Version Bump, #358981; Dropped ppc due to missing KEYWORDS in DEPs

(Portage version: 2.2.0_alpha28/cvs/Linux x86_64)

6 files changed, 1122 insertions, 7 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 8397700eb464..7e5273d51432 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.36 2011/03/22 09:46:20 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.37 2011/03/22 13:53:26 jlec Exp $
+
+*vmd-1.9 (22 Mar 2011)
+
+  22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+  +vmd-1.9.ebuild, +files/vmd-1.9-gentoo-base.patch,
+  +files/vmd-1.9-gentoo-plugins.patch, metadata.xml:
+  Version Bump, #358981; Dropped ppc due to missing KEYWORDS in DEPs
 
   22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
   Restrict fltk version being able to return includedir
diff --git a/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch b/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch
new file mode 100644
index 000000000000..4fb7da420de9
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch
@@ -0,0 +1,295 @@
+ vmd-1.9/bin/vmd.sh   |    3 ++
+ vmd-1.9/configure    |   88 +++++++++++++++++++-------------------------------
+ vmd-1.9/src/Makefile |    6 +---
+ 3 files changed, 37 insertions(+), 60 deletions(-)
+
+diff --git a/vmd-1.9/bin/vmd.sh b/vmd-1.9/bin/vmd.sh
+index 2da6656..6e5308f 100755
+--- a/vmd-1.9/bin/vmd.sh
++++ b/vmd-1.9/bin/vmd.sh
+@@ -400,6 +400,7 @@ esac
+ 
+ # 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_$ARCH" ]
+@@ -410,6 +411,7 @@ then
+ fi
+ 
+ # Surf -- used to generate molecular surfaces
++export SURF_BIN="gentoo-surf"
+ if [ -z "$SURF_BIN" ]
+ then
+   if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
+@@ -420,6 +422,7 @@ then
+ fi
+ 
+ # Tachyon -- used to generate ray traced graphics
++export TACHYON_BIN="gentoo-tachyon"
+ if [ -z "$TACHYON_BIN" ]
+ then
+   if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
+diff --git a/vmd-1.9/configure b/vmd-1.9/configure
+index 926bab0..d8c1459 100755
+--- a/vmd-1.9/configure
++++ b/vmd-1.9/configure
+@@ -13,10 +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/$install_name";
+ 
+ 
+ # optionally override hard-coded defaults above with environment variables
+@@ -132,28 +132,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) {
+ # 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
+@@ -413,7 +391,7 @@ $arch_rcflags     = "No resource compiler required on this platform.";
+ 
+ $arch_cc          = "cc";
+ $arch_ccpp        = "CC";
+-$arch_nvcc        = "/usr/local/encap/cuda-3.0/bin/nvcc";
++$arch_nvcc        = "gentoo-nvcc";
+ $arch_nvccflags   = "--ptxas-options=-v " . 
+                     "-gencode arch=compute_10,code=sm_10 " .
+                     "-gencode arch=compute_13,code=sm_13 " .
