gentoo resync : 04.05.2021

9 files changed, 6 insertions, 576 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 95348a04517a..8778c0e1caa5 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest
index 8ab95b157670..7e8efe4ee960 100644
--- a/sci-chemistry/modeller/Manifest
+++ b/sci-chemistry/modeller/Manifest
@@ -1,3 +1,3 @@
 DIST modeller-9.25.tar.gz 44820658 BLAKE2B b3e8a3cc8cc70689a25bc5ed2eee294d67bef8eea9ed4b64d41aba3a27c0bc428ae58e74d734da0eaab7e4fabb213d098b9ba66b9569557159ac7d4a58244b0a SHA512 93f273aba0ec0f884cde5bbcc24769a09386bfc6bf1744d80001e41924b1a682225ba3c554fb9898ef3bfd1fd8451f9458bb92431b20f2f51b01781e79686c91
-EBUILD modeller-9.25.ebuild 3844 BLAKE2B 6190491bec7c4ca0bbca56675b6a5dd36ffe4381ebb779ae9fdb4760e71a04a503ff452e1d45ee297f8474152eb0e91dc10de74184e4bee8c48dac22191a81b3 SHA512 9e44ef9659c7cc6ce5d3c21a4c3706e9fffe38872312c3da1443d6200c6dcf879827537b0e131409f54268658ff9774176580babb3c4506fa216ec51f89b7cd7
+EBUILD modeller-9.25.ebuild 3847 BLAKE2B 410b9f2e700d683f4e08fc973096fab394707b718a36c1266a157ac5778b9210b725db00aabc541ac0f361fb5e3d6b728c218ad9b2bd277247d8c787b8ff5de3 SHA512 6b5d1b11aa56a2fc552ea41c41c9aea023bb3a782af21a498e042c96599d47dc84058137f03e25e16177d5ce1be59af3fce9b09043b15cb9433685ab86119785
 MISC metadata.xml 374 BLAKE2B d93e2ad2f09971909382ad65fc5f5033487979b0694f9dc656439573973f55ce1865e5a30584e55e1c48fdd93898601ac2b11e269fb2b1c5adc3ff8dde66f35d SHA512 1c61c58e1cfbbb42342f7a87625e0044e51523f7a2f7270ecfea537c622965e64195fc88eb8f70fac648a0154a19f4a852b88383de1dcd6e17ff0ac0dc6e22d8
diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild
index 7dd6a1001545..3e44bd99585c 100644
--- a/sci-chemistry/modeller/modeller-9.25.ebuild
+++ b/sci-chemistry/modeller/modeller-9.25.ebuild
@@ -37,7 +37,7 @@ pkg_setup() {
 	esac
 }
 
-python_prepare_all(){
+python_prepare_all() {
 	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
 	rm -rf modlib/modeller/python_library || die
 	sed -i '1 i\#!/usr/bin/python' bin/modslave.py || die
@@ -45,7 +45,7 @@ python_prepare_all(){
 	distutils-r1_python_prepare_all
 }
 
-python_compile(){
+python_compile() {
 	cd src/swig || die
 	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
 	distutils-r1_python_compile
@@ -56,7 +56,7 @@ python_install() {
 	distutils-r1_python_install
 }
 
-python_install_all(){
+python_install_all() {
 	cd "${S}" || die
 	sed \
 		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index cb3604b3dddf..3a4f34fe7be6 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,5 @@
 AUX pymol-2.4.0-fix_bug119.patch 1078 BLAKE2B 78ed2953dcb20197de0a06c2c9c4c9f59be79cecbedfc910e7e530e5ad58452aab0da8540f4a4737023a3d56eba51530dfb1f2dfd59cdaf91192b6cd90383610 SHA512 ff4adb6de9c03f165e062698fe6359ab187ccf7cccba05c2e90363b44a53e5d4371e4942f21f26dd89ca8d1b7f9865f48e18f7d9a0214a5c6f453bee0ab49bb7
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523 SHA512 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a
