diff options
author | Hiroki Sato <hrs@FreeBSD.org> | 2012-04-23 04:48:03 +0000 |
---|---|---|
committer | Hiroki Sato <hrs@FreeBSD.org> | 2012-04-23 04:48:03 +0000 |
commit | 7b3d6adf5fcac6dec0d7a3d99b42f83120aee8db (patch) | |
tree | 5f22566bdbf0caebf508b347cfb03cc28e5c68c5 /science | |
parent | Maintainer wishes to release this back to the wild. (diff) |
Update to 1.9.1.
Submitted by: bjk
Notes
Notes:
svn path=/head/; revision=295293
Diffstat (limited to 'science')
-rw-r--r-- | science/vmd/Makefile | 16 | ||||
-rw-r--r-- | science/vmd/distinfo | 8 | ||||
-rw-r--r-- | science/vmd/files/patch-AtomParser.C | 11 | ||||
-rw-r--r-- | science/vmd/files/patch-Make-arch | 51 | ||||
-rw-r--r-- | science/vmd/files/patch-OpenGLExtensions.C | 21 | ||||
-rw-r--r-- | science/vmd/files/patch-bin_vmd.csh | 14 | ||||
-rw-r--r-- | science/vmd/files/patch-bin_vmd.sh | 15 | ||||
-rw-r--r-- | science/vmd/files/patch-configure | 125 | ||||
-rw-r--r-- | science/vmd/files/patch-lib_tachyon_unix_Make-arch | 2 | ||||
-rw-r--r-- | science/vmd/files/patch-plugins__hesstrans__Makefile | 11 | ||||
-rw-r--r-- | science/vmd/files/patch-utilities.C | 11 | ||||
-rw-r--r-- | science/vmd/pkg-plist | 800 |
12 files changed, 533 insertions, 552 deletions
diff --git a/science/vmd/Makefile b/science/vmd/Makefile index 74f86ab62cfb..6bf43d184d3d 100644 --- a/science/vmd/Makefile +++ b/science/vmd/Makefile @@ -6,16 +6,16 @@ # PORTNAME= vmd -PORTVERSION= 1.8.7 -PORTREVISION= 3 +DISTVERSION= 1.9.1 CATEGORIES= science graphics python tcl tk -MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.98.7/:tachyon \ +MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b2/:tachyon \ + http://www.photonlimited.com/~johns/tachyon/files/0.99b2/:tachyon \ http://www.ks.uiuc.edu/Research/vmd/extsrcs/:stride DISTFILES= ${VMD_DIST} \ ${TACHYON_DIST}:tachyon \ ${STRIDE_DIST}:stride -MAINTAINER= kaduk-fbsd@mit.edu +MAINTAINER= bjk@freebsd.org COMMENT= A molecular visualization program BUILD_DEPENDS= makedepend:${PORTSDIR}/devel/makedepend \ @@ -35,8 +35,8 @@ ONLY_FOR_ARCHS= i386 amd64 RESTRICTED= License has restrictions -VMD_DIST= ${PORTNAME}-${PORTVERSION}.src.tar.gz -TACHYON_DIST= tachyon-0.98.7.tar.gz +VMD_DIST= ${PORTNAME}-${DISTVERSION}.src.tar.gz +TACHYON_DIST= tachyon-0.99b2.tar.gz # I get stride.tar.gz from ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/ # but the www.ks.uiuc.edu site (that gives Stride_src.tar.Z) is closer # to vmd upstream (and google actually knows about it). @@ -72,7 +72,7 @@ post-patch: ${REINPLACE_CMD} "s/-ltk8.5/-ltk85/" ${WRKSRC}/configure ${REINPLACE_CMD} "s/-ltcl8.5/-ltcl85/" ${WRKSRC}/configure ${REINPLACE_CMD} "s%\$$python_dir/lib_\$$config_arch%${PREFIX}%" ${WRKSRC}/configure - ${REINPLACE_CMD} "s/python2.2/${PYTHON_VERSION}/" ${WRKSRC}/configure + ${REINPLACE_CMD} "s/python2.5/${PYTHON_VERSION}/" ${WRKSRC}/configure ${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/Makefile ${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/*/Makefile ${REINPLACE_CMD} "s%log2f(\([^ ,]*\))%logf(\1)/(float)M_LN2%g" ${WRKSRC}/src/Orbital.C @@ -81,7 +81,7 @@ post-patch: do-build: ${SETENV} ${MAKE_ENV} ${GMAKE} bsd -C ${WRKSRC}/lib/tachyon/unix && ${MV} ${WRKSRC}/lib/tachyon/compile/bsd/tachyon ${WRKSRC}/lib/tachyon/tachyon_${VMD_ARCH} - ${SETENV} ${MAKE_ENV} PLUGINDIR=${WRKSRC}/plugins ${GMAKE} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins + ${SETENV} ${MAKE_ENV} TCLLIB=-L${PREFIX}/lib/tcl8.5 TCLINC=-I${PREFIX}/include/tcl8.5 PLUGINDIR=${WRKSRC}/plugins ${GMAKE} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins ${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.5 TK_INCLUDE_DIR=${PREFIX}/include/tk8.5 ${GMAKE} ${VMD_TARGET} -C ${WRKSRC} ${SETENV} ${MAKE_ENV} ${GMAKE} all -C ${WRKSRC}/src ${SETENV} ${MAKE_ENV} ${GMAKE} depend -C ${WRKSRC}/lib/surf && ${SETENV} ${MAKE_ENV} ${GMAKE} surf -C ${WRKSRC}/lib/surf && ${MV} ${WRKSRC}/lib/surf/surf ${WRKSRC}/lib/surf/surf_${VMD_ARCH} diff --git a/science/vmd/distinfo b/science/vmd/distinfo