+@@ -451,7 +429,7 @@ chop($arch_no_math_float);
+ 
+ ################ Plugin options
+ #
+-$plugin_dir	= "../plugins";
++$plugin_dir	= "gentoo-plugindir";
+ $plugin_include = "-I$plugin_dir/include";
+ $plugin_library = "";
+ $plugin_libs    = "";
+@@ -464,7 +442,7 @@ $plugin_defines = "";
+ @plugin_extra   = ();
+ 
+ if ($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";
+@@ -564,8 +542,8 @@ $fltkopengl_defines     = "-DVMDOPENGL -DVMDFLTKOPENGL";
+ ################ 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          = ();
+@@ -626,8 +604,8 @@ $tcl_include      = "-I$stock_tcl_include_dir";
+ 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           = ();
+@@ -1004,8 +982,8 @@ $mpi_libs        = "-L/usr/mpi/gcc/mvapich-1.0.0/lib -lmpich -libverbs -libumad
+ #######################
+ $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          = ();
+@@ -1076,6 +1054,7 @@ $pthreads_libs     = "-lpthread";
+ #$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";
+@@ -1085,7 +1064,7 @@ $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/l
+ $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        = "$stock_python_library -lpthread";
+ @python_h           = ('PythonTextInterp.h',
+                        'VMDTkinterMenu.h',
+ 		       'py_commands.h',
+@@ -1807,8 +1786,8 @@ if ($config_arch eq "LINUX") {
+ 
+     # XFree 4.0 Direct Rendering Interface and GLX 
+     $opengl_dir         = "/usr/X11R6";
+-    $opengl_include     = "-I$opengl_dir/include";
+-    $opengl_library     = "-L$opengl_dir/lib";
++    $opengl_include     = "-Igentoo-opengl-include";
++    $opengl_library     = "-Lgentoo-opengl-libs";
+     $opengl_libs        = "-lGL -lGLU"; 
+     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
+ 
+@@ -1836,15 +1815,15 @@ if ($config_arch eq "LINUX") {
+       $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 -O3";
+-      $arch_copts       = "-m32 -Wall -O3";
++      $arch_shldopts    = "gentoo-ldflags";
++      $arch_opt_flag    = "gentoo-cflags";
++      $arch_copts       = "gentoo-cflags";
+ 
+       if ($config_static) {
+         $arch_lopts       = "-static";
+@@ -1864,8 +1843,8 @@ if ($config_arch eq "LINUX") {
+     $arch_cppopts     = "";
+ 
+     if ($config_cuda) {
+-      $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
+-      $cuda_library     = "-L/usr/local/encap/cuda-3.0/lib";
++      $arch_nvccflags .= "gentoo-nvflags $cuda_include";
++      $cuda_library     = "-Lgentoo-cuda-lib";
+     }
+     # a hack - to be removed, just keeps make happy
+     $arch_template_repository = "foobar";
+@@ -1955,7 +1934,7 @@ if ($config_arch eq "LINUXAMD64") {
+       $arch_template_repository = "foobar";
+       $arch_shlibname   = "so";
+       $arch_shcppopts   = "-fPIC";
+-      $arch_shldopts    = "";
++      $arch_shldopts    = "gentoo-ldflags";
+ 
+       if ($config_static) {
+         # link everything statically (this won't work due to libGL issues)
+@@ -1986,7 +1965,7 @@ if ($config_arch eq "LINUXAMD64") {
+ 
+     if ($config_cuda) {
+       $arch_nvccflags   .= " --machine 64 -O3 $cuda_include";
+-      $cuda_library     = "-L/usr/local/encap/cuda-3.0/lib64";
++      $cuda_library     = "-Lgentoo-cuda-lib";
+     }
+ 
+     $arch_lex		= "flex"; # has problems with vendor lex
+@@ -2354,7 +2333,7 @@ if ($config_arch eq "MACOSXX86" || $config_arch eq "MACOSXX86_64") {
+       # $arch_nvccflags   .= " -O3 $cuda_include";
+       # make it continue to work with the older rev of CUDA for now
+       $arch_nvccflags   = " --ptxas-options=-v -O3 $cuda_include";
+-      $cuda_library     = "-L/usr/local/cuda/lib";
++      $cuda_library     = "-Lgentoo-cuda-lib";
+     }
+     if ($config_opencl) {
+       $opencl_libs        = "-framework OpenCL";
+@@ -2545,7 +2524,7 @@ if ($config_arch eq "SOLARISX86" || $config_arch eq "SOLARISX86_64") {
+           $arch_nvcc        = "/usr/local/cuda/bin/nvcc";
+           $arch_nvccflags   .= " -m64 -O3 -I/usr/local/cuda/include";
+           $cuda_libs        = "-lcudart";
+-          $cuda_library     = "-L/usr/local/cuda/lib";
++          $cuda_library     = "-Lgentoo-cuda-lib";
+         }
+       } else {
+         print "Configured for a 32-bit build.\n";
+@@ -2927,11 +2906,11 @@ LIBDIRS     = $LIBDIRS
+ 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)
+@@ -2979,7 +2958,7 @@ $config_progname: y.tab.h \$(VMD_OBJS)
