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authorhrs <hrs@FreeBSD.org>2012-04-23 12:48:03 +0800
committerhrs <hrs@FreeBSD.org>2012-04-23 12:48:03 +0800
commit0ec1b4890bfefe8723d96532a95d63c9fa34c236 (patch)
tree600b5c65083400ff8a68c3be23d140c8d8b6653c /science
parent8402dc4bf884057a8b091141ebe113607a111fc7 (diff)
downloadfreebsd-ports-gnome-0ec1b4890bfefe8723d96532a95d63c9fa34c236.tar.gz
freebsd-ports-gnome-0ec1b4890bfefe8723d96532a95d63c9fa34c236.tar.zst
freebsd-ports-gnome-0ec1b4890bfefe8723d96532a95d63c9fa34c236.zip
Update to 1.9.1.
Submitted by: bjk
Diffstat (limited to 'science')
-rw-r--r--science/vmd/Makefile16
-rw-r--r--science/vmd/distinfo8
-rw-r--r--science/vmd/files/patch-AtomParser.C11
-rw-r--r--science/vmd/files/patch-Make-arch51
-rw-r--r--science/vmd/files/patch-OpenGLExtensions.C21
-rw-r--r--science/vmd/files/patch-bin_vmd.csh14
-rw-r--r--science/vmd/files/patch-bin_vmd.sh15
-rw-r--r--science/vmd/files/patch-configure125
-rw-r--r--science/vmd/files/patch-lib_tachyon_unix_Make-arch2
-rw-r--r--science/vmd/files/patch-plugins__hesstrans__Makefile11
-rw-r--r--science/vmd/files/patch-utilities.C11
-rw-r--r--science/vmd/pkg-plist800
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
-lib/vmd/plugins/noarch/tcl/irspecgui1.1/irspecgui.tcl
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-lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.pdb
-lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.psf
-lib/vmd/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp
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-lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/CVS/Entries
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-lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/CYS.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLN.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLU.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLY-end.mfrag
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lib/vmd/plugins/noarch/tcl/palettetool1.0/palettetool.tcl
lib/vmd/plugins/noarch/tcl/palettetool1.0/pkgIndex.tcl
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lib/vmd/plugins/noarch/tcl/pdbtool1.0/pdbtool.tcl
lib/vmd/plugins/noarch/tcl/pdbtool1.0/pkgIndex.tcl
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lib/vmd/plugins/noarch/tcl/psipred1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/psipred1.1/psipred.tcl
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lib/vmd/plugins/noarch/tcl/ramaplot1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/ramaplot1.1/ramaplot.tcl
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-lib/vmd/plugins/noarch/tcl/resptool1.1/resptool.tcl
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+lib/vmd/plugins/noarch/tcl/readcharmmpar1.2/par_all36_lipid.prm
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+lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all36_lipid.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_amber2charmm.inp
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+lib/vmd/plugins/noarch/tcl/remote0.1/remote.tcl
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+lib/vmd/plugins/noarch/tcl/resptool1.2/resptool.tcl
lib/vmd/plugins/noarch/tcl/rmsd1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/rmsd1.0/rmsd.tcl
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-lib/vmd/plugins/noarch/tcl/rmsdtt2.0/rmsdtt.tcl
-lib/vmd/plugins/noarch/tcl/rnaview1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/rnaview1.0/rnaview.tcl
+lib/vmd/plugins/noarch/tcl/rmsdtt3.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/rmsdtt3.0/rmsdtt.tcl
+lib/vmd/plugins/noarch/tcl/rmsdvt1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/rmsdvt1.0/rmsdvt.tcl
+lib/vmd/plugins/noarch/tcl/rmsdvt1.0/rmsdvt-gui.tcl
+lib/vmd/plugins/noarch/tcl/rmsdvt1.0/modal.tcl
lib/vmd/plugins/noarch/tcl/ruler1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/ruler1.0/ruler.tcl
-lib/vmd/plugins/noarch/tcl/runante0.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/runante0.1/runante.tcl
-lib/vmd/plugins/noarch/tcl/saltbr1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/saltbr1.0/saltbr.tcl
+lib/vmd/plugins/noarch/tcl/runante0.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/runante0.2/runante.tcl
+lib/vmd/plugins/noarch/tcl/runsqm0.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/runsqm0.2/runsqm.tcl
+lib/vmd/plugins/noarch/tcl/saltbr1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/saltbr1.1/saltbr.tcl
lib/vmd/plugins/noarch/tcl/seqdata1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/seqdata1.1/seqdata.tcl