index 434b34b20e8e..d86f624a7010 100644 --- a/science/vmd/distinfo +++ b/science/vmd/distinfo @@ -1,6 +1,6 @@ -SHA256 (vmd-1.8.7.src.tar.gz) = 72fe2fb7eff4c805a886ea929c7e143a3a1be57cc817b5d1719d29e591d80316 -SIZE (vmd-1.8.7.src.tar.gz) = 23853864 -SHA256 (tachyon-0.98.7.tar.gz) = f22b86ed8c85bb12abc20c703f01238bce676c097dae66c81a6bbb7c08a60341 -SIZE (tachyon-0.98.7.tar.gz) = 3269840 +SHA256 (vmd-1.9.1.src.tar.gz) = 54aa88e03d86d763383e7b98592a152c9d68e78383e13af0dd2aca09b002491f +SIZE (vmd-1.9.1.src.tar.gz) = 30748110 +SHA256 (tachyon-0.99b2.tar.gz) = 3bd8dd6ad78c6b2153e985645b385357eb42f3908a2269a7cfe7f9afa35da012 +SIZE (tachyon-0.99b2.tar.gz) = 3352908 SHA256 (Stride_src.tar.Z) = c40f7de64947ebab7ec49511c0d264b08bc0fcbc703014bdc85d83a7389be230 SIZE (Stride_src.tar.Z) = 100329 diff --git a/science/vmd/files/patch-AtomParser.C b/science/vmd/files/patch-AtomParser.C deleted file mode 100644 index b27d2b19b3ec..000000000000 --- a/science/vmd/files/patch-AtomParser.C +++ /dev/null @@ -1,11 +0,0 @@ ---- src/AtomParser.C-xxx Fri Dec 5 13:21:53 2003 -+++ src/AtomParser.C Thu Aug 12 00:24:00 2004 -@@ -114,7 +114,7 @@ - #define YYCONST - #endif - --#if !defined(_MSC_VER) && !defined(__APPLE__) -+#if !defined(_MSC_VER) && !defined(__APPLE__) && !defined(ARCH_FREEBSD) && !defined(ARCH_FREEBSDAMD64) - #include <values.h> - #endif - diff --git a/science/vmd/files/patch-Make-arch b/science/vmd/files/patch-Make-arch index f981afc108cf..9bad558a0bf2 100644 --- a/science/vmd/files/patch-Make-arch +++ b/science/vmd/files/patch-Make-arch @@ -1,38 +1,31 @@ ---- Make-arch.orig Mon Feb 7 13:09:55 2005 -+++ ../plugins/Make-arch Fri Mar 25 16:54:01 2005 -@@ -12,6 +12,7 @@ - @echo " AIX5_64" - @echo " AIX6_64" - @echo " FREEBSD" -+ @echo " FREEBSDAMD64" - @echo " HPUX11" - @echo " IRIX6" - @echo " IRIX6_64" -@@ -259,8 +260,25 @@ +--- ../plugins/Make-arch.orig 2011-03-11 22:38:25.000000000 -0500 ++++ ../plugins/Make-arch 2011-03-12 00:08:41.000000000 -0500 +@@ -277,8 +277,8 @@ "CC = gcc" \ "CXX = g++" \ - "DEF = -D" \ + "DEF = -D" \ - "CCFLAGS = -O2 -Wall -I/usr/local/include/tcl8.5" \ - "CXXFLAGS = -O2 -Wall" \ + "CCFLAGS = ${CFLAGS} -O2 -Wall -I/usr/local/include/tcl8.5" \ -+ "CXXFLAGS = ${CFLAGS} -O2 -Wall -I/usr/local/include/tcl8.5" \ -+ "TCLLDFLAGS = -L/usr/local/lib -ltcl85" \ -+ "NETCDFLDFLAGS = -lnetcdf " \ -+ "AR = ar" \ -+ "NM = nm -p" \ -+ "RANLIB = touch" \ -+ "SHLD = gcc -shared" -+ -+FREEBSDAMD64: -+ $(MAKE) dynlibs staticlibs \ ++ "CXXFLAGS = ${CFLAGS} -O2 -Wall" \ + "TCLLDFLAGS = -L/usr/local/lib -ltcl85" \ + "NETCDFLDFLAGS = -lnetcdf " \ + "AR = ar" \ +@@ -288,14 +288,14 @@ + + FREEBSDAMD64: + $(MAKE) dynlibs staticlibs bins \ +- "ARCH = FREEBSD" \ + "ARCH = FREEBSDAMD64" \ -+ "COPTO = -fPIC -m64 -o " \ -+ "LOPTO = -fPIC -m64 -o " \ -+ "CC = gcc" \ -+ "CXX = g++" \ -+ "DEF = -D" \ + "COPTO = -fPIC -m64 -o " \ + "LOPTO = -fPIC -m64 -o " \ + "CC = gcc" \ + "CXX = g++" \ + "DEF = -D" \ +- "CCFLAGS = -m64 -O2 -Wall -I/usr/local/include/tcl8.5" \ +- "CXXFLAGS = -m64 -O2 -Wall" \ + "CCFLAGS = ${CFLAGS} -m64 -O2 -Wall -I/usr/local/include/tcl8.5" \ -+ "CXXFLAGS = ${CFLAGS} -m64 -O2 -Wall -I/usr/local/include/tcl8.5" \ ++ "CXXFLAGS = ${CFLAGS} -m64 -O2 -Wall" \ "TCLLDFLAGS = -L/usr/local/lib -ltcl85" \ - "NETCDFLDFLAGS = -lnetcdf " \ + "NETCDFLDFLAGS = -lnetcdf " \ "AR = ar" \ diff --git a/science/vmd/files/patch-OpenGLExtensions.C b/science/vmd/files/patch-OpenGLExtensions.C deleted file mode 100644 index 5f24ce33c59c..000000000000 --- a/science/vmd/files/patch-OpenGLExtensions.C +++ /dev/null @@ -1,21 +0,0 @@ ---- src/OpenGLExtensions.C-xxx Fri Dec 5 13:21:59 2003 -+++ src/OpenGLExtensions.C Fri Aug 27 16:42:14 2004 -@@ -157,7 +157,17 @@ - #endif - - #if !defined(_MSC_VER) && !defined(__APPLE__) --#if !defined(__linux) && !defined(ARCH_SOLARISX86) && !defined(ARCH_SOLARISX86_64) && (defined(GLX_VERSION_1_4) || defined(ARCH_SOLARIS2)) -+/* -+ Why the !defined(ARCH_FREEBSD)? Typically the X libraries that -+ come with FreeBSD work with