+ 	if [ ! -r ./$arch_template_repository ]; then \\
+ 	  ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
+ 	fi; \\
+-	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
++	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
+ 	\$(COMPILERC) \$(RCFLAGS)
+ 
+ install:
+@@ -3017,8 +2996,7 @@ install:
+ 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$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 ; \\
+diff --git a/vmd-1.9/src/Makefile b/vmd-1.9/src/Makefile
+index 18eff40..c301f91 100644
+--- a/vmd-1.9/src/Makefile
++++ b/vmd-1.9/src/Makefile
+@@ -446,7 +446,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS)
+ 	if [ ! -r ./ ]; then \
+ 	  ln -s ../src/ ./ ; \
+ 	fi; \
+-	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
++	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
+ 	$(COMPILERC) $(RCFLAGS)
+ 
+ install:
+@@ -459,10 +459,6 @@ install:
+ 	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_WIN32 ]; then \
+            $(MOVE) "/usr/local/lib/vmd/vmd_WIN32" "/usr/local/lib/vmd/OLD_vmd_WIN32" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_WIN32" ; fi
+ 	-$(COPY) ../WIN32/vmd_WIN32 "/usr/local/lib/vmd"
diff --git a/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch
new file mode 100644
index 000000000000..d6b1afb0cafd
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch
@@ -0,0 +1,612 @@
+ plugins/Make-arch                             |    3 +-
+ plugins/Makefile                              |   20 ++++---
+ plugins/autopsf/Makefile                      |    4 +-
+ plugins/catdcd/Makefile                       |    4 +-
+ plugins/cionize/Makefile                      |    4 +-
+ plugins/clustalw/Makefile                     |    2 +-
+ plugins/cluster/Makefile                      |    2 +-
+ plugins/hesstrans/Makefile                    |    2 +-
+ plugins/libbiokit/Makefile                    |   14 +++---
+ plugins/molfile_plugin/Makefile               |   62 ++++++++++++------------
+ plugins/molfile_plugin/src/cifplugin/Makefile |   66 ++++++++++++------------
+ plugins/phylotree/Makefile                    |    2 +-
+ plugins/rnaview/Makefile                      |    2 +-
+ plugins/stamp/Makefile                        |    2 +-
+ 14 files changed, 96 insertions(+), 93 deletions(-)
+
+diff --git a/plugins/Make-arch b/plugins/Make-arch
+index 5d59ef3..ab57459 100755
+--- a/plugins/Make-arch
++++ b/plugins/Make-arch
+@@ -336,7 +336,8 @@ LINUX:
+ 	"AR = ar" \
+ 	"NM = nm -p" \
+ 	"RANLIB = touch" \
+-	"SHLD = gcc -shared"
++	"SHLD = gcc -shared" \
++	"SHXXLD = g++ -shared"
+ 	
+ LINUXALPHA:
+ 	$(MAKE) dynlibs staticlibs bins \
+diff --git a/plugins/Makefile b/plugins/Makefile
+index 19f0e8b..57cbe32 100644
+--- a/plugins/Makefile
++++ b/plugins/Makefile
+@@ -132,25 +132,27 @@ distrib:
+ 
+ include Make-arch
+ 
+-molfilelibs:
+-	cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
+-	cd molfile_plugin; $(MAKE) staticlibs && cd .. || exit 1
++molfilelibs_static:
++	$(MAKE) -C molfile_plugin staticlibs
++
++molfilelibs_dyn:
++	$(MAKE) -C molfile_plugin dynlibs
+ 
+ win32molfilelibs:
+ 	cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
+ 	cd molfile_plugin; $(MAKE) win32staticlibs && cd .. || exit 1
+ 
+-dynlibs: molfilelibs
+-	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) dynlibs && cd .. || exit 1 ; done
++dynlibs: molfilelibs_dyn
++	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir dynlibs; done
+ 
+-staticlibs: molfilelibs
+-	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) staticlibs && cd .. || exit 1 ; done
++staticlibs: molfilelibs_static
++	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir staticlibs; done
+ 
+ win32staticlibs: win32molfilelibs
+ 	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs && cd .. || exit 1 ; done
+ 
+-bins:
+-	for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) bins && cd .. || exit 1 ; done
++bins: molfilelibs_dyn
++	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir bins; done
+ 
+ win32bins:
+ 	for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) win32bins && cd .. || exit 1 ; done
+diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile
+index e63d3c4..d217ed8 100644
+--- a/plugins/autopsf/Makefile
++++ b/plugins/autopsf/Makefile
+@@ -49,8 +49,8 @@ AUTOPSFOBJS=${ARCHDIR}/psfatom.o  \
+ 
+ ${ARCHDIR}/psfcheck.so : ${AUTOPSFOBJS}
+ 	if [ -n "${TCLSHLD}" ]; \