-EBUILD pymol-2.4.0-r1.ebuild 3109 BLAKE2B fde18d90cc695279c3118a937f2d556b675a138029f72d6c16114fd37adfc34668a2e7c6f8b2b4d6fd3625d272aa7273129656d45ca6f049995bcb4f0392ec98 SHA512 9e8f43b7950693682703bf1170538bf89afcaf3b264bbae1458f7ac109509e6829992ee01ad137ef1937aa2f2489fb14b875516e1da164528c3074b0b10d8c2c
+EBUILD pymol-2.4.0-r1.ebuild 3106 BLAKE2B ca3e75218437da7eecb7f6cd4feb737386cfed4a002121659cf4147f141fc380dac3d3c18b9a0ea1dd3d614dd05df391545b3cad65905d1d7a52beace3c54b97 SHA512 cd03c112d9210fa24206de44e55dc8ed1bfde7a51c4278902355f01fd5d5846fb12afb3318796c9e4f57b1e5e7cae58812cf81267d9c7f776c5a35f6a0eb3082
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
index 7fb154b68509..c710896747d8 100644
--- a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
@@ -11,7 +11,7 @@ inherit desktop optfeature flag-o-matic xdg distutils-r1
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="https://www.pymol.org/"
 SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+	https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz
 	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
 	"
 RESTRICT="mirror"
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 3cc7356b53af..bac8374180d8 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,10 +1,4 @@
-AUX vmd-1.9.4-gentoo-paths.patch 11523 BLAKE2B 3e02c73b49a3686ce00deb44f4bca0809c527a53d7fb13315c5799c5e9fe1d8ada9664452e41f49ad084abed96d2e5a6d01b000e49393e97eeb5fb2378af888f SHA512 da8e723d12ca7728d67dffcd0bf2e9c856764917d3f3ef07756febbc981bae20b061e0ead3fa617de18b94918d855c09f68c24a979c6f9f0cdea12b343a22756
-AUX vmd-1.9.4-tmpdir.patch 398 BLAKE2B cf61240688f111d4763f458f0e10319a8154c5427172ba99d4bcfc7a9d8fd559fe7777c1ff703f81b68b2f10ec2a8c4af5cf61fd91d147aec2f4fafcf6753c82 SHA512 c5f96b3ef880ccdcf86d3927308c85aeaf3260ed0e54d60cbf186a0d63f6a88da16e49b14d6815d97bfd1ff4500bf9ce99d183d26ee78b67fed388e2217a7f10
-DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
-DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
 DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc
-DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
 DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40
-EBUILD vmd-1.9.4_alpha43.ebuild 8072 BLAKE2B 7d840693f56d8e6e93c8ff90de5f2cc8cc129154559619734b0e0eeb3a38e5291a49fd935562907ab4f8a784873572cedb0068317f020f9dfc41491b92b93743 SHA512 c939215fe71c16bd75b51c2afeb1b2956c619f17d4cc1fc5654a3d4872b905c77c78fb15311e031a3b663c06c457f85bd007d4155bfcde59459e6fef6c8966bc
 EBUILD vmd-1.9.4_alpha51.ebuild 7604 BLAKE2B 95a6087ebee108f1444fbef54e96478e32d0a2bd958c9a5679e9b087d9e43d8d46c0847e2babbef3906c7eaf20bfd2c4b9959476a61ea9cc0e0c4ca4504bbd17 SHA512 d52b6964ea258e30c7a8a337412a813a70ae10ad62b311ef27b87beb13c5afb844ff9380566a24e6e8191f2b13f15d0637d053d8ea3f54ba89be48eeb9707f85
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
deleted file mode 100644
index ca74b868d8f4..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
+++ /dev/null
@@ -1,276 +0,0 @@
---- a/bin/vmd.sh.old	2020-09-09 18:02:09.135798193 +0200
-+++ b/bin/vmd.sh	2020-09-09 18:37:22.355511675 +0200
-@@ -436,6 +436,7 @@
- 
- # set the path to a few external programs
- # Stride -- used to generate cartoon representations etc.