glXGetProcAddress. However, if the -+ nvidia-driver port is installed, it seems not to work. But using -+ glXGetProcAddressARB seems to work whether or not the nvidia-driver -+ port is installed. (To be honest, I do feel that this is a bit hackish, -+ and maybe this will break something in other environments, but lets face -+ that bridge when we come to it - email me at stephen@math.missouri.edu -+ about it.) -+*/ -+#if !defined(ARCH_FREEBSD) && !defined(__linux) && !defined(ARCH_SOLARISX86) && !defined(ARCH_SOLARISX86_64) && (defined(GLX_VERSION_1_4) || defined(ARCH_SOLARIS2)) - // GLX 1.4 form found on commercial Unix systems that - // don't bother providing the ARB extension version that Linux prefers. - return glXGetProcAddress((const GLubyte *) procname); diff --git a/science/vmd/files/patch-bin_vmd.csh b/science/vmd/files/patch-bin_vmd.csh deleted file mode 100644 index a13d8716deb3..000000000000 --- a/science/vmd/files/patch-bin_vmd.csh +++ /dev/null @@ -1,14 +0,0 @@ ---- bin/vmd.csh.orig 2010-12-08 20:55:17.000000000 -0500 -+++ bin/vmd.csh 2010-12-08 21:10:21.000000000 -0500 -@@ -218,6 +218,11 @@ - # The standard options - if (`uname -m` == "i386") then - set ARCH=FREEBSD -+ else if (`uname -m` == "amd64") then -+ set ARCH=FREEBSDAMD64 -+ else -+ echo "Error: unsupported FreeBSD version $MACHVER" -+ exit 1 - endif - set VMD_WINTERM=xterm - set VMD_WINOPTS='-sb -sl 1000 -e' diff --git a/science/vmd/files/patch-bin_vmd.sh b/science/vmd/files/patch-bin_vmd.sh deleted file mode 100644 index 5689cfdf44cc..000000000000 --- a/science/vmd/files/patch-bin_vmd.sh +++ /dev/null @@ -1,15 +0,0 @@ ---- bin/vmd.sh.orig 2010-12-08 21:07:16.000000000 -0500 -+++ bin/vmd.sh 2010-12-08 21:15:46.000000000 -0500 -@@ -256,6 +256,12 @@ - if [ `uname -m` = "i386" ] - then - ARCH=FREEBSD -+ elif [ `uname -m` = "amd64" ] -+ then -+ ARCH=FREEBSDAMD64 -+ else -+ echo "Error: unsupported FreeBSD version $MACHVER" -+ exit 1 - fi - VMD_WINTERM=xterm - VMD_WINOPTS='-sb -sl 1000 -e' diff --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure index ce3c93112e3c..7f1d31386128 100644 --- a/science/vmd/files/patch-configure +++ b/science/vmd/files/patch-configure @@ -13,24 +13,7 @@ # optionally override hard-coded defaults above with environment variables -@@ -48,6 +48,7 @@ - # AIX5 - compile on an RS/6000 machine (gcc/g++/xlc/xlC) - # AIX6 - compile on an RS/6000 machine (gcc/g++/xlc/xlC) - # FREEBSD - compile on a FreeBSD machine (gcc/g++) -+# FREEBSDAMD64 - compile on a FreeBSD machine (gcc/g++) - # HPUX11 - compile on an HP-UX 11.0 machine (cc/CC/cc/aCC) - # IRIX6 - compile on an SGI, IRIX 6.X or later, 32-bit ABI - # IRIX6_64 - compile on an SGI, IRIX 6.X or later, 64-bit ABI -@@ -153,7 +154,7 @@ - - #################### Parse command line options ########### - # list of allowed architectures --@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64'); -+@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'FREEBSDAMD64', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64'); - - if ($#ARGV == -1) { - $text = `cat configure.options`; -@@ -747,8 +748,8 @@ +@@ -788,8 +788,8 @@ # This may be commented out if not required. $libtachyon_defines = "-DVMDLIBTACHYON"; $libtachyon_dir = "$vmd_library_dir/tachyon"; @@ -41,111 +24,7 @@ $libtachyon_libs = "-ltachyon"; @libtachyon_cc = (); @libtachyon_cu = (); -@@ -1478,9 +1479,11 @@ - $def_imageviewer="display %s"; - - # 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_dir = "/usr/local"; -+# -DGLX_GLXEXT_LEGACY is required for patched OpenGLExtensions.C to compile. -+# See patched OpenGLExtensions.C for explanation. -+ $opengl_include = "-DGLX_GLXEXT_LEGACY -I$opengl_dir/include"; -+ $opengl_library = "-L$opengl_dir/lib -L/usr/local/lib"; - $opengl_libs = "-lGL -lGLU"; - - $arch_lex = "flex"; -@@ -1492,17 +1495,17 @@ - $arch_shld = "g++ -shared"; - $arch_shlibname = "so"; - $arch_shcppopts = "-fPIC"; -- $arch_shldopts = "-L/usr/local/lib -L/usr/X11R6/lib"; -+ $arch_shldopts = "-L/usr/local/lib"; - - $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3"; - $arch_copts = "-m32 -Wall -O3"; - - if ($config_static) { - $arch_lopts = "-static"; -- $mesa_libs = "-lMesaGL -lMesaGLU -L/usr/X11R6/lib -lXext -lX11"; -+ $mesa_libs = "-lMesaGL -lMesaGLU -L/usr/local/lib -lXext -lX11"; - } else { - $arch_lopts = ""; -- $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib -lXext -lX11"; -+ $mesa_libs = "-lGL -lGLU -L/usr/local/lib -lXext -lX11"; - } - - if ($config_shared) { -@@ -1515,7 +1518,66 @@ - - # this is to make tcl happy, - # also needed for plugins -- $system_libs .