+-	then ${TCLSHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+-	else ${SHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
++	then ${TCLSHLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
++	else ${SHXXLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
+ 	fi
+ 
+ ${ARCHDIR}/psfatom.o : psfatom.h psfatom.C
+diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
+index 7a8f0f8..dc0d7a5 100644
+--- a/plugins/catdcd/Makefile
++++ b/plugins/catdcd/Makefile
+@@ -45,8 +45,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi
+ 	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
+ 
+ # all other platforms
+-${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
+-	${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
++${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
+ 
+ ${ARCHDIR}/hash.o: hash.h hash.c
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
+diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
+index c5fe136..5e9a379 100644
+--- a/plugins/cionize/Makefile
++++ b/plugins/cionize/Makefile
+@@ -52,8 +52,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI
+ 	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
+ 
+ # all other platforms
+-${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
++${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
+ 
+ ${ARCHDIR}/hash.o: hash.h hash.c
+ 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
+diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
+index b8fbba5..988ad06 100644
+--- a/plugins/clustalw/Makefile
++++ b/plugins/clustalw/Makefile
+@@ -66,7 +66,7 @@ OBJS = ${ARCHDIR}/alnscore.o \
+ ${ARCHDIR}/clustalw.exe: ${OBJS}
+ 	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
+ ${ARCHDIR}/clustalw: ${OBJS}
+-	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
++	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
+     
+     
+ # Objects.
+diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
+index 99d347e..c2d30ae 100644
+--- a/plugins/cluster/Makefile
++++ b/plugins/cluster/Makefile
+@@ -48,7 +48,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS}
+ 
+ # all other platforms
+ ${ARCHDIR}/cluster : ${OBJS}
+-	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
+ 
+ ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o
+diff --git a/plugins/hesstrans/Makefile b/plugins/hesstrans/Makefile
+index 903e88b..50fa625 100644
+--- a/plugins/hesstrans/Makefile
++++ b/plugins/hesstrans/Makefile
+@@ -67,7 +67,7 @@ HESSTRANSOBJS=${ARCHDIR}/newmat1.o \
+ ${ARCHDIR}/hesstrans.so : ${HESSTRANSOBJS}
+ 	if [ -n "${TCLSHLD}" ]; \
+ 	then ${TCLSHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+-	else ${SHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
++	else ${SHXXLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+ 	fi
+ 
+ #
+diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
+index 7a66d08..da764dd 100644
+--- a/plugins/libbiokit/Makefile
++++ b/plugins/libbiokit/Makefile
+@@ -98,7 +98,7 @@ OBJS = ${DYNLIBOBJS} \
+ ${ARCHDIR}/tcl_libbiokit.so : ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS}
+ 	if [ -n "${TCLSHLD}" ]; \
+ 	then ${TCLSHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+-	else ${SHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
++	else ${SHXXLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+ 	fi
+ ${ARCHDIR}/tcl_libbiokit_wrap.o : ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp
+ 	${CXX} ${CXXFLAGS} ${TCLINC} ${INCDIR} -c ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp $(COPTO)${ARCHDIR}/tcl_libbiokit_wrap.o
+@@ -111,7 +111,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i
+ ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
+ 	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
+ ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
+ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
+ 
+@@ -119,7 +119,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
+ ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
+ 	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
+ ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
+ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
+ 
+@@ -127,7 +127,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
+ ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
+ 	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
+ ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
+ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
+ 