-+export STRIDE_BIN="gentoo-stride"
- if [ -z "$STRIDE_BIN" ]
- then
-   if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
-@@ -446,6 +447,7 @@
- fi
- 
- # Surf -- used to generate molecular surfaces
-+export SURF_BIN="gentoo-surf"
- if [ -z "$SURF_BIN" ]
- then
-   if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
-@@ -456,6 +458,7 @@
- fi
- 
- # Tachyon -- used to generate ray traced graphics
-+export TACHYON_BIN="gentoo-tachyon"
- if [ -z "$TACHYON_BIN" ]
- then
-   if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
---- a/configure.old	2020-09-09 18:05:55.778655084 +0200
-+++ b/configure	2020-09-09 18:38:01.607083112 +0200
-@@ -13,11 +13,10 @@
- $install_name = "vmd";
- 
- # Directory where VMD startup script is installed, should be in users' paths.
--$install_bin_dir="/usr/local/bin";
-+$install_bin_dir="gentoo-bindir";
- 
- # Directory where VMD files and executables are installed
--$install_library_dir="/usr/local/lib/$install_name";
--
-+$install_library_dir="gentoo-libdir/$install_name";
- 
- # optionally override hard-coded defaults above with environment variables
- if ($ENV{VMDINSTALLNAME}) {
-@@ -143,29 +142,6 @@
- # Configure script code begins here
- ############################################################################
- 
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
--  print "\n";
--  print "VMD plugin directory not found.\n";
--  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--  print "into a 'plugins' directory linked or located in this directory.\n";
--  print "Be sure your PLUGINDIR environment variable is set before running\n";
--  print "'make distrib' in the plugin build area.\n";
--  print "\n";
--  die "Halting configuration until VMD plugins are built.\n";
--} else {
--  if (!(-e "plugins/include/vmdplugin.h")) {
--    print "\n";
--    print "VMD plugin include files or directory not found.\n";
--    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--    print "into a 'plugins' directory linked or located in this directory.\n";
--    print "Be sure your PLUGINDIR environment variable is set before running\n";
--    print "'make distrib' in the plugin build area.\n";
--    print "\n";
--    die "Halting configuration until VMD plugins are built.\n";
--  }
--} 
--
- #################### Parse command line options   ###########
- # list of allowed architectures
- @archlist=('AIX6_64', 'ANDROIDARMV7A', 'BLUEGENEQ', 'BLUEWATERS', 'CRAY_XC', 'CRAY_XK', 'FREEBSD', 'FREEBSDAMD64', 'LINUX', 'LINUXAMD64', 'LINUXARM64', 'LINUXCARMA', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'OPENPOWER', 'SUMMIT', 'SUMMITDEV', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -493,7 +469,7 @@
- 
- $arch_cc          = "cc";
- $arch_ccpp        = "CC";
--$arch_nvcc        = "/usr/local/cuda-10.2/bin/nvcc";
-+$arch_nvcc        = "gentoo-nvcc";
- $arch_nvccflags   = "-lineinfo --ptxas-options=-v " . 
-                     "-gencode arch=compute_30,code=compute_30 " .
-                     "-gencode arch=compute_30,code=sm_35 " .
-@@ -537,7 +513,7 @@
- 
- ################ Plugin options
- #
--$plugin_dir	= "../plugins";
-+$plugin_dir    = "gentoo-plugindir";
- $plugin_include = "-I$plugin_dir/include";
- $plugin_library = "";
- $plugin_libs    = "";
-@@ -550,7 +526,7 @@
- @plugin_extra   = ();
- 
- if ($config_staticplugin) {
--  $molfile_dir = "$plugin_dir/$config_arch/molfile";
-+  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
-   $plugin_include .= " -I$molfile_dir";
-   $plugin_library .= " -L$molfile_dir";
-   $plugin_libs    .= " -lmolfile_plugin";
-@@ -715,8 +691,8 @@
- ################ FLTK GUI
- $fltk_defines     = "-DVMDGUI -DVMDFLTK";
- $fltk_dir         = "$vmd_library_dir/fltk";
--$fltk_include     = "-I$fltk_dir/include";
--$fltk_library     = "-L$fltk_dir/$config_arch";
-+$fltk_include     = "-Igentoo-fltk-include";
-+$fltk_library     = "-Lgentoo-fltk-libs";
- $fltk_libs        = "-lfltk -lX11";
- #@fltk_cc          = ('forms_ui.c');
- @fltk_cu          = ();
-@@ -777,8 +753,8 @@
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
- $tcl_library      = "-L$stock_tcl_library_dir";
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
--$tcl_libs         = "-ltcl8.5";  
--if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
-+$tcl_libs         = "-ltcl";  
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
- 
- @tcl_cc           = ();
- @tcl_cu           = ();
-@@ -1289,8 +1265,8 @@
- # This may be commented out if not required.