= " -ldl"; -+ # $system_libs .= " -ldl"; -+ -+ if ($config_python) { -+ # this is to make python happy -+ $system_libs .= " -lutil"; -+ } -+ -+ # this is necessary for the embedded Python interpreter to dynamically -+ # load shared libraries. It increases the size of the binary by 200k. -+ $arch_lopts .= " -Xlinker -export-dynamic"; -+} -+ -+ -+ -+if ($config_arch eq "FREEBSDAMD64") { -+ $def_imageviewer="display %s"; -+ if ($config_lp64) { -+ print "LP64 ABI is already the default on this platform.\n"; -+ } -+ -+ # XFree 4.0 Direct Rendering Interface and GLX -+ $opengl_dir = "/usr/local"; -+# -DGLX_GLXEXT_LEGACY is required for patched OpenGLExtensions.C to compile. -+# See patched OpenGLExtensions.C for explanation. -+ $opengl_include = "-DGLX_GLXEXT_LEGACY -I$opengl_dir/include"; -+ $opengl_library = "-L$opengl_dir/lib -L/usr/local/lib"; -+ $opengl_libs = "-lGL -lGLU"; -+ -+ $arch_lex = "flex"; -+ $arch_yacc = "bison -b y -d "; # If standard yacc doesn't work -+ -+ $arch_cc = "gcc"; -+ $arch_ccpp = "g++"; -+ $arch_depend_flag = "-MM"; -+ $arch_shld = "ld -shared"; -+ $arch_shlibname = "so"; -+ $arch_shcppopts = "-fPIC"; -+ $arch_shldopts = "-L/usr/local/lib -L/usr/local/lib"; -+ -+ $arch_opt_flag = "-m64 -Wall -O3 -ffast-math"; -+ $arch_copts = "-m64 -Wall -O3 -ffast-math"; -+ -+ if ($config_static) { -+ $arch_lopts = "-static"; -+ $mesa_libs = "-lMesaGL -lMesaGLU -L/usr/local/lib -lXext -lX11"; -+ } else { -+ $arch_lopts = ""; -+ $mesa_libs = "-lGL -lGLU -L/usr/local/lib -lXext -lX11"; -+ } -+ -+ if ($config_shared) { -+ $arch_lopts = "-shared"; -+ } -+ -+ # a hack - to be removed, just keeps make happy -+ $arch_template_repository = "foobar"; -+ -+ # this is to make tcl happy, -+ # also needed for plugins -+ # $system_libs .= " -ldl"; - - if ($config_python) { - # this is to make python happy -@@ -2715,10 +2777,10 @@ +@@ -2942,10 +2942,10 @@ # compiler and compiler directives CC = $arch_cc diff --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch index ade246db35aa..aa8049780694 100644 --- a/science/vmd/files/patch-lib_tachyon_unix_Make-arch +++ b/science/vmd/files/patch-lib_tachyon_unix_Make-arch @@ -1,6 +1,6 @@ --- Make-arch-orig Fri Mar 25 14:34:38 2005 +++ lib/tachyon/unix/Make-arch Fri Mar 25 14:34:50 2005 -@@ -950,7 +950,7 @@ +@@ -989,7 +989,7 @@ $(MAKE) all \ "ARCH = bsd" \ "CC = gcc" \ diff --git a/science/vmd/files/patch-plugins__hesstrans__Makefile b/science/vmd/files/patch-plugins__hesstrans__Makefile new file mode 100644 index 000000000000..8397e904bf12 --- /dev/null +++ b/science/vmd/files/patch-plugins__hesstrans__Makefile @@ -0,0 +1,11 @@ +--- ../plugins/hesstrans/Makefile.orig 2012-03-19 19:58:44.000000000 -0400 ++++ ../plugins/hesstrans/Makefile 2012-03-19 19:59:01.000000000 -0400 +@@ -12,7 +12,7 @@ + ARCHDIR=${COMPILEDIR}/lib_${ARCH}/tcl/hesstrans$(VERSION) + SRCDIR=src + INCDIR=-Isrc +-CXXFLAGS = -g $(CXXFLAGS) ++CXXFLAGS += -g + VPATH = src ${ARCHDIR} + + ## diff --git a/science/vmd/files/patch-utilities.C b/science/vmd/files/patch-utilities.C deleted file mode 100644 index 41abe5f0c839..000000000000 --- a/science/vmd/files/patch-utilities.C +++ /dev/null @@ -1,11 +0,0 @@ ---- src/utilities.C.orig Sat Jan 22 16:15:24 2005 -+++ src/utilities.C Sat Jan 22 16:15:45 2005 -@@ -396,7 +396,7 @@ - return stringdup("Windows User"); - } - #else --#if defined(ARCH_FREEBSD) || defined(__APPLE__) || defined(__linux) -+#if