush
-	test? ( ${RDEPEND} )
-	"
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	rm -rf minfx bmrblib extern/numdifftools || die
-	tc-export CC
-	need-wxwidgets unicode
-}
-
-src_compile() {
-	escons
-}
-
-src_test() {
-	VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback"
-	virtualmake
-}
-
-src_install() {
-	dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf}
-
-	python_moduleinto ${PN}
-	python_domodule *
-
-	rm ${PN} README || die
-
-	make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@"
-}
diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest
deleted file mode 100644
index 483d19fd9cfe..000000000000
--- a/sci-chemistry/sparky/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-AUX 3.115-fix-c++14.patch 849 BLAKE2B fde4158bf18e4cba23e0bb93972b10236e88e8cd3db055b81e328ff2fbddd38c8f6a051525e949b237adebd7a534aaa7639863aa17c3536fe35387e930ca5806 SHA512 80bbfe8a2e853f8be84ed48da99605805a42bb05b091c851ddbefb5513745cdf51c5396e97ad4e3be7dd199270fb069e239e0c24f6642d956fd6571d8b14a7e1
-AUX 3.115-ldflags.patch 2713 BLAKE2B 26873b508c9b0ecd5122712b8e599393bdf1787e9608b4e7e451d1db95ba2831af42e8f9d2637181f21e3206689bd115601fdcb7b48c0011cc30a83037bec087 SHA512 1c439cc04af3e8e403257ccd45eecb16f0e36d4b51a28ab5ddda269bde271d23a20bb453cda48e03f58c31a9a614d4b19ca2b6aa7f75bdfec1f79b70e8c361de
-AUX 3.115-makefile.patch 580 BLAKE2B 4beeca38c910e583235d2aef66137165fe4ae58f48591e4567f50a1d702ea0391e467dd6f4baab4019a05a8b5051329b0485fc1cc56a38c6bfcbd53a06034a09 SHA512 9ddd99de93656301f307aabb3284e86fe68f4c7957f0b5ff81da4615f850fc36b686908de84816f0ff8a3d75169ccd0d4d7cb5bb8afd88d96c913f766e7ee19a
-AUX 3.115-paths.patch 415 BLAKE2B 9e959f54626f3eb34e963a571cb9a92e92f87af4fd593972490dc3bf299ba8b9e42a47768f78ea8463f0fb1c76274ec334be8f4d5b1e52d339aa90eec7b7dd19 SHA512 44c44c99cf2c5c51c8e506267efc4efc50eb2277ccdab362943da0c45c63f9e797ae699e99eda3ce6ca0b4e0a886393d1917ce8614eea3086e97446fc3c0c674
-AUX 3.115-wrapper-r1.patch 1518 BLAKE2B a5dd56c76a36f1a1e67599b1dcb25ba9f8edd639220d9f3c248d64b7bee88a108482137ec70acb5ee466048abf5939122842ae827ffba23dcef7c895dbf20f56 SHA512 be2c18a40ceabdb1c25a7849e1ee00438092f264c486e93b3bfb412fc417902a3b22b672d28a6cc104fedc5477ea2c0de66bc40dd5d4d607ed0201eee4d368a7
-DIST sparky-source-3.115.tar.gz 4103686 BLAKE2B c7811aa135b10f21b8807447e2ab173f407ccc1446ff1307006f7f885e6e69983647991600720e02e4e738bb68338de01bc5d57577eacf20298db6d53a54b183 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89
-EBUILD sparky-3.115-r2.ebuild 3192 BLAKE2B 172ded57706c8aac3a4f9d268fd75f410d35dffc9c26352695c3961c2508dc08773e3a9c857d530ab47341ac3977daac78939661d14c8334da4eadba7852e610 SHA512 f2f5fe11666e85feca9d90c5fb6c9d93f42b9bde269f311a943c37b334d617d7dcdbc5ee45cb555fb6af278a648c0c0ab4ec28027143675ee0cc2c77dc41c10a
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/sparky/files/3.115-fix-c++14.patch b/sci-chemistry/sparky/files/3.115-fix-c++14.patch
deleted file mode 100644
index 3a05ea7d85ce..000000000000
--- a/sci-chemistry/sparky/files/3.115-fix-c++14.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Fix the custom new/new[] operators in order to account for changed
-noexcept semantics in C++11.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=596012
-
-Patch by Peter Levine
-
---- a/c++/memalloc.cc
-+++ b/c++/memalloc.cc
-@@ -39,7 +39,10 @@
- 
- // ----------------------------------------------------------------------------
- //
--void *operator new(size_t size) throw(std::bad_alloc)
-+void *operator new(size_t size)
-+#if __cplusplus < 201103L
-+throw(std::bad_alloc)
-+#endif
- {
-   void *value = allocate(size);
-   if (tracking_memory)
-@@ -72,7 +75,10 @@
- 
- // ----------------------------------------------------------------------------
- //
--void *operator new[](size_t size) throw(std::bad_alloc)
-+void *operator new[](size_t size)
-+#if __cplusplus < 201103L
-+throw(std::bad_alloc)
-+#endif
- {
-   void *value = allocate(size);
-   if (tracking_memory)
diff --git a/sci-chemistry/sparky/files/3.115-ldflags.patch b/sci-chemistry/sparky/files/3.115-ldflags.patch
deleted file mode 100644
index bd4020387682..000000000000
--- a/sci-chemistry/sparky/files/3.115-ldflags.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/c++/Makefile b/c++/Makefile
-index aeb4daa..5cab356 100644
---- a/c++/Makefile
-+++ b/c++/Makefile
-@@ -131,28 +131,28 @@ $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk:
- 	chmod 755 $@
- 
- sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS)
--	$(CXX) -o $@ main.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) -o $@ main.o $(SPARKY_OBJS) $(LDLIBS)
- 
- ucsfdata$(EXE_SUFFIX): ucsfdata.o $(NMR_OBJS)
--	$(CXX) -o $@ ucsfdata.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ ucsfdata.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- pipe2ucsf$(EXE_SUFFIX): pipe2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ pipe2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ pipe2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- vnmr2ucsf$(EXE_SUFFIX): vnmr2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- bruk2ucsf$(EXE_SUFFIX): bruk2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ bruk2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ bruk2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- peaks2ucsf$(EXE_SUFFIX): peaks2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ peaks2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ peaks2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- matrix2ucsf$(EXE_SUFFIX): matrix2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ matrix2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ matrix2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- spy.so: python.o $(SPARKY_OBJS)
--	$(CXX) $(LDSHARED) -o $@ python.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS)
-+	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ python.o $(SPARKY_OBJS) $(LDLIBS)
- 
- winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc
- 	$(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc
-@@ -161,7 +161,7 @@ python.o: python.cc
- 	$(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
- 
- _tkinter.so: _tkinter.o
--	$(CXX) $(LDSHARED) -o $@ _tkinter.o $(LDFLAGS) $(TKLIBS)
-+	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS)
- 
- _tkinter.o: _tkinter.c
- 	$(CC) $(CFLAGS) $(TKFLAGS) $(PYFLAGS) -c $(SPARKY_SRC)/_tkinter.c
-@@ -188,8 +188,8 @@ PYLDFLAGS	= -L$(PYTHON_LIB)/config -lpython$(PYTHON_VERSION)
- PYIFLAGS	= -I$(PYTHON_INC)
- 
- debug-sparky: main-debug.o python.o _tkinter.o $(SPARKY_OBJS)
--	$(CXX) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \
--		$(LDFLAGS) $(PYLDFLAGS) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \
-+		$(PYLDFLAGS) $(LDLIBS)
- 
- main-debug.o: main-debug.cc
- 	$(CXX) $(CXXFLAGS) $(PYIFLAGS) -c $(SPARKY_SRC)/main-debug.cc
diff --git a/sci-chemistry/sparky/files/3.115-makefile.patch b/sci-chemistry/sparky/files/3.115-makefile.patch
deleted file mode 100644
index 7c810dcbd8ae..000000000000
--- a/sci-chemistry/sparky/files/3.115-makefile.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/Makefile b/Makefile
-index bb27034..30979bd 100644
---- a/Makefile
-+++ b/Makefile
-@@ -48,6 +48,12 @@ TKINTER_PYMOD	= _tkinter$(PYMOD_SUFFIX)
- all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force
- 	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@
- 
-+libraries:
-+	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(SPY_PYMOD) $(TKINTER_PYMOD)
-+
-+binaries:
-+	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(EXECUTABLES) debug-sparky
-+
- Makefile.dep TAGS: force
- 	cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@
- 
diff --git a/sci-chemistry/sparky/files/3.115-paths.patch b/sci-chemistry/sparky/files/3.115-paths.patch
deleted file mode 100644
index 20d9a801ecd6..000000000000
--- a/sci-chemistry/sparky/files/3.115-paths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/c++/paths.h b/c++/paths.h
-index 2a21366..38aff52 100644
---- a/c++/paths.h
-+++ b/c++/paths.h
-@@ -19,7 +19,7 @@
- // Installation subdirectories and files
- //
- #define SPARKY_MANUAL		"manual"
--#define SPARKY_LIB		"lib"
-+#define SPARKY_LIB		"."