- $libtachyon_defines     = "-DVMDLIBTACHYON";
- $libtachyon_dir         = "$vmd_library_dir/tachyon";
--$libtachyon_include     = "-I$libtachyon_dir/include";
--$libtachyon_library     = "-L$libtachyon_dir/lib_$config_arch";
-+$libtachyon_include     = "-Igentoo-libtachyon-include";
-+$libtachyon_library     = "-Lgentoo-libtachyon-libs";
- $libtachyon_libs        = "-ltachyon";
- @libtachyon_cc          = ();
- @libtachyon_cu          = ();
-@@ -1541,8 +1517,8 @@
- #######################
- $netcdf_defines     = "";
- $netcdf_dir         = "$vmd_library_dir/netcdf";
--$netcdf_include     = "-I$netcdf_dir/include";
--$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
-+$netcdf_include     = "-Igentoo-netcdf-include";
-+$netcdf_library     = "-Lgentoo-netcdf-libs";
- $netcdf_libs        = "-lnetcdf";
- @netcdf_cc          = ();
- @netcdf_cu          = ();
-@@ -1595,6 +1571,7 @@
- #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
- $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
- $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
-+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
- 
- #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
- #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
-@@ -1604,7 +1581,7 @@
- $python_defines     = "-DVMDPYTHON";
- $python_include     = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
- $python_library     = "-L$stock_python_library_dir";
--$python_libs        = "-lpython2.5 -lpthread";
-+$python_libs        = "$stock_python_library -lpthread";
- @python_h           = ('PythonTextInterp.h',
-                        'VMDTkinterMenu.h',
- 		       'py_commands.h',
-@@ -2350,8 +2327,8 @@
- 
-     # XFree 4.0 Direct Rendering Interface and GLX 
-     $opengl_dep_dir         = "/usr/X11R6";
--    $opengl_dep_include     = "-I$opengl_dep_dir/include";
--    $opengl_dep_library     = "-L$opengl_dep_dir/lib";
-+    $opengl_dep_include     = "-Igentoo-opengl-include";
-+    $opengl_dep_library     = "-Lgentoo-opengl-libs";
-     $opengl_dep_libs        = "-lGL"; 
-     # $opengl_dep_libs      = "-L/usr/X11R6/lib -lGL -lXext -lX11";
- 
-@@ -2381,15 +2358,15 @@
-       $arch_lopts       .= "-i-static ";
-     } else {
-       # compling with GCC
--      $arch_cc          = "gcc";
--      $arch_ccpp        = "g++";
-+      $arch_cc          = "gentoo-gcc";
-+      $arch_ccpp        = "gentoo-g++";
-       $arch_depend_flag = "-MM";
--      $arch_shld        = "g++ -shared";
-+      $arch_shld        = "gentoo-g++ -shared";
-       $arch_shlibname   = "so";
-       $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
--      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
--      $arch_copts       = "-m32 -Wall -Wno-unknown-pragmas -O3";
-+      $arch_shldopts    = "gentoo-ldflags";
-+      $arch_opt_flag    = "gentoo-cflags";
-+      $arch_copts       = "gentoo-cflags";
- 
-       if ($config_static) {
-         $arch_lopts       = "-static";
-@@ -2407,14 +2384,13 @@
- 
-     $arch_cppopts     = "";
-     if ($config_cuda) {
--      $arch_nvcc     = "/usr/local/cuda-4.0/bin/nvcc";
-       $arch_nvccflags  = "--ptxas-options=-v " . 
-                     "-gencode arch=compute_13,code=sm_13 " .
-                     "-gencode arch=compute_20,code=sm_20 " .
-                     "-gencode arch=compute_20,code=compute_20 " .