defined(ARCH_FREEBSD) || defined(ARCH_FREEBSDAMD64) || defined(__APPLE__) || defined(__linux) - return stringdup(getlogin()); - #else - return stringdup(cuserid(NULL)); diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist index daff3ee26865..310cefe335c5 100644 --- a/science/vmd/pkg-plist +++ b/science/vmd/pkg-plist @@ -5,6 +5,9 @@ lib/vmd/Announcement lib/vmd/LICENSE lib/vmd/README lib/vmd/doc/ug.pdf +lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0/catdcd +lib/vmd/plugins/%%VMD_ARCH%%/bin/cionize1.0/cionize +lib/vmd/plugins/%%VMD_ARCH%%/molfile/abinitplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/babelplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/basissetplugin.so @@ -41,6 +44,7 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/mol2plugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/moldenplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/msmsplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/namdbinplugin.so +lib/vmd/plugins/%%VMD_ARCH%%/molfile/offplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/pbeqplugin.so @@ -63,25 +67,91 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspposcarplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxdatcarplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxmlplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/vtfplugin.so +lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/xbgfplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/xsfplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/xyzplugin.so -lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hessTest.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3/psfcheck.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3/autopsf.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/cionize.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw +lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw_help +lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/mafft.tcl lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.so -lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.tcl lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/pkgIndex.tcl -lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so -lib/vmd/plugins/LINUX/tcl/intersurf1.1/color_func.tcl -lib/vmd/plugins/LINUX/tcl/intersurf1.1/intersurf_gui.tcl -lib/vmd/plugins/LINUX/tcl/intersurf1.1/license.txt -lib/vmd/plugins/LINUX/tcl/intersurf1.1/nicostuf.tcl -lib/vmd/plugins/LINUX/tcl/intersurf1.1/pkgIndex.tcl -lib/vmd/plugins/WIN32/tcl/intersurf1.1/bin/intersurf.dll -lib/vmd/plugins/WIN32/tcl/intersurf1.1/color_func.tcl -lib/vmd/plugins/WIN32/tcl/intersurf1.1/intersurf_gui.tcl -lib/vmd/plugins/WIN32/tcl/intersurf1.1/license.txt -lib/vmd/plugins/WIN32/tcl/intersurf1.1/nicostuf.tcl -lib/vmd/plugins/WIN32/tcl/intersurf1.1/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/q +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/metric.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit_profcombine.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit_entropy.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/seqqr +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/structqr +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/qpair +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/rmsd +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/percid +lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/tcl_libbiokit.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/libalchemify.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/mutator_gui.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/mutator.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/upgmaclu +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_widget.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_nodeprops.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_nexus.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_newick.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_matrixviewer.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_je.