- #define SPARKY_PRINT		"print-prolog.ps"	// under lib directory
- #define SPARKY_RESOURCE		"Sparky"		// under lib directory
- #define SPARKY_SAMPLE_DATA	"example"
diff --git a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch
deleted file mode 100644
index d83b5b8510cc..000000000000
--- a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff --git a/bin/sparky b/bin/sparky
-index 8b51212..270723a 100644
---- a/bin/sparky
-+++ b/bin/sparky
-@@ -4,18 +4,6 @@
- #
- 
- # -----------------------------------------------------------------------------
--# Figure out Sparky installation directory from $0.
--#
--set sparky_exe = "$0"
--while (-l "$sparky_exe")
--  set ls_sparky_exe = `ls -l "$sparky_exe"`
--  set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'`
--end
--set sparky_bin = `dirname "$sparky_exe"`
--set sparky_bin = `cd "$sparky_bin"; pwd`
--set sparky_inst = `dirname "$sparky_bin"`
--
--# -----------------------------------------------------------------------------
- # Sparky uses the SPARKY_INSTALL environment variable to find its
- # application resource file and print prolog file.
- #
-@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL		"$sparky_inst"
- # If Python is available start Sparky as a Python extension.
- # Otherwise the standalone version of Sparky is started.
- #
--set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5"
-+set PYTHON = GENTOO_PYTHON
- if (! -e "$PYTHON") then
-   set PYTHON = python2.5
- endif
-@@ -79,7 +67,7 @@ if ($status == 0) then
-   # ---------------------------------------------------------------------------
-   # Add the Sparky package and Tkinter to the Python path
-   #
--  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk"
-+  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky"
-   if ($?PYTHONPATH) then
-     setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH"
-   else
diff --git a/sci-chemistry/sparky/metadata.xml b/sci-chemistry/sparky/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/sparky/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/sparky/sparky-3.115-r2.ebuild b/sci-chemistry/sparky/sparky-3.115-r2.ebuild
deleted file mode 100644
index e664747fea13..000000000000
--- a/sci-chemistry/sparky/sparky-3.115-r2.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit flag-o-matic prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Graphical NMR assignment and integration program for large polymers"
-HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/"
-SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib-${PV}/${PN}-source-${PV}.tar.gz"
-
-LICENSE="sparky"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	app-shells/tcsh
-	dev-lang/tcl:0=
-	dev-lang/tk:0="
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${PN}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-ldflags.patch
-	"${FILESDIR}"/${PV}-wrapper-r1.patch
-	"${FILESDIR}"/${PV}-paths.patch
-	"${FILESDIR}"/${PV}-makefile.patch
-	"${FILESDIR}"/${PV}-fix-c++14.patch
-)
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	TKVER=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-	PYVER=${EPYTHON#python}
-}
-
-src_prepare() {
-	default
-
-	sed -i \
-		-e "s:^\(set PYTHON =\).*:\1 ${PYTHON}:g" \
-		-e "s:^\(setenv SPARKY_INSTALL[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir)/${PN}:g" \
-		-e "s:tcl8.4:tcl${TKVER}:g" \
-		-e "s:tk8.4:tk${TKVER}:g" \
-		-e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir):g" \
-		"${S}"/bin/sparky || die
-	eprefixify "${S}"/bin/sparky
-}
-
-src_compile() {
-	emake \
-		SPARKY="${S}" \
-		PYTHON_VERSION="${PYVER}" \
-		PYTHON_PREFIX="${EPREFIX}/usr" \
-		PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \
-		PYTHON_INC="$(python_get_includedir)" \
-		TK_PREFIX="${EPREFIX}/usr" \
-		TCLTK_VERSION="${TKVER}" \
-		TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \
-		CXX="$(tc-getCXX)" \
-		CC="$(tc-getCC)" \
-		LDSHARED="-shared" \
-		binaries
-
-	rm c++/*.o || die
-
-	emake \
-		SPARKY="${S}" \
-		PYTHON_VERSION="${PYVER}" \
-		PYTHON_PREFIX="${EPREFIX}/usr" \
-		PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \
-		PYTHON_INC="$(python_get_includedir)" \
-		TK_PREFIX="${EPREFIX}/usr" \
-		TCLTK_VERSION="${TKVER}" \
-		TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \
-		CXX="$(tc-getCXX)" \
-		CC="$(tc-getCC)" \
-		CXXFLAGS="${CXXFLAGS} -fPIC" \
-		CFLAGS="${CFLAGS} -fPIC" \
-		LDSHARED="-shared -fPIC" \
-		libraries
-}
-
-src_install() {
-	# The symlinks are needed to avoid hacking the complete code to fix the locations
-	dobin c++/{{bruk,matrix,peaks,pipe,vnmr}2ucsf,ucsfdata,sparky-no-python} bin/${PN}
-
-	insinto /usr/share/${PN}/
-	doins lib/{print-prolog.ps,Sparky}
-	dosym ../../share/${PN}/print-prolog.ps /usr/$(get_libdir)/${PN}/print-prolog.ps
-	dosym ../../share/${PN}/Sparky /usr/$(get_libdir)/${PN}/Sparky
-
-	python_moduleinto ${PN}
-	python_domodule python/*.py c++/{spy.so,_tkinter.so}
-	dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python
-
-	rm manual/{pkzip.cfg,Makefile} || die
-	mv {manual/,}manual.ps || die
-	local DOCS=( README manual.ps )
-	local HTML_DOCS=( manual/. )
-	einstalldocs
-	newdoc python/README README.python
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual
-
-	if use examples; then
-		dodoc -r example
-		dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example
-	fi
-}
diff --git a/sci-chemistry/viewmol/Manifest b/sci-chemistry/viewmol/Manifest
deleted file mode 100644
index 7de430c5ed44..000000000000