lib/vmd/plugins/noarch/tcl/seqdata1.1/seqdata_aln.tcl
@@ -470,34 +608,36 @@ lib/vmd/plugins/noarch/tcl/seqedit1.1/seqedit_widget_edit.tcl
lib/vmd/plugins/noarch/tcl/seqedit1.1/seqedit_widget_select.tcl
lib/vmd/plugins/noarch/tcl/seqedit1.1/seqedit_widget_statusbar.tcl
lib/vmd/plugins/noarch/tcl/seqedit1.1/taxonomy_options.tcl
-lib/vmd/plugins/noarch/tcl/solvate1.3/pkgIndex.tcl
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-lib/vmd/plugins/noarch/tcl/solvate1.3/wat.pdb
-lib/vmd/plugins/noarch/tcl/solvate1.3/wat.psf
-lib/vmd/plugins/noarch/tcl/solvate1.3/wat.top
-lib/vmd/plugins/noarch/tcl/ssrestraints1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/ssrestraints1.0/ssrestraints.tcl
-lib/vmd/plugins/noarch/tcl/ssrestraints1.0/ssrestraints_stride.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.5/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.5/solvate.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.5/wat.pdb
+lib/vmd/plugins/noarch/tcl/solvate1.5/wat.psf
+lib/vmd/plugins/noarch/tcl/solvate1.5/wat.top
+lib/vmd/plugins/noarch/tcl/ssrestraints1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/ssrestraints1.1/ssrestraints.tcl
+lib/vmd/plugins/noarch/tcl/ssrestraints1.1/ssrestraints_stride.tcl
lib/vmd/plugins/noarch/tcl/stingtool1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/stingtool1.0/stingtool.tcl
-lib/vmd/plugins/noarch/tcl/symmetrytool1.2/pkgIndex.tcl
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-lib/vmd/plugins/noarch/tcl/timeline2.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/timeline2.0/timeline.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.0/README
-lib/vmd/plugins/noarch/tcl/topotools1.0/par_CG.prm
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-lib/vmd/plugins/noarch/tcl/topotools1.0/top_CG.prm
-lib/vmd/plugins/noarch/tcl/topotools1.0/topoangles.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.0/topoatoms.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.0/topobonds.tcl
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-lib/vmd/plugins/noarch/tcl/topotools1.0/topolammps.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.0/topotools.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.0/topoutils.tcl
+lib/vmd/plugins/noarch/tcl/symmetrytool1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/symmetrytool1.3/symmetry.tcl
+lib/vmd/plugins/noarch/tcl/timeline2.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/timeline2.3/timeline.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/README
+lib/vmd/plugins/noarch/tcl/topotools1.2/par_CG.prm
+lib/vmd/plugins/noarch/tcl/topotools1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/top_CG.prm
+lib/vmd/plugins/noarch/tcl/topotools1.2/topoangles.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topoatoms.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topobonds.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topocgcmm.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topodihedrals.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topogromacs.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topohelpers.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topoimpropers.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topolammps.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topotools.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topoutils.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.2/topovarxyz.tcl
lib/vmd/plugins/noarch/tcl/trunctraj1.5/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/acepar19.inp
lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/acepar22_prot.inp
@@ -554,12 +694,18 @@ lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/toprna10r_22.inp
lib/vmd/plugins/noarch/tcl/trunctraj1.5/trunctraj.tcl
lib/vmd/plugins/noarch/tcl/utilities1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/utilities1.0/utilities.tcl
-lib/vmd/plugins/noarch/tcl/vdna2.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/vdna2.0/vdna.tcl
-lib/vmd/plugins/noarch/tcl/viewmaster2.2/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/viewmaster2.2/viewmaster.tcl
-lib/vmd/plugins/noarch/tcl/vmdmovie1.7/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/vmdmovie1.7/vmdmovie.tcl
+lib/vmd/plugins/noarch/tcl/vdna2.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vdna2.2/vdna.tcl
+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
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generated by cgit (git 2.34.1) at 2024-12-17 03:46:14 +0800