*/*: Drop more Py2 last-rited pkgs

Bug: https://bugs.gentoo.org/715966
Closes: https://bugs.gentoo.org/714628
Closes: https://bugs.gentoo.org/606680
Closes: https://bugs.gentoo.org/686238
Closes: https://bugs.gentoo.org/710214
Closes: https://bugs.gentoo.org/710028
Closes: https://bugs.gentoo.org/710032
Closes: https://bugs.gentoo.org/656934
Closes: https://bugs.gentoo.org/592718
Closes: https://bugs.gentoo.org/446122
Closes: https://bugs.gentoo.org/547210
Closes: https://bugs.gentoo.org/359785
Closes: https://bugs.gentoo.org/571396
Closes: https://bugs.gentoo.org/600754
Closes: https://bugs.gentoo.org/677830
Closes: https://bugs.gentoo.org/710716
Closes: https://bugs.gentoo.org/651940
Closes: https://bugs.gentoo.org/695132
Closes: https://bugs.gentoo.org/708978
Closes: https://bugs.gentoo.org/710058

Signed-off-by: Aaron Bauman <bman@gentoo.org>

48 files changed, 0 insertions, 1742 deletions

diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
deleted file mode 100644
index 1a146495e053..000000000000
--- a/sci-chemistry/apbs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a
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/eden/Manifest b/sci-chemistry/eden/Manifest
deleted file mode 100644
index ef7017e4ec14..000000000000
--- a/sci-chemistry/eden/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST eden_V5.3.tar.gz 1139981 BLAKE2B 237f054accbba72fcde3a43716915a8037412a26aee861839c4a6e404276126a3955e6e0a3c76078b2253658f3ab9bcf8ad628bba059421c5171d0394c41052b SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5
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/p3d/Manifest b/sci-chemistry/p3d/Manifest
deleted file mode 100644
index 93d8b80b2f94..000000000000
--- a/sci-chemistry/p3d/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST p3d-0.4.3.tar.gz 7213577 BLAKE2B b614957be16ede7567bd6412d183b3cb79638a5033672afd725cafaf393e306d5d227e1bca444ea17d60a3cd3bb5d3b2c910f2bfc68a118d3bffcd29944b4c29 SHA512 b4cf472b849ece96fe0b2b7f633c496fe3d12bf8cb82a2af10180ce5c27c5465dd0c16cb912d22c56c933b68c06e7de28c0c640da29eaa6bc6f95009bf10277f
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/${PN}
-		doins -r pdbs exampleScripts
-	fi
-}
diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest
deleted file mode 100644
index f507aec00c53..000000000000
--- a/sci-chemistry/pdb-tools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pdbTools_0.2.1.tar.gz 103835 BLAKE2B ad4b5c8d6eb000c79a6d2797519b99027350fa34f6d543f6302f1a9edbe3497afe1a7b5c5c0e7243081cc709d9f1c37da5fc31605a0a225413851ce7288f64c9 SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724
diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml
deleted file mode 100644
index 25095bc4b42e..000000000000
--- a/sci-chemistry/pdb-tools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="google-code">pdb-tools</remote-id>
-    <remote-id type="github">harmslab/pdbtools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
deleted file mode 100644
index 090b7c041dfe..000000000000
--- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit fortran-2 python-single-r1 toolchain-funcs
-
-MY_PN="pdbTools"
-
-DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files"
-HOMEPAGE="https://github.com/harmslab/pdbtools"
-SRC_URI="https://${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 0663d5136267..000000000000
--- a/sci-chemistry/pdb2pqr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f
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 57d019e2f920..000000000000
--- a/sci-chemistry/prodecomp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d
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-caver/Manifest b/sci-chemistry/pymol-plugins-caver/Manifest
deleted file mode 100644
index 4d7abe5d823c..000000000000
--- a/sci-chemistry/pymol-plugins-caver/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Caver2_1_2_pymol_plugin.zip 5698331 BLAKE2B e1accfaea6faf1e8c545b88c965228ccb62710d4015ff681506971feba6bd18a4a8b0b6e6caf621c99830ba529a6ec17873cdd3d5e52ad6dc6f67d9457e4eb87 SHA512 9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c
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 672421ffa008..000000000000
--- a/sci-chemistry/pymol-plugins-dssp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pymol-plugins-dssp-110430.py.xz 6836 BLAKE2B d8a58d1ad85aaa45acdcac40d022bac8035baf9c95c05e2cd6abb1dd82f1cd390515e04b4c65ff96902655a366ca2e4eab8e86060dffb27ea146298f827fbd7c SHA512 521e0a32ca6d2c8c21c690815b0654bb44303bd7fb9a1eb76227030b2ad7311fadb0d748e49b8bbc16cd5e69acba375b5353de7bffef1ff69686e62021fe64f4
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-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest
deleted file mode 100644
index 521213fb730c..000000000000
--- a/sci-chemistry/pymol-plugins-promol/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pymol-plugins-promol-3.0.2.zip 2219295 BLAKE2B 7e81de98ee20f6b22fabeca35b0825250c3b839b9ea51f6c0b51f15062c73810474bd377d0e39d3c2ac0d61f1b5cfb4174c53f1dfc67a11dfcd707eee417a7ed SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7
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/sparky/Manifest b/sci-chemistry/sparky/Manifest
deleted file mode 100644
index abb7a3bc2696..000000000000
--- a/sci-chemistry/sparky/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sparky-source-3.115.tar.gz 4103686 BLAKE2B c7811aa135b10f21b8807447e2ab173f407ccc1446ff1307006f7f885e6e69983647991600720e02e4e738bb68338de01bc5d57577eacf20298db6d53a54b183 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89
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
-}