--- a/sci-chemistry/viewmol/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX 2.4.1-change-default-paths.patch 2745 BLAKE2B c604ab1ffbe992b49671f0f1c713ce95fa2cec18b39d625856bdf8cbc226f8965f3fc13b22003a8ec812954daf2533cac4a001255e07a5cd3bf0eeaeed6524dd SHA512 9dda6e39f43706f9868eb02402137573d58e90b14940ad5d10ede6088e49d2ebd8a114ffda3cf4a69bee5874cc0a16b83bb4ea86281203765c5d861cb8dac6dd
-AUX 2.4.1-remove-icc-check.patch 1020 BLAKE2B 63c0b2c68be4bc745f8dbc184f1ca90bc0b5e2964508e686c811cb1a3f46d5ed8f401f789fce8e8f15b89e1ccaf7a657a2de830c2e829d6782f285031a89ee3c SHA512 ea2a1a58730561fcf2bc05a0f23dc2108cf2fd97d228a7a6305d3323abda5ce3510793dbebf2253cef9e6d60326889079bc6a9639228b1b2bfd9d9a3b8c03ebb
-DIST viewmol-2.4.1.src.tgz 2229379 BLAKE2B c7d3d9f0a0a728f13be718e2b85a645d1824d2c9efd920a05a0693dfb5904e18da20fcef8080e99f497280effdb71cb21c58d9aeadf49d2477e1c931caa49389 SHA512 42701d570d97e77b84597950a9068dfdf48faf4e551957383c8eea38f082c1ad136c17b7cbd3903673478506116d6fc08d1288842e74d6a9776526c685083584
-EBUILD viewmol-2.4.1-r3.ebuild 2225 BLAKE2B 74563226fe1bcbe418bde909f202eead15aedf7610a592f8d6d7ae1b2e0d47cf2bdec2a91e21772f978512ddbe0cc0739028694f85a2fa13adcaa9fe9e79a6c6 SHA512 b290d08a50662422876d093b973ba7b4e44fe759258325d1f796beb8f929575861a0b8367d52b1ab8a5976dea8e5b805894454867f32751fbd768bd6c9a3476c
-MISC metadata.xml 342 BLAKE2B 3d43fda7cef989246f20968757c7c9710832915b5aa7623026185e69f79901fdeed5503c04a87d7395bcc0f9fd47313a017673903df74cc7a55999fb5c24467a SHA512 f77c63597bc5df26ba6dd136ee943f78562c5d99fefc1b435633c602a6eb3433600976884085ea8aa8f87f2f79fd495e9b51f918290bc1751e66d7515fe4e039
diff --git a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch
deleted file mode 100644
index 4b1edef7ef8b..000000000000
--- a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-diff --git a/source/getrc.c b/source/getrc.c
-index a39b436..c130096 100644
---- a/getrc.c
-+++ b/getrc.c
-@@ -87,7 +87,7 @@ extern XtAppContext app;
- 
- static char viewmolpath[MAXLENLINE];
- 
--#define DEFAULTPATH "/usr/local/lib/viewmol"
-+#define DEFAULTPATH "@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR/viewmol"
- 
- int getrc(void)
- {
-diff --git a/source/install b/source/install
-index 580865b..f136af3 100755
---- a/install
-+++ b/install
-@@ -54,24 +54,27 @@ fi
- cp $dirorig/viewmol $ROOT/bin
- chmod 711 $ROOT/bin/viewmol
- 
--# install other files needed in $ROOT/lib/viewmol
--if [ ! -d $ROOT/lib/viewmol/$dir ]
-+# install other files needed in $ROOT/GENTOOLIBDIR/viewmol
-+if [ ! -d $ROOT/GENTOOLIBDIR/viewmol/$dir ]
- then
--  mkdir -p $ROOT/lib/viewmol/$dir
--  chmod 755 $ROOT/lib/viewmol/$dir
-+  mkdir -p $ROOT/GENTOOLIBDIR/viewmol/$dir
-+  chmod 755 $ROOT/GENTOOLIBDIR/viewmol/$dir
- fi
- cd $dirorig
--cp tm bio readgamess readgauss readmopac readpdb $ROOT/lib/viewmol/$dir
--chmod 711 $ROOT/lib/viewmol/$dir/*
-+cp tm bio readgamess readgauss readmopac readpdb $ROOT/GENTOOLIBDIR/viewmol/$dir
-+chmod 711 $ROOT/GENTOOLIBDIR/viewmol/$dir/*
- cd ../..
--cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/lib/viewmol
--chmod 755 $ROOT/lib/viewmol/*
--cp -r doc examples locale scripts tests $ROOT/lib/viewmol
--find $ROOT/lib/viewmol -type f -exec chmod a+r {} \;
--find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \;
--sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc
--chmod -R 644 $ROOT/lib/viewmol/viewmolrc
--if [ -d /usr/X11R6/lib/X11/app-defaults ]
-+cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/GENTOOLIBDIR/viewmol
-+chmod 755 $ROOT/GENTOOLIBDIR/viewmol/*
-+mkdir -p $ROOT/usr/share/viewmol $ROOT/usr/share/doc/GENTOODOCDIR/ $ROOT/GENTOOLIBDIR/viewmol/
-+cp -r examples scripts tests $ROOT/usr/share/viewmol
-+cp -r locale $ROOT/GENTOOLIBDIR/viewmol/
-+cp -r doc/* examples scripts tests $ROOT/usr/share/doc/GENTOODOCDIR/
-+find $ROOT/GENTOOLIBDIR/viewmol -type f -exec chmod a+r {} \;
-+find $ROOT/GENTOOLIBDIR/viewmol -type d -exec chmod a+rx {} \;
-+sed 's/\/source//g' viewmolrc > $ROOT/GENTOOLIBDIR/viewmol/viewmolrc
-+chmod -R 644 $ROOT/GENTOOLIBDIR/viewmol/viewmolrc
-+if [ -d $ROOT/X11R6/GENTOOLIBDIR/X11/app-defaults ]
- then
-   locale=`echo $LANG | cut -c1-2`
-   if [ "$locale" = "en" ]
-@@ -82,6 +85,6 @@ then
-     # The C locale is defined by default for rpm builds, overwrite it
-     locale="en_US"
-   fi
--  cp locale/${locale}/Viewmol /usr/X11R6/lib/X11/app-defaults
--  chmod a+r /usr/X11R6/lib/X11/app-defaults/Viewmol
-+  cp locale/${locale}/Viewmol ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults
-+  chmod a+r ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults/Viewmol
- fi
diff --git a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch
deleted file mode 100644
index fd91e0a5a434..000000000000
--- a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/getmachine
-+++ b/getmachine
-@@ -269,19 +269,11 @@
-            makedir
-            cat ../.config.$os > makefile
-            use_icc=`type icc 2> /dev/null`
--           if [ "$use_icc" = "" ]
--           then
- 	     findProcessor
- 	     echo 'COMPILER=gcc' >> makefile
-              echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile
-              echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile
-              echo "LDFLAGS=$LINKFORSHARED" >> makefile
--           else
--	     echo 'COMPILER=icc' >> makefile
--             echo 'OPT=-O2 -ipo' >> makefile
--             echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile
--             echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile
--           fi
-            echo 'SCANDIR=' >> makefile
-            echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile
-            echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile
diff --git a/sci-chemistry/viewmol/metadata.xml b/sci-chemistry/viewmol/metadata.xml
deleted file mode 100644
index 335c7edd503b..000000000000