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_export.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_data.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_analysis.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/cluster.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/libpmepot.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot_gui.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/libpsfgen.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/ug.pdf +lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/specden.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/signalproc.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftpack.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/data_io_lib.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftcmds.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/sgsmooth.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp +lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp.defaults +lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pdb.directories +lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/dssp.directories +lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Root +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Repository +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Entries +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_A.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_C.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_G.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_I.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_P.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_T.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_U.pdb +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/misc_rna.par +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/ps_image.par +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/raster3d.par +lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/vrml_image.par +lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/volutil +lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/volutil.tcl lib/vmd/plugins/include/molfile_plugin.h lib/vmd/plugins/include/vmdconio.h lib/vmd/plugins/include/vmdplugin.h @@ -90,18 +160,17 @@ lib/vmd/plugins/noarch/tcl/apbsrun1.3/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/apbsrun1.3/radii.dat lib/vmd/plugins/noarch/tcl/atomedit1.0/atomedit.tcl lib/vmd/plugins/noarch/tcl/atomedit1.0/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-api.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-gui.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-settings.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-template.namd -lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/namdrun.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/autoimd1.6/ug.pdf -lib/vmd/plugins/noarch/tcl/autoionize1.2/autoionize.tcl -lib/vmd/plugins/noarch/tcl/autoionize1.2/autoionizegui.tcl -lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top -lib/vmd/plugins/noarch/tcl/autoionize1.2/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd-api.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd-gui.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd-settings.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd-template.namd +lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/namdrun.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/autoimd1.7/ug.pdf +lib/vmd/plugins/noarch/tcl/autoionize1.3/autoionize.tcl +lib/vmd/plugins/noarch/tcl/autoionize1.3/autoionizegui.tcl +lib/vmd/plugins/noarch/tcl/autoionize1.3/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/bignum1.0/bignum.tcl lib/vmd/plugins/noarch/tcl/bignum1.0/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/biocore1.1/biocore.tcl @@ -124,12 +193,18 @@ lib/vmd/plugins/noarch/tcl/cgtools1.0/protein.cgc lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.par lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.top