-                     "--ftz=true ";
--      $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
--      $cuda_library     = "-L/usr/local/cuda-4.0/lib";
-+      $arch_nvccflags .= "gentoo-nvflags $cuda_include";
-+      $cuda_library     = "-Lgentoo-cuda-lib";
-       $cuda_libs       = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
-     }
-     # this is to make tcl happy
-@@ -2513,7 +2489,7 @@
- 
-     if ($config_cuda) {
-       $arch_nvccflags   .= " --machine 64 -O3 $cuda_include";
--      $cuda_library     = "-L/usr/local/cuda-10.2/lib64";
-+      $cuda_library     = "-Lgentoo-cuda-lib";
-     }
- 
-     $arch_lex		= "flex"; # has problems with vendor lex
-@@ -3502,11 +3478,11 @@
- DEFINES     = $DEFINES
- 
- # compiler and compiler directives 
--CC          = $arch_cc
--CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CC          = gentoo-gcc
-+CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
- 
--CCPP	    = $arch_ccpp
--CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CCPP        = gentoo-g++
-+CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
- 
- NVCC        = $arch_nvcc
- NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-@@ -3555,7 +3531,7 @@
- $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX)
- 	\$(ECHO) "Linking " \$\@ "..."; \\
- 	\$(CD) $vmd_arch_dir ; \\
--	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
-+	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
- 	\$(COMPILERC) \$(RCFLAGS)
- 
- install:
-@@ -3596,8 +3572,7 @@
- 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
- 	\$(CD) $vmd_bin_dir ; \\
- 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
--	if [ ! -x "/bin/csh" ]; then \\
--		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
-+	if [ -x "/bin/bash" ]; then \\
- 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
---- a/src/Makefile.old	2020-09-09 18:22:46.234818925 +0200
-+++ b/src/Makefile	2020-09-09 18:37:22.356511690 +0200
-@@ -647,7 +647,7 @@
- vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX)
- 	$(ECHO) "Linking " $@ "..."; \
- 	$(CD) ../LINUXAMD64 ; \
--	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
-+	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
- 	$(COMPILERC) $(RCFLAGS)
- 
- install:
-@@ -660,10 +660,6 @@
- 	if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
- 		$(MAKEDIR) "/usr/local/lib/vmd"/doc; \
- 	fi
--	-$(COPY) ../Announcement  "/usr/local/lib/vmd"
--	-$(COPY) ../README        "/usr/local/lib/vmd"
--	-$(COPY) ../LICENSE       "/usr/local/lib/vmd"
--	-$(COPY) ../doc/ug.pdf        "/usr/local/lib/vmd"/doc
- 	if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
-            $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
- 	-$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
deleted file mode 100644
index 295811db0580..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/scripts/vmd/chemical2vmd.old	2020-09-09 18:40:56.795215443 +0200
-+++ b/scripts/vmd/chemical2vmd	2020-09-09 18:41:09.648348701 +0200
-@@ -61,7 +61,7 @@
- 
- 
- # Make a temp. file to store the load command
--$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'};
-+$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'};
- sub tmpfile {
-     local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$;
-     local ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
deleted file mode 100644
index 417828a3209f..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ /dev/null
@@ -1,277 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-
-MY_PV="${PV/_alpha/a}"
-MY_P="${PN}-${MY_PV}"
-SRC_URI="
-	${MY_P}.src.tar
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
-	https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-CDEPEND="
-	>=dev-lang/tk-8.6.1:0=
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep 'dev-python/numpy[${PYTHON_MULTI_USEDEP}]')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )
-"
-DEPEND="${CDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-	dev-lang/swig
-"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/chemical-mime-data
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-"
-
-S="${WORKDIR}/${MY_P}"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${MY_P}.src.tar from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz"
-	elog "https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch"
-	elog "Place them into your DISTDIR directory"
-	elog
-	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
-	elog "file may get downloaded as a compressed tarball or not. In that case"
-	elog "you will need to ensure you uncompress the file and rename it"
-	elog "to ${MY_P}.src.tar"
-}
-
-src_prepare() {
-	# Apply user patches from ${WORKDIR} to allow patching on patches
-	# subdir too
-	cd "${WORKDIR}"
-	xdg_src_prepare
-
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
-	eapply "${DISTDIR}"/${PN}-1.9.4-gentoo-plugins.patch
-
-	use cuda && cuda_sanitize
-
-	# Prepare plugins
-	cd plugins || die
-
-	sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch
-
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
-	eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
-		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	# Open PDB files with VMD
-	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}