--- a/sci-chemistry/viewmol/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">viewmol</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild b/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild
deleted file mode 100644
index a82367bac3b7..000000000000
--- a/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk(-)"
-
-inherit prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Open-source graphical front end for computational chemistry programs"
-HOMEPAGE="http://viewmol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/viewmol/${P}.src.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	media-libs/libpng:0=
-	media-libs/tiff:0
-	virtual/glu
-	virtual/opengl
-	x11-libs/libX11
-	x11-libs/libXi
-	x11-libs/libXmu
-	x11-libs/libXt
-	x11-libs/motif:0
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/source"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-remove-icc-check.patch
-	"${FILESDIR}"/${PV}-change-default-paths.patch
-)
-
-src_prepare() {
-	default
-
-	eprefixify getrc.c
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i install getrc.c || die
-	sed "s:GENTOODOCDIR:${PF}:g" -i install || die
-
-	mkdir "$(uname -s)" || die
-	cd "$(uname -s)" || die
-
-	cat >> ".config.$(uname -s)" <<- EOF || die
-		LIBTIFF = -L"${EPREFIX}/usr/$(get_libdir)"
-		TIFFINCLUDE = "${EPREFIX}/usr/include"
-
-		LIBPNG = -L"${EPREFIX}/usr/$(get_libdir)"
-		PNGINCLUDE = "${EPREFIX}/usr/include"
-
-		PYTHONVERSION = ${EPYTHON}
-		PYTHONINCLUDE = $(python_get_CFLAGS)
-		PYTHONLIB = $(python_get_LIBS)
-
-		COMPILER = $(tc-getCC)
-		CFLAGS = ${CFLAGS} -DLINUX
-		LDFLAGS = ${LDFLAGS}
-		SCANDIR=
-		INCLUDE=\$(TIFFINCLUDE) -I\$(PNGINCLUDE) \$(PYTHONINCLUDE)
-		LIBRARY=\$(LIBTIFF) \$(LIBPNG) \$(PYTHONLIB)
-		LIBS=-L"${EPREFIX}/usr/$(get_libdir)" -ltiff -lpng -lz -lGLU -lGL -L"${EPREFIX}/usr/X11R6/lib" -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm
-	EOF
-
-	cp .config.$(uname -s) makefile || die
-	cat ../Makefile >> makefile || die
-}
-
-src_compile() {
-	emake -C "$(uname -s)" viewmol_ tm_ bio_ readgamess_ readgauss_ readmopac_ readpdb_
-	"${EPREFIX}"/bin/bash makeTranslations || die
-}
-
-src_install() {
-	./install "${ED%/}"/usr || die
-
-	# fix broken layout
-	mv "${ED%/}"/usr/{usr/share,} || die
-	rm -rf "${ED%/}"/usr/usr || die
-	mv "${ED%/}"/usr/{$(get_libdir)/${PN}/locale,share} || die
-	mv "${ED%/}"/usr/{$(get_libdir),libexec} || die
-}
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 1cd5411f26dc..7185dba46aa6 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,15 +1,7 @@
-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-cuda.patch 15569 BLAKE2B a26ce893fd2808b7ce1ad36f6d2d690be482d24805f44030434fd3aadaa9f9a834ae8b73d7f1c759161e20041c2372181b90ae17f71eab50c94e6b38e3b133a3 SHA512 ba6f435601a53d5ed26ceab9ab86a9734e6a3b60f9cb61be5c9f59676a5145a4c64a538ddadf446e82608ade5a3d86ec6b8cb7257d9c402e245f845371feb571
 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 7255 BLAKE2B d59ea537a43555104edd2effc973274abae483d739bf5051efce7c1ad15e131ff0156ce2129cf882c88194f359c69eb163571e23f47025ae26cc6f85ab4999a2 SHA512 bafeb7c0448920feaa77855d29cffd2e3d9df1994c528bb738ac01551d6eb5fea4d3e681f5d4c189366e8dff973c9f8c5633f18648c31026ce749041eb5358ee
-EBUILD vmd-1.9.3-r1.ebuild 7612 BLAKE2B 62e0208cbe8fac390d942885f1e12713a88dc29eac68aa708dacfa9a2c0c0eff94982795ddc3bce47c459e8153692978744efdf520518705db0892208761dd9d SHA512 4529071928c4b63ebc35d92ff9ef7713a38d49d5579cf4351a979806ae81eb9ce3e02c438a9ce127eba217039341ae2c53e74710aa0151d4e9b0db865458facb
-EBUILD vmd-1.9.3-r4.ebuild 7793 BLAKE2B 9f023e8efb5a095d2d6b46198a4137298d7e61c697e7f1eeb57ecfa5f1df7102840b9c42f4ceeb8c5052c59031d572a50eda0a2799a11432487b15a21e97eb5c SHA512 22326601bd6908b3495ebef7e9b45f3482dbd73c8b6bd54582d02e4721bcc483ef02ea67d8e582b59777cbfc923e4464a707281a06b6459de64a7f1e301d9268
 EBUILD vmd-1.9.3-r5.ebuild 7822 BLAKE2B 2a3933c1008dcde65b37846ae5cfc993036d387a9a62a4cb207865187a22e8cf41401000171d083e059abc17c43adf773490aafcfbc576480b241fd359f6fb88 SHA512 9abc8facc673387ee0fcc77b27e4f421f2c7cb590b451b5d8ce4165a66be27ad1b69a45d9c939718a4359f1c76591855219bdb5956947aa2408d61f338eb78ca
-EBUILD vmd-1.9.3.ebuild 7210 BLAKE2B a4c7a26b5c137c67adb5ea4b49acf0b8866a5b5a30840816a7c5a62c12355dfbb3bf17b2dfff39501c9d63e5bf3b479624c9186f7eaef65db455a9f29fe543a3 SHA512 fea1bf7019ae20f796be0c9fb9a5f912a491de16ecabeb6327b366120621c65401f8b4d32a575cf8d231b2c40d54f7c38537f3ce6a217856e1ec44fe49420e38
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
deleted file mode 100644
index 67eb11bbd36b..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 +
- vmd-1.9.1/src/CUDAQuickSurf.cu     | 1 +
- 2 files changed, 2 insertions(+)
-
-diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu
-index 5bfe7bf..36faaf0 100755
---- a/src/CUDAMarchingCubes.cu
-+++ b/src/CUDAMarchingCubes.cu
-@@ -45,6 +45,7 @@
- #include "CUDAMarchingCubes.h"
- #include <thrust/scan.h>
- #include <thrust/functional.h>
-+#include <thrust/device_ptr.h>
- 
- // The number of threads to use for triangle generation 
- // (limited by shared memory size)
-diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu
-index a21ebde..56a42c8 100755
---- a/src/CUDAQuickSurf.cu
-+++ b/src/CUDAQuickSurf.cu
-@@ -22,6 +22,7 @@
- #include <stdlib.h>
- #include <string.h>
- #include <cuda.h>
-+#include <thrust/device_ptr.h>
- 
- #if CUDART_VERSION < 4000
- #error The VMD QuickSurf feature requires CUDA 4.0 or later
diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
deleted file mode 100644
index 3f9ea5c8c2ef..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- plugins/molfile_plugin/src/maeffplugin.cxx | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx
-index cfe1223..41d92bb 100644
---- a/plugins/molfile_plugin/src/maeffplugin.cxx
-+++ b/plugins/molfile_plugin/src/maeffplugin.cxx
-@@ -1979,7 +1979,7 @@ namespace {
-       }
-     }
-     catch (std::exception &e) {
--      fprintf(stderr, e.what());
-+      fprintf(stderr, "%s", e.what());
-       return MOLFILE_ERROR;
-     }
-     return MOLFILE_SUCCESS;
diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
deleted file mode 100644
index 92daf0304775..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ /dev/null
@@ -1,256 +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 cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar.gz"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${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
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	dev-lang/swig"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-	"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar.gz from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-}
-
-src_prepare() {
-	use cuda && cuda_sanitize
-
-	epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	epatch \
-		"${WORKDIR}"/${P}-gentoo-plugins.patch \
-		"${FILESDIR}"/${P}-format-security.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
-
-	epatch "${WORKDIR}"/${P}-gentoo-base.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 $(fltk-config --libs)):g" \
-		-e "s:gentoo-netcdf-include:${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 $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
deleted file mode 100644
index f42cb4d104fe..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
+++ /dev/null
@@ -1,267 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1:0=
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )
-"
-DEPEND="${CDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-	dev-lang/swig
-"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-	elog
-	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
-	elog "file may get downloaded as a compressed tarball or not. In that case"
-	elog "you will need to ensure you uncompress the file and rename it"
-	elog "as ${P}.src.tar"
-}
-
-src_prepare() {
-	default
-
-	use cuda && cuda_sanitize
-
-	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
-
-	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
-	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
-		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
deleted file mode 100644
index 39e7a9751cee..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
+++ /dev/null
@@ -1,271 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${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
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	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/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
deleted file mode 100644
index 88394af1970d..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ /dev/null
@@ -1,255 +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 cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	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}
-	virtual/pkgconfig
-	dev-lang/swig"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-	"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar.gz from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-}
-
-src_prepare() {
-	use cuda && cuda_sanitize
-
-	epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	epatch \
-		"${WORKDIR}"/${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
-
-	epatch "${WORKDIR}"/${P}-gentoo-base.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 $(fltk-config --libs)):g" \
-		-e "s:gentoo-netcdf-include:${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 $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}
diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest
index abcd5ed980d5..df8a29f5511f 100644
--- a/sci-chemistry/votca-csg/Manifest
+++ b/sci-chemistry/votca-csg/Manifest
@@ -3,6 +3,7 @@ DIST votca-csg-1.4.tar.gz 346527 BLAKE2B 8f0a41f9aa9fd865e2e544d5fd587d93d631edc
 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-1.6.1.tar.gz 474044 BLAKE2B 36ededfffe7af5b87b2a031f69afbb9cc727af9454466163312e48c23719f6fe3cb727de96c419ae6e7d4901576013bd76f84d8e7e394cc65df4d83bd1ce30bb SHA512 b8f0f1bf2ca57ee9e2050b4a76e1d725ccb0908314886415f36d4e4554953b4e1c93f7c05502afb77f9b7b5ef3059ebbf7f223b965ba72ae45736798fa2e6ad9
+DIST votca-csg-1.6.2.tar.gz 522982 BLAKE2B e0376e04e7baabaa45cab2cc87ff3d7574a35a4a50d87763bb42232eb6f110904b9fb5cdee0a8f2b4057a441a8ca5e276a8d44e14ec3609301832c2ed18cfd94 SHA512 e1d88cc9d18718f323355736afaf309940234001abb39414dd4990f1ff231ef3e8f71d51c78929c422c296b96f304fa17f6c9671071148ff1446bdc1eb442708
 DIST votca-csg-1.6.tar.gz 464175 BLAKE2B 1871c7edc4b4e848a06049a7c687e906f166312777bdbf5c65be8efe8d5032582fdca9dc7eca453b7013901f409326b0583c79731c68fa2b4e6366f021958b0b SHA512 76cda93023d46a66ae31edcec0ece709ddc70a9be9d098721b945006c197ed3b6cbd1e643158797be518c4fe66f7b23d3e8d8735cbd9e155db3db0d79929cfbe
 DIST votca-csg-1.6_rc1.tar.gz 479265 BLAKE2B c4ba3c81eefd375eea6f8c0b1cd60f9cc80898fb7e8e811ecc286f06d94bd4316edfca277649ec3f7f8b751b2f2928ca2dfe61cc3b1c3060a324ea783c62003f SHA512 6622648ddc3308ca2f8e98d6dbcd28e33a4e0fb44d96ef94ebcaa2e87e5ba3ca2ab83dcc1de4fd0803dbc20ba7192f5fdd2c935b364ed4e2122b5948c10d4936
 DIST votca-csg-manual-1.4.1.pdf 1282641 BLAKE2B 370b7c8997649555fd2360b999cf381c340a74c3747afda23d0e9d346367cc6d14d4e9a0e9ac82184945427d30050dd623dd1b6d8218c6ff3d2f17331987aaae SHA512 e89f41af05eaeb9ea499e8625cc98e2632ec647ec2d8c9c9052dcd4d2935d082b29b51495514e3e06e73ce42b8cda7017fc523a013569378e2bc86bf88ad32d4
@@ -10,6 +11,7 @@ DIST votca-csg-manual-1.4.pdf 1281983 BLAKE2B 5659c2e327ba7bb00fac15adfb578288d5