lib/vmd/plugins/noarch/tcl/cgtools1.0/water.cgc +lib/vmd/plugins/noarch/tcl/chirality1.1/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/chirality1.1/chirality_gui.tcl +lib/vmd/plugins/noarch/tcl/chirality1.1/chirality.tcl +lib/vmd/plugins/noarch/tcl/cispeptide1.1/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/cispeptide1.1/cispeptide_gui.tcl +lib/vmd/plugins/noarch/tcl/cispeptide1.1/cispeptide.tcl lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/clonerep1.1/clonerep.tcl -lib/vmd/plugins/noarch/tcl/clonerep1.1/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/colorscalebar1.2/colorscalebar.tcl -lib/vmd/plugins/noarch/tcl/colorscalebar1.2/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/clonerep1.2/clonerep.tcl +lib/vmd/plugins/noarch/tcl/clonerep1.2/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/colorscalebar1.3/colorscalebar.tcl +lib/vmd/plugins/noarch/tcl/colorscalebar1.3/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/contactmap1.1/contactmap.tcl lib/vmd/plugins/noarch/tcl/contactmap1.1/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/dataimport1.0/dataimport.tcl @@ -138,33 +213,48 @@ lib/vmd/plugins/noarch/tcl/demomaster1.0/demomaster.tcl lib/vmd/plugins/noarch/tcl/demomaster1.0/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/dipwatch1.2/dipwatch.tcl lib/vmd/plugins/noarch/tcl/dipwatch1.2/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/dowser1.0/dowser.tcl -lib/vmd/plugins/noarch/tcl/dowser1.0/dowser_gui.tcl -lib/vmd/plugins/noarch/tcl/dowser1.0/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/dowser1.1/dowser.tcl +lib/vmd/plugins/noarch/tcl/dowser1.1/dowser_gui.tcl +lib/vmd/plugins/noarch/tcl/dowser1.1/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/exectool1.2/exectool.tcl lib/vmd/plugins/noarch/tcl/exectool1.2/jobmanager.tcl lib/vmd/plugins/noarch/tcl/exectool1.2/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/extendedpdb1.0/extendedpdb.tcl lib/vmd/plugins/noarch/tcl/extendedpdb1.0/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/gofrgui1.1/gofrgui.tcl -lib/vmd/plugins/noarch/tcl/gofrgui1.1/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/hbonds1.1/hbonds.tcl -lib/vmd/plugins/noarch/tcl/hbonds1.1/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_guiProcs.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_guiInterface.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_GeomOpt.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_GenZMatrix.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_GenDihScan.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_GenBonded.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_DihOpt.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_ChargeOpt.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_BuildPar.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_BondAngleOpt.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk.tcl +lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_SharedFcns.tcl +lib/vmd/plugins/noarch/tcl/gofrgui1.2/gofrgui.tcl +lib/vmd/plugins/noarch/tcl/gofrgui1.2/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/hbonds1.2/hbonds.tcl +lib/vmd/plugins/noarch/tcl/hbonds1.2/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/heatmapper1.0/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/heatmapper1.0/heatmapper.tcl lib/vmd/plugins/noarch/tcl/idatm0.1/idatm.tcl lib/vmd/plugins/noarch/tcl/idatm0.1/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/ilstools1.2/acetylene.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/carbondioxide.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/carbonmonoxide.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/ethene.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/hydrogen.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/ilstools.tcl -lib/vmd/plugins/noarch/tcl/ilstools1.2/methane.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/nitricoxide.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrogen.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrogendioxide.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrousoxide.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/oxygen.xyz -lib/vmd/plugins/noarch/tcl/ilstools1.2/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/ilstools1.4/acetylene.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/carbondioxide.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/carbonmonoxide.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/ethene.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/hydrogen.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/ilstools.tcl +lib/vmd/plugins/noarch/tcl/ilstools1.4/methane.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/nitricoxide.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/nitrogen.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/nitrogendioxide.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/nitrousoxide.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/oxygen.xyz +lib/vmd/plugins/noarch/tcl/ilstools1.4/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/imdmenu1.0/imdmenu.tcl lib/vmd/plugins/noarch/tcl/imdmenu1.0/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/inorganicbuilder.tcl @@ -189,113 +279,147 @@ lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.inp lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.pdb lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.top lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/pkgIndex.tcl 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+lib/vmd/plugins/noarch/tcl/viewchangerender1.6/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/viewchangerender1.6/vcr_gui.tcl +lib/vmd/plugins/noarch/tcl/viewchangerender1.6/vcr.tcl +lib/vmd/plugins/noarch/tcl/viewmaster2.5/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/viewmaster2.5/viewmaster.tcl +lib/vmd/plugins/noarch/tcl/vmddebug1.0/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/vmddebug1.0/debugatomsel.tcl +lib/vmd/plugins/noarch/tcl/vmddebug1.0/vmddebug.tcl +lib/vmd/plugins/noarch/tcl/vmdmovie1.9/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/vmdmovie1.9/vmdmovie.tcl lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/README lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/CVS/Entries @@ -1027,6 +1173,8 @@ lib/vmd/shaders/CVS/Root lib/vmd/shaders/vmd.frag lib/vmd/shaders/vmd.vert lib/vmd/shaders/vmdsphere.frag +lib/vmd/shaders/vmdspheresprite.frag +lib/vmd/shaders/vmdspheresprite.vert lib/vmd/shaders/vmdsphere.vert lib/vmd/stride_%%VMD_ARCH%% lib/vmd/surf_%%VMD_ARCH%% @@ -1035,107 +1183,129 @@ lib/vmd/vmd_%%VMD_ARCH%% lib/vmd/vmd_completion.dat @dirrm lib/vmd/doc +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin/cionize1.0 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin @dirrm lib/vmd/plugins/%%VMD_ARCH%%/molfile +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1 @dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2 +@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3 @dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl @dirrm lib/vmd/plugins/%%VMD_ARCH%% -@dirrm lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin -@dirrm lib/vmd/plugins/LINUX/tcl/intersurf1.1 -@dirrm lib/vmd/plugins/LINUX/tcl -@dirrm lib/vmd/plugins/LINUX -@dirrm lib/vmd/plugins/WIN32/tcl/intersurf1.1/bin -@dirrm lib/vmd/plugins/WIN32/tcl/intersurf1.1 -@dirrm lib/vmd/plugins/WIN32/tcl -@dirrm lib/vmd/plugins/WIN32 @dirrm lib/vmd/plugins/include @dirrm lib/vmd/plugins/noarch/tcl/apbsrun1.3 @dirrm lib/vmd/plugins/noarch/tcl/atomedit1.0 -@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.6 -@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.2 +@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.7 +@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.3 @dirrm lib/vmd/plugins/noarch/tcl/bignum1.0 @dirrm lib/vmd/plugins/noarch/tcl/biocore1.1 @dirrm lib/vmd/plugins/noarch/tcl/blast1.1 @dirrm 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