+@@ -135,7 +135,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
+ ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
+ 	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
+ ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
+ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
+ 
+@@ -143,7 +143,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
+ ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
+ 	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
+ ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
+ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
+ 
+@@ -151,7 +151,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
+ ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
+ 	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
+ ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
+-	${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
+ ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
+     
+diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
+index 172a217..345f64c 100644
+--- a/plugins/molfile_plugin/Makefile
++++ b/plugins/molfile_plugin/Makefile
+@@ -15,7 +15,7 @@ INCDIR = -I../include -I${SRCDIR}
+ VPATH = src ../include ${ARCHDIR}
+ 
+ SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
+@@ -142,7 +142,7 @@ abinitplugin.so: ${ARCHDIR}/abinitplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -163,13 +163,13 @@ babelplugin.so: ${ARCHDIR}/babelplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
+ 
+ parmplugin.so: ${ARCHDIR}/parmplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
+@@ -187,40 +187,40 @@ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
+ 
+ graspplugin.so: ${ARCHDIR}/graspplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ msmsplugin.so: ${ARCHDIR}/msmsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ stlplugin.so: ${ARCHDIR}/stlplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cubeplugin.so: ${ARCHDIR}/cubeplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ edmplugin.so: ${ARCHDIR}/edmplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ brixplugin.so: ${ARCHDIR}/brixplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pltplugin.so: ${ARCHDIR}/pltplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ rst7plugin.so: ${ARCHDIR}/rst7plugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ parm7plugin.so: ${ARCHDIR}/parm7plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vtfplugin.so: ${ARCHDIR}/vtfplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -235,7 +235,7 @@ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -265,52 +265,52 @@ moldenplugin.so: ${ARCHDIR}/moldenplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ phiplugin.so: ${ARCHDIR}/phiplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ grdplugin.so: ${ARCHDIR}/grdplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dxplugin.so: ${ARCHDIR}/dxplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ situsplugin.so: ${ARCHDIR}/situsplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ spiderplugin.so: ${ARCHDIR}/spiderplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mapplugin.so: ${ARCHDIR}/mapplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ avsplugin.so: ${ARCHDIR}/avsplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ fs4plugin.so: ${ARCHDIR}/fs4plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pqrplugin.so: ${ARCHDIR}/pqrplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mol2plugin.so: ${ARCHDIR}/mol2plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ bgfplugin.so: ${ARCHDIR}/bgfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gridplugin.so: ${ARCHDIR}/gridplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ carplugin.so: ${ARCHDIR}/carplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mdfplugin.so: ${ARCHDIR}/mdfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -325,7 +325,7 @@ basissetplugin.so: ${ARCHDIR}/basissetplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xsfplugin.so: ${ARCHDIR}/xsfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ jsplugin.so: ${ARCHDIR}/jsplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
+index 1dfa768..bd6eceb 100644
+--- a/plugins/molfile_plugin/src/cifplugin/Makefile
++++ b/plugins/molfile_plugin/src/cifplugin/Makefile
+@@ -13,8 +13,8 @@ INCDIR = -I../include -I${SRCDIR}
+ 
+ VPATH = src ../include ${ARCHDIR}
+ 
+-SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