 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-manual-1.6.1.pdf 1248350 BLAKE2B d4433974e38785fb968bd357ed2914515b2a22a78d6417597265bb1420b5af8b7b9849533a5faba571bcf635eff8385b244b2252bf7a20d3adb9318cd7115b03 SHA512 d627a9c7a71b8ac5e8d6ca109f0ea56978706b0dd1408aaf10b75b4b52f40b6150063248477ca2b5922f603e8d582ddd4dec3de73b3991db5fbb7bf204d347a3
+DIST votca-csg-manual-1.6.2.pdf 1241907 BLAKE2B 9d51682099081cb8301eed10e7bb4f3afea89561626da5f3b361939d8d9b4ed15bb49392074bc19c530d413f4913afbf4ce612ee62e0e4d22c30f856a2019cbb SHA512 a85094bfa9ae2fcef52f42af162eb1a94ed30de9d7785aac03d7591177f6982dd315874566ce2671df508a3139ce8816c6becf0e0c1d0bfb9b675063810eb3e7
 DIST votca-csg-manual-1.6.pdf 1248178 BLAKE2B 5213d55787041db81fe8563febbf130db6aed9233e569039b66d69cfb173131353d45bef824640ee7b0a3fed7821ede4d5a6ce6ffc14d1548499317afdc0248a SHA512 e91d4b8397b67808c9671b9adbaad41fd9a0ede90066e220839d86f21a9bbcd4e433534faf1dfbca106d55af5a6cce0425a5bdfa3eb30ebe14469594da0129ca
 DIST votca-csg-manual-1.6_rc1.pdf 1248403 BLAKE2B b702eff4a36d27d592147f115f4e9080cbf580b6401141a14865395f0cb927c35f60035f92724e71e5edadbbe3e317f93989eb6f2e0a0e7b9f685e56851546d2 SHA512 2514bd2fee4bae787a3f8c07d1f1d90061a2b503255efe0730ed164bb002c7e7ad7309ccd3b5b931994f70b7ed99afde28955d9ea1b34c86df21bfcb8bfb39bb
 DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 BLAKE2B e9acf8e421f6fce4d97be2d51fb559979c6fd3e6b042525cedf32cadeab1dddc5b1aaf80bbbfd387da3bce71672759c2e84d317c789f616dc71834c72a581fff SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90
@@ -17,6 +19,7 @@ DIST votca-csg-tutorials-1.4.tar.gz 6348417 BLAKE2B 612fcbc4457a57be74e5306bf86d
 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
 DIST votca-csg-tutorials-1.6.1.tar.gz 5945945 BLAKE2B 18ea7e406acf70e37049b1f8676551d96b20825fba25bb9c1e674b0f94f5ee41bd74ce77619880dfb2e2f1f8fb0b40de9ce8a5e9e9d8470639af057376a19632 SHA512 82d60fcea4859e1caa6138147848427dbdb1ddcf4e0713b6f2d50cd624ceacdbce1ceb8e98fb85d079d8d9de02f501ec8c9236243fe75761e44486f27207249b
+DIST votca-csg-tutorials-1.6.2.tar.gz 5945110 BLAKE2B 2871c89c763c8624deb877f90da10cd2021ec5b10a0d8473c4523b70a179247ad2e809aa5b0aab7c36a324d929b55f3b2070822914043382424b87fbf34ef05b SHA512 40f377a824f6c10be759adf3e1b87dbc5392b00e4a377ba04d998f96aa9b7ceb986c2e5cfac16ea3047f08d2d76deb7e9f3aadfba794f58b8f131861f7a7ff04
 DIST votca-csg-tutorials-1.6.tar.gz 5946764 BLAKE2B 018bd00c86c0a85baf35afd2ea4206c96dee8f948dcbf331b53e6f685b69bf2c909731b15ba3261c86cee9e1960ec5cfa7b2ee0c6dcfabbbbc110789840184ad SHA512 36d3a66c19d230f2002170851345da7063aeef1f29841945b8a182f73922617823815dde5d7289fb0f80e771ac03780adacdf95af4814235edbf69a4772b3696
 DIST votca-csg-tutorials-1.6_rc1.tar.gz 5946622 BLAKE2B 7bf0c7083ca7b148d16f7b77b9f785c11b16a8124a5435522e8c065859f4c2ae560c622f04021918b2683c9955d5a1b674c84fad179319f5fedb86616bbe24e7 SHA512 1c89f95944f8277a995d9d6d7dacfae2ae1be54a9a7b19c53d3464a4bdf5da0556e862033ba0a5f442b1ee5bd79bafd478655856fe266f4285c98e14512ce259
 EBUILD votca-csg-1.4.1.ebuild 3204 BLAKE2B e447a6859d7ee4d722701f96634667529bd183f10dd4affeb2713023edfe52ab73988df7ef912963bd154b893bd2d401d2fd110a729040a2a2c52ec5fd44985c SHA512 df94c127269df2a2eaa9643005eeeae6925b458fbb0cb4d1661757a49e5ab4926a613c532e4df4475b34768e904d2388270c868c9ad675cd110e2b1737153e3d
@@ -24,7 +27,8 @@ EBUILD votca-csg-1.4.ebuild 3200 BLAKE2B 041deefd8fc208525c636d00665f7ea70d0efaf
 EBUILD votca-csg-1.5.1.ebuild 2552 BLAKE2B a64b31b3b6a9297b6ead93e9f5605ace929fecf98ee377eff17a0b529b9176fe5d251e9efb5dada1c7d29b144b7e89dcd95ff3c6921b7584f225f842bc93f94b SHA512 3d96fac05c344f0986597ec6ce50f07a19327113d3b02238df60ce28ab2788f91a224f9c70ecdaaf6cfe6206f00f8e86e4ad2dde1c68c5c0a32f5d20eee658cd
 EBUILD votca-csg-1.5.ebuild 2550 BLAKE2B 7fb2a4280fca23370169fbf04c3b9251065f06d56d7df29a26f3bbaf642e3296e400a23cc3c7524a830cee0dd881e598569c82bbcfacbec35198dd564d379828 SHA512 9516699dbfab66505053d701a31440ce0ca16484b6b0f60b072f6d5a54740449c90ea96461e08d598933dd7f7803278dbc4e19df381f5b57c541b9d3de90c9d5
 EBUILD votca-csg-1.6.1.ebuild 2369 BLAKE2B a6d8e7e9049f55f2e916614586bb6ec68e1223ea25cff260ee884f94f137afb798c51983ab7df7b54e918fc1b9eb4c315e380b1a4649e361b999753d11e5c210 SHA512 f72714b948a8c0ca93061aeeb9ff3bc358d8b0c0b5e369dbb732569ad302edf9198753e8e0921fae9cab5deb6ef3e5111d921c3fd4c0a4a8ec3deb41afb43825
+EBUILD votca-csg-1.6.2.ebuild 2340 BLAKE2B 97934fdd4b56cfbc58d5c2f47179ed3f747600ae870fe86fc7829fcdecb8e72e67ec129b49cc25e0a04b1dccb878ae79f7e693f59184da4e447eacbceb794b12 SHA512 30e0ef70ef8cf7c791a8579b01440fb7013ed4344a2132e955e17d1b8a5edac7982dae46d796122f8066584583f4b9356a478b512334ec4f0dae647ed4fa8f6e
 EBUILD votca-csg-1.6.ebuild 2365 BLAKE2B 585240513e8b06c9c35aab0dfb75962c59e2d42853837eaa67d86c728c5cd3d8485061a4974c71898caba41d6d44a1cf93ba27c16824427b767f965e8f9a07ab SHA512 38b6ff068367ac79717f9a364b2b6a83824cec0c804af934f15d3f19ca1cf50eddd8b94cc64c0b035724a6abca2f32a40ec598396c646f5a31c0ea0748bff976
 EBUILD votca-csg-1.6_rc1.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac
-EBUILD votca-csg-9999.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac
+EBUILD votca-csg-9999.ebuild 2340 BLAKE2B 97934fdd4b56cfbc58d5c2f47179ed3f747600ae870fe86fc7829fcdecb8e72e67ec129b49cc25e0a04b1dccb878ae79f7e693f59184da4e447eacbceb794b12 SHA512 30e0ef70ef8cf7c791a8579b01440fb7013ed4344a2132e955e17d1b8a5edac7982dae46d796122f8066584583f4b9356a478b512334ec4f0dae647ed4fa8f6e
 MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1
diff --git a/sci-chemistry/votca-csg/votca-csg-1.6.2.ebuild b/sci-chemistry/votca-csg/votca-csg-1.6.2.ebuild
new file mode 100644
index 000000000000..c77bb3e40fa8
--- /dev/null
+++ b/sci-chemistry/votca-csg/votca-csg-1.6.2.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake 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/${PN/-//}.git"
+	KEYWORDS=""
+	PDEPEND="${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}
+	>=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_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call
+	for i in "${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"
+	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-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
index 0e02baa215a8..c77bb3e40fa8 100644
--- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild
+++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils multilib
+inherit bash-completion-r1 cmake multilib
 
 IUSE="doc examples extras +gromacs hdf5"
 PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )"
@@ -62,11 +62,11 @@ src_configure() {
 		-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5')
 		-DWITH_RC_FILES=OFF
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
 
 src_install() {
-	cmake-utils_src_install
+	cmake_src_install
 	newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call
 	for i in "${ED}"/usr/bin/csg_*; do
 		[[ ${i} = *csg_call ]] && continue
diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest
index 26ba926b94b7..da02e1913994 100644
--- a/sci-chemistry/votca-csgapps/Manifest
+++ b/sci-chemistry/votca-csgapps/Manifest
@@ -3,6 +3,7 @@ DIST votca-csgapps-1.4.tar.gz 21072 BLAKE2B 30c2f6692544741bfbec09efea2f68ae48cd
 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
 DIST votca-csgapps-1.6.1.tar.gz 20128 BLAKE2B 509f684b84e7ebb718fbcf5b48adc732dc8c6b9f6478269e243dda3c980a5d91a46208863ac6227a07d90f6e2ea4e5cf2b50a7b34b6dbe2567d9a95ede4ee1de SHA512 06e396c20990f7bb22ae8c888a36585b40a61280aa53a521c01128bbaadc1f449f85d4f41380ee3ce290defb64eca285be7dde1cd888f4cb69805695511a5b90
+DIST votca-csgapps-1.6.2.tar.gz 19549 BLAKE2B 8aad4ff143a2073b4d17a4af0766898882ed011be4de814b6dca3cb4c1776fbee925fb4fef4ba1fd20d3aa3097440caeaab7fddb68b35322b5123868e7e2fbea SHA512 f88f8ea41773b846ed7b3b910ad81c58a6dc1aabea5ae8ead030709c095e229b29443213854d358b4fa6518d8373b9a2acab741be2bbc33fec22d8f267f6cfe3
 DIST votca-csgapps-1.6.tar.gz 20130 BLAKE2B 0c34fba42a70f756043aae89f51b94cc0a9c9a85680ed78c56b4c05f834d94c74aff59e4adf6155e5fab81d057da58ec420d843532af57beeaa6e81f82432d92 SHA512 5a85abaf6b09a225604f33f2e0cfb774525159e9bce89efd7ebfc0c9c37342e472503ff51c3065be2a4b87e95671f55164c630477f404f94b0510a83e262352f
 DIST votca-csgapps-1.6_rc1.tar.gz 20138 BLAKE2B 9374911f761fd78f01721e8e10f3b9c14f2ba894735735e4d09f5e29eb1d1b69f4fa081699d7a93abfad2ebe55d6439edbb6db547618e6d2cfbaf7bbc8a79ca8 SHA512 153bd6e537175c9908739c60ce80830ebf57c0686f11b21fc541995cb5355d4a3f7f7ee7d1707bb85f5fc859bf260a3a167450175ffe8feb92044e8018be996b
 EBUILD votca-csgapps-1.4.1.ebuild 653 BLAKE2B 208ae3538fcf42296a4a1077d222a9d6f752648834dc8f74941546fa2bdffb6fd9ea60ad31d124b8de52c3f59c089f48d4395b5166989fec19191076570e1bf0 SHA512 13ab1d118aea4f16664566f4e13965cc46a9e67e37157e23ad8c76a68d5db89b8db5b95104c23cf9cc16f78315dc9f632708cbd3920a545d964e2226dc6f9ff2
@@ -10,7 +11,8 @@ EBUILD votca-csgapps-1.4.ebuild 649 BLAKE2B 4b219583f5d5a1f7f4ed7635b4fedce2619d
 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-1.6.1.ebuild 676 BLAKE2B 7e91e674c0e4602b174877aac82562e75f9bcc5a8a5291910f5f801bb8335acc43417594c9a616ebe6fadd72ca165860a2bc3e2b4508e6d8546e1c59542c4cc1 SHA512 4b23fda3ec2857c773ffe2947ede48903f88a664c4e41f07637cbd2859b05c91108295791b53a02a33eab4777c53f89e30fb378721eec402e4abead2c2e8def4
+EBUILD votca-csgapps-1.6.2.ebuild 659 BLAKE2B e0c0b1b95d98f743f356923fae13cd7747dcb3846f2bf066e34624db9080ea16fb171319dc97ed4357d816622ade101375f0e41d9e549496701211916622aeae SHA512 24c0567317c698a1105a6999c8e696c7763fdfb8cb811d3749cbf717028cc6770d03cd56e46aa6b009ae8c40f03fe27fb9db988f007ef4be433191903984711b
 EBUILD votca-csgapps-1.6.ebuild 672 BLAKE2B 2737abc16e6a06485fb9e542bd620f3ee1c9b63f4fde290558e0674a4cd2488162d917f8654c108080c9370c49fe027e60fe417d33bf6a6be5d14ebd667dfd4f SHA512 af87122c3f45b6003b314373e2a87035a37f6540221c01f31b40573a9ed9973bb9124f35342e601c9c0667db9ee60042b7aca5dbf495079518d5cf62961da852
 EBUILD votca-csgapps-1.6_rc1.ebuild 665 BLAKE2B 893814bcc1e8413a5c6454c32092aa51e3633f2917aedf47bc928c603554acf064a299208e9a1c8cf58437cebdee00f6d07fd30424540081ef3d0c7f2636d8d0 SHA512 a32d204985dd20ef8389cbfd44f6e45d44542480d0593ddaa17d5976e193db687f26d1e818251325c939552c7e9a1c1f95ec20ca952834cc4a4ca6c4836ea2b7
-EBUILD votca-csgapps-9999.ebuild 665 BLAKE2B 893814bcc1e8413a5c6454c32092aa51e3633f2917aedf47bc928c603554acf064a299208e9a1c8cf58437cebdee00f6d07fd30424540081ef3d0c7f2636d8d0 SHA512 a32d204985dd20ef8389cbfd44f6e45d44542480d0593ddaa17d5976e193db687f26d1e818251325c939552c7e9a1c1f95ec20ca952834cc4a4ca6c4836ea2b7
+EBUILD votca-csgapps-9999.ebuild 659 BLAKE2B e0c0b1b95d98f743f356923fae13cd7747dcb3846f2bf066e34624db9080ea16fb171319dc97ed4357d816622ade101375f0e41d9e549496701211916622aeae SHA512 24c0567317c698a1105a6999c8e696c7763fdfb8cb811d3749cbf717028cc6770d03cd56e46aa6b009ae8c40f03fe27fb9db988f007ef4be433191903984711b
 MISC metadata.xml 457 BLAKE2B 9d392be6c061ebd3d975308065fcdec4ee061268f4b8b79e122b183d2e4f7259fdb9e165b8b3f030f1edbbc4f112757b1de7a50929ac112d5633143f9585699a SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563
diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.6.2.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.2.ebuild
new file mode 100644
index 000000000000..4f5d6d7d4aa7
--- /dev/null
+++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit cmake
+
+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=""