+@@ -84,10 +84,10 @@ mesg:
+ #
+ 
+ biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cifplugin.so: ${ARCHDIR}/cifplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -105,10 +105,10 @@ babelplugin.so: ${ARCHDIR}/babelplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ parmplugin.so: ${ARCHDIR}/parmplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
+@@ -126,40 +126,40 @@ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
+ 
+ graspplugin.so: ${ARCHDIR}/graspplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ msmsplugin.so: ${ARCHDIR}/msmsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ stlplugin.so: ${ARCHDIR}/stlplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cubeplugin.so: ${ARCHDIR}/cubeplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ edmplugin.so: ${ARCHDIR}/edmplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ brixplugin.so: ${ARCHDIR}/brixplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pltplugin.so: ${ARCHDIR}/pltplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ rst7plugin.so: ${ARCHDIR}/rst7plugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ parm7plugin.so: ${ARCHDIR}/parm7plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vtfplugin.so: ${ARCHDIR}/vtfplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -174,7 +174,7 @@ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+@@ -201,58 +201,58 @@ moldenplugin.so: ${ARCHDIR}/moldenplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ phiplugin.so: ${ARCHDIR}/phiplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ grdplugin.so: ${ARCHDIR}/grdplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dxplugin.so: ${ARCHDIR}/dxplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ situsplugin.so: ${ARCHDIR}/situsplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ spiderplugin.so: ${ARCHDIR}/spiderplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mapplugin.so: ${ARCHDIR}/mapplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ avsplugin.so: ${ARCHDIR}/avsplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ fs4plugin.so: ${ARCHDIR}/fs4plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pqrplugin.so: ${ARCHDIR}/pqrplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mol2plugin.so: ${ARCHDIR}/mol2plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ bgfplugin.so: ${ARCHDIR}/bgfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gridplugin.so: ${ARCHDIR}/gridplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ carplugin.so: ${ARCHDIR}/carplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mdfplugin.so: ${ARCHDIR}/mdfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gamessplugin.so: ${ARCHDIR}/gamessplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xsfplugin.so: ${ARCHDIR}/xsfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ #
+ # object files
+diff --git a/plugins/phylotree/Makefile b/plugins/phylotree/Makefile
+index 6442747..0aceb4d 100644
+--- a/plugins/phylotree/Makefile
++++ b/plugins/phylotree/Makefile
+@@ -54,7 +54,7 @@ ${ARCHDIR}/upgmaclu.exe : ${OBJS}
+ 
+ # all other platforms
+ ${ARCHDIR}/upgmaclu : ${OBJS}
+-	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
++	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
+ 
+ ${ARCHDIR}/upgmaclu.o: ${SRCDIR}/upgmaclu.c
+ 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/upgmaclu.c $(COPTO)${ARCHDIR}/upgmaclu.o
+diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
+index 503695e..e7019a6 100644
+--- a/plugins/rnaview/Makefile
++++ b/plugins/rnaview/Makefile
+@@ -67,7 +67,7 @@ OBJS = ${ARCHDIR}/analyze.o \
+ ${ARCHDIR}/rnaview.exe: ${OBJS}
+ 	LINK ${OBJS} /OUT:${ARCHDIR}/rnaview.exe
+ ${ARCHDIR}/rnaview: ${OBJS}
+-	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
++	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
+ 
+ ${ARCHDIR}/analyze.o: ${SRCDIR}/analyze.c
+ 	${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/analyze.c $(COPTO)${ARCHDIR}/analyze.o
+diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
+index f0fb515..aa8f6b6 100644
+--- a/plugins/stamp/Makefile
++++ b/plugins/stamp/Makefile
+@@ -101,7 +101,7 @@ OBJS = ${ARCHDIR}/a3to1.o \
+ ${ARCHDIR}/stamp.exe: ${OBJS}
+ 	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
+ ${ARCHDIR}/stamp: ${OBJS}
+-	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
++	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
+     
+     
+ # Objects.
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
index 3ecc4ccc7f98..16543e0c81b8 100644
--- a/sci-chemistry/vmd/metadata.xml
+++ b/sci-chemistry/vmd/metadata.xml
@@ -12,9 +12,8 @@
 	<herd>sci-chemistry</herd>
 	<use>
 		<flag name='msms'>Add support for MSMS SAS calcualtion tool</flag>
-		<flag name='povray'>Add support for povray raytracer for HQ
-			images</flag>
-		<flag name='tachyon'>Add support for tachyon raytracer for HQ
-			images</flag>
+		<flag name='povray'>Add support for povray raytracer for HQ	images</flag>
+		<flag name='tachyon'>Add support for tachyon raytracer for HQ images</flag>
+		<flag name='cuda'>Use nvidia cuda toolkit for speeding up computations</flag>
 	</use>
 </pkgmetadata>
diff --git a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
index 7ac31adee35d..96a0c3c74252 100644
--- a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.6 2011/03/22 09:46:20 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.7 2011/03/22 13:53:26 jlec Exp $
 
 EAPI="3"
 
@@ -28,13 +28,13 @@ DEPEND="
 	)
 	dev-lang/perl
 	dev-python/numpy
-	sci-biology/stride
 	sci-libs/netcdf
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1
 	x11-libs/libXft"
 
 RDEPEND="${DEPEND}
+	sci-biology/stride
 	x11-terms/xterm
 	msms? ( sci-chemistry/msms-bin )
 	povray? ( media-gfx/povray )
diff --git a/sci-chemistry/vmd/vmd-1.9.ebuild b/sci-chemistry/vmd/vmd-1.9.ebuild
new file mode 100644
index 000000000000..11849f30434f
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.ebuild
@@ -0,0 +1,202 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.ebuild,v 1.1 2011/03/22 13:53:26 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils multilib python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda msms povray static-libs tachyon xinerama"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+DEPEND="
+	|| (
+		>=dev-lang/tk-8.5[-truetype]
+		=dev-lang/tk-8.4*
+	)
+	dev-lang/perl
+	dev-lang/swig
+	dev-python/numpy
+	sci-libs/netcdf
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	xinerama? ( x11-libs/libXinerama )"
+
+RDEPEND="${DEPEND}
+	sci-biology/stride
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+	tachyon? ( media-gfx/tachyon )"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_TEXTRELS="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_PRESTRIPPED="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_DT_HASH_amd64="usr/lib64/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+
+pkg_nofetch() {
+	elog "Please download ${A} from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and then move it to "
+	elog "${DISTDIR}"
+}
+
+src_prepare() {
+	cd "${WORKDIR}"/plugins
+
+	epatch "${FILESDIR}"/${P}-gentoo-plugins.patch
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed -e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o\":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o\":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	use static-libs || sed 's:staticlibs::g' -i Make-arch
+
+	# prepare vmd itself
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${P}-gentoo-base.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags: -O3 -v:g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+#	local NUMPY_INCLUDE="numpy/core/include"
+#	sed -e "s:gentoo-python-include:${EPREFIX}$(python_get_includedir):" \
+#		-e "s:gentoo-python-lib:${EPREFIX}$(python_get_libdir):" \
+#		-e "s:gentoo-python-link:$(PYTHON):" \
+#		-e "s:gentoo-numpy-include:${EPREFIX}$(python_get_sitedir)/${NUMPY_INCLUDE}:" \
+#		-i configure || die "failed setting up python"
+
+	sed \
+		-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+		-i configure || die
+
+	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"
+}
+
+src_configure() {
+	local myconf="OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+	use static-libs || myconf+=" NOSTATICPLUGINS"
+#	use tachion && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="${EPREFIX}$(python_get_libdir)" \
+		PYTHON_LIBRARY="$(python_get_library -l)" \
+		NUMPY_INCLUDE_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include"
+
+	./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+
+	emake \
+		TCLINC="-I${EPREFIX}/usr/include" \
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFLIB="$(pkg-config --libs-only-L netcdf)" \
+		NETCDFINC="$(pkg-config --cflags-only-I netcdf)" \
+		NETCDFLDFLAGS="$(pkg-config --libs netcdf)" \
+		LINUX || die
+
+	# build vmd
+	cd "${S}"/src
+	emake || die "failed to build vmd"
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib || die "failed to install plugins"
+
+	# install vmd
+	cd "${S}"/src
+	emake install || die "failed to install vmd"
+
+	# install docs
+	cd "${S}"
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf || die
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${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 "${FILESDIR}"/vmd.png || die "Failed to install vmd icon"
+	insinto /usr/share/applications
+	doins "${FILESDIR}"/vmd.desktop || die "Failed to install desktop entry"
+}