+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.md )
diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild
index 463cba8e0e38..4f5d6d7d4aa7 100644
--- a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild
+++ b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit cmake-utils
+inherit cmake
 
 if [ "${PV}" != "9999" ]; then
 	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest
index 6a89b861c3c8..acae167993cd 100644
--- a/sci-chemistry/votca-xtp/Manifest
+++ b/sci-chemistry/votca-xtp/Manifest
@@ -3,6 +3,7 @@ DIST votca-xtp-1.4.tar.gz 15214266 BLAKE2B 435ba1603495d904ccce20b4fa665d3a1c62f
 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-1.6.1.tar.gz 1405246 BLAKE2B b32db1e50ebfd79683ea2bf990293d9dfcf7703f3d95467a3fac5f98ec98e9bf1d29bab079e8f328fab8998144af186e7f47e99d9312763f7d73a1ae364ce58a SHA512 8b1bb235e70c239d0c57ceac65cd384841ea136d61f28bc72cbe2cfb47f9d776d42e06180acd1d8da93d0a0586e0bc3884ed82830d0f31c498ce225ca79a45aa
+DIST votca-xtp-1.6.2.tar.gz 1405868 BLAKE2B 4e5700cec41ede632b97904259040aef2b79f9698547bf508584e49ff5cb16ab627c31732136de67bed3f70af9bf890a25bf511e8d9278821107760fc29441b7 SHA512 64610239ef5b902daa4ff475b4fea194912ef2a50e24214fcecf7d63336208a642c5ae5f02b0f21d04a78acaef224ba9a29b06b9380dbd6a43553e704efc54fe
 DIST votca-xtp-1.6.tar.gz 1404955 BLAKE2B 1599281ea1cd6b5a93b1d91f69a793af7bb9cd2fbf70157e5d40a5bfc72f973f3d97338f92157c2c482ad041f8afda298282b1f83dda66d0bb189bdc07bb5a23 SHA512 cb99c31fe7f1af53b8ccf50cc9cc304ed5c5b5d1a165e1a72a456c0bbf5ac8bb9263c9eff829acc74be348192afbf80fd4d80a2c20d1dd5d7f909b1b50368670
 DIST votca-xtp-1.6_rc1.tar.gz 13586771 BLAKE2B d5b72a7389b77df0570eac0021870bba3fa66a89b3a2df1e08632b1c1827884d101ef8d972762dae35e44e53e7a9fe9278d3204eec09c35d091ab3427b055be4 SHA512 0b54eddcf944967b1d41f75f4887eba9edc3be18b94d319e93e795a24f58a2877d7f60afd806290eacb41d329d1b1206ebaab83874d6be2d5b026f06dbc19dfd
 DIST votca-xtp-manual-1.4.1.pdf 1066873 BLAKE2B 8cbd4b55b013794a19a8b5867b929b8e2d9084e6780d777b2a2bbaea23006f4f4ec5b26bd4a07c59e1c6726f23471eb1756b668636e0c4e656a0807e64197586 SHA512 fdf1147f24785524f5e96020fcd29c32bbeef520eebf6afba32b59d7e777d586c452919478d2734c3f021e558b1147b945cdbc0833402be2b16e5af3a8e37f5f
@@ -14,7 +15,8 @@ EBUILD votca-xtp-1.4.ebuild 1618 BLAKE2B bab1c2d4cd442bc2208f87ff16ed1218aaf6c34
 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-1.6.1.ebuild 992 BLAKE2B ec7860af210b86c57cecb6adb3ef42130f208a60f23f65dadde98ac751cf8dc0981861b5126c2f97b6e7e20e4d6ab78a847c4e644d21fdf741b91784ce85bdfe SHA512 7174ba2da6f0bc38e2532c525a98c2d4e5641bd6879b9a1d5ed133fbfcd0523420398793edb6a86d033b759e8e6fb5550312608639517c50c4d17876ef9a9cfc
+EBUILD votca-xtp-1.6.2.ebuild 975 BLAKE2B 95533f87c2afefb78002e83099299e40b00fc5bd16e8e054810fa60f6d039ae1c35452f1fd14e586e9d8adbadf1293d85e93b0906b324854b0bc71e85231ba97 SHA512 497c6b1c081e56b64ca33bc0089946c32b1b0ec977f38a7bafba976087ea192d70b1535d49394a87b347b68872dd3b91970b647dd8bccc72713556daa955cd61
 EBUILD votca-xtp-1.6.ebuild 988 BLAKE2B a0829b922e31fe3e14c60422ebaff3e26da19320b78d22fcdf22de032d9983a98f019a2469ffe9807cc34585fc8655c5a5cc7f80e81c8547e95aa9e569e240c5 SHA512 7643ea1c4b2c123169f8c3a06c4d04e5bccb9070afe70bcbe8c935f956b78ce29c83223e9c54df8915164f0107ffec50b50a639ba0c4407f9cb3e70ee5f93023
 EBUILD votca-xtp-1.6_rc1.ebuild 981 BLAKE2B 029f87e4554e2d353b5ce31f3901b5d18ae56ae4165878066e93d2de5f4ff4c65b9532be077127ec4e605b22ff0c765b841a6f9978cc7e503e50554b0e7ff7b7 SHA512 e2d58abe5b8f8d6b3e2a696a0b0a0f7b27f0af4a88d00d2fc59053dbccd9b7fa840579a5bc3b854bcdf3ce9266d10bacd962d4bada0b5ed325e0074c2d873d3d
-EBUILD votca-xtp-9999.ebuild 981 BLAKE2B 029f87e4554e2d353b5ce31f3901b5d18ae56ae4165878066e93d2de5f4ff4c65b9532be077127ec4e605b22ff0c765b841a6f9978cc7e503e50554b0e7ff7b7 SHA512 e2d58abe5b8f8d6b3e2a696a0b0a0f7b27f0af4a88d00d2fc59053dbccd9b7fa840579a5bc3b854bcdf3ce9266d10bacd962d4bada0b5ed325e0074c2d873d3d
+EBUILD votca-xtp-9999.ebuild 975 BLAKE2B 95533f87c2afefb78002e83099299e40b00fc5bd16e8e054810fa60f6d039ae1c35452f1fd14e586e9d8adbadf1293d85e93b0906b324854b0bc71e85231ba97 SHA512 497c6b1c081e56b64ca33bc0089946c32b1b0ec977f38a7bafba976087ea192d70b1535d49394a87b347b68872dd3b91970b647dd8bccc72713556daa955cd61
 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e
diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.6.2.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.6.2.ebuild
new file mode 100644
index 000000000000..116b226b03f4
--- /dev/null
+++ b/sci-chemistry/votca-xtp/votca-xtp-1.6.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake multilib
+
+IUSE=""
+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=""
+fi
+
+DESCRIPTION="Votca excitation and charge properties module"
+HOMEPAGE="http://www.votca.org"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+
+RDEPEND="
+	~sci-libs/votca-tools-${PV}
+	>=dev-cpp/eigen-3.3
+	sci-libs/hdf5[cxx]
+	~sci-chemistry/votca-csg-${PV}
+	sci-libs/libxc"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+DOCS=( README.md NOTICE CHANGELOG.md )
+
+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
+}
diff --git a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild
index 9e3b8ca0fa6d..116b226b03f4 100644
--- a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild
+++ b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils multilib
+inherit bash-completion-r1 cmake multilib
 
 IUSE=""
 if [ "${PV}" != "9999" ]; then
author	V3n3RiX <venerix@redcorelinux.org>	2020-08-25 10:45:55 +0100
committer	V3n3RiX <venerix@redcorelinux.org>	2020-08-25 10:45:55 +0100
commit	3cf7c3ef441822c889356fd1812ebf2944a59851 (patch)
tree	c513fe68548b40365c1c2ebfe35c58ad431cdd77 /sci-chemistry
parent	05b8b0e0af1d72e51a3ee61522941bf7605cd01c (diff)