git: 9d387d6d8e68 - main - science/vmd: Update to 1.9.4a57
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Wed, 16 Nov 2022 00:36:17 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=9d387d6d8e68d73411813a0c70f3295d514aee6f
commit 9d387d6d8e68d73411813a0c70f3295d514aee6f
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-11-16 00:32:46 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-11-16 00:36:16 +0000
science/vmd: Update to 1.9.4a57
Unbreak build: 1.9.3 incompatible with latest python tools
Clean up portlint and stage qa issues
---
science/vmd/Makefile | 46 +-
science/vmd/distinfo | 6 +-
science/vmd/files/patch-Make-arch | 2 +-
science/vmd/files/patch-Makefile | 8 +-
science/vmd/files/patch-configure | 205 +++++-
science/vmd/files/patch-lib_stride_Makefile | 2 +-
...patch-surf_Makefile => patch-lib_surf_Makefile} | 6 +-
science/vmd/files/patch-lib_tachyon_unix_Make-arch | 258 ++++++-
science/vmd/pkg-plist | 806 ++++++++++++---------
9 files changed, 952 insertions(+), 387 deletions(-)
diff --git a/science/vmd/Makefile b/science/vmd/Makefile
index 7ef3fc782db0..c5d758ac0042 100644
--- a/science/vmd/Makefile
+++ b/science/vmd/Makefile
@@ -1,6 +1,6 @@
PORTNAME= vmd
-DISTVERSION= 1.9.3
-PORTREVISION= 11
+DISTVERSION= 1.9.4
+DISTVERSIONSUFFIX= a57
CATEGORIES= science graphics python tcl tk
MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \
http://www.photonlimited.com/~johns/tachyon/files/0.99b6/:tachyon \
@@ -17,6 +17,8 @@ WWW= http://www.ks.uiuc.edu/Research/vmd/
LICENSE= VMD BSD3CLAUSE STRIDE
LICENSE_COMB= multi
+ONLY_FOR_ARCHS= amd64 i386
+
BUILD_DEPENDS= makedepend:devel/makedepend \
${PYNUMPY}
LIB_DEPENDS= libexpat.so:textproc/expat2 \
@@ -24,6 +26,13 @@ LIB_DEPENDS= libexpat.so:textproc/expat2 \
libnetcdf.so:science/netcdf
RUN_DEPENDS= ${PYNUMPY}
+USES= gl gmake perl5 python shebangfix sqlite tcl tk xorg
+SHEBANG_FILES= ${WRKDIR}/plugins/topotools/*.tcl \
+ ${WRKDIR}/plugins/mdff/resetmaps.sh
+USE_PERL5= build
+USE_GL= gl glu
+USE_XORG= x11
+
LICENSE_FILE_VMD= ${WRKSRC}/LICENSE
LICENSE_PERMS_VMD= no-auto-accept
LICENSE_NAME_VMD= Visual Molecular Dynamics Software License Agreement
@@ -37,14 +46,6 @@ LICENSE_PERMS_STRIDE= dist-mirror pkg-mirror auto-accept
LICENSE_NAME_STRIDE= Stride Copyright Notice
LICENSE_DISTFILES_STRIDE=${STRIDE_DIST}
-USES= gl gmake perl5 python shebangfix sqlite tcl tk xorg
-SHEBANG_FILES= ${WRKDIR}/plugins/topotools/*.tcl
-USE_PERL5= build
-USE_GL= gl glu
-USE_XORG= x11
-
-ONLY_FOR_ARCHS= amd64 i386
-
CONFIGURE_ENV= PYTHON_INCLUDE_DIR=${PYTHON_INCLUDEDIR} \
PYTHON_LIBRARY_DIR=${PYTHON_LIBDIR} \
NUMPY_INCLUDE_DIR=${PYTHON_SITELIBDIR}/numpy/core/include \
@@ -71,13 +72,21 @@ MAKE_ENV= EXPATINC=-I${LOCALBASE}/include \
TCLLDFLAGS=-ltcl${TCL_VER:S/.//} \
TKLDFLAGS="-ltk${TK_VER:S/.//} -lX11"
-VMD_DIST= ${PORTNAME}-${DISTVERSION}.src.tar.gz
+VMD_DIST= ${PORTNAME}-${DISTVERSION}${DISTVERSIONSUFFIX}.src.tar.gz
TACHYON_DIST= tachyon-0.99b6.tar.gz
STRIDE_DIST= stride.tar.gz
STRIDE_DOC= stride.doc
.include <bsd.port.pre.mk>
+.if !exists(${DISTDIR}/${VMD_DIST})
+IGNORE= license restrictions require manual fetching of the distribution\
+ source. Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\
+ with a browser. You will be required to register, log in, and accept\
+ the University of Illinois agreement before you can download the\
+ ${VMD_DIST} source. Place this distfile in ${DISTDIR} and try again.
+.endif
+
.if ${ARCH} == "amd64"
VMD_ARCH= FREEBSDAMD64
.else
@@ -86,15 +95,6 @@ VMD_ARCH= FREEBSD
PLIST_SUB+= VMD_ARCH=${VMD_ARCH}
-# Check for VMD sources
-.if !exists(${DISTDIR}/${VMD_DIST})
-IGNORE= license restrictions require manual fetching of the distribution\
- source. Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\
- with a browser. You will be required to register, log in, and accept\
- the University of Illinois agreement before you can download the\
- ${VMD_DIST} source file. Place this file in ${DISTDIR} and try again.
-.endif
-
do-extract:
${MKDIR} ${WRKDIR} ${WRKSRC}/lib/stride
${TAR} -xzf ${DISTDIR}/${VMD_DIST} -C ${WRKDIR}
@@ -148,9 +148,9 @@ post-install:
${REINPLACE_CMD} -i '' -e 's|${STAGEDIR}||g' ${STAGEDIR}${PREFIX}/bin/vmd
${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/*${VMD_ARCH} \
${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/molfile/*.so
-.for f in tcl/autopsf1.6/psfcheck.so tcl/hesstrans1.0/hesstrans.so \
+.for f in tcl/autopsf1.8/psfcheck.so tcl/hesstrans1.0/hesstrans.so \
tcl/mutator1.5/libalchemify.so tcl/pmepot1.0/libpmepot.so \
- tcl/psfgen1.6/libpsfgen.so tcl/rnaview1.1/rnaview \
+ tcl/psfgen2.0/libpsfgen.so tcl/rnaview1.1/rnaview \
tcl/signalproc1.1/specden.so tcl/signalproc1.1/fftcmds.so \
tcl/signalproc1.1/sgsmooth.so tcl/volutil1.3/volutil \
tcl/clustalw1.1/clustalw tcl/libbiokit1.1/tcl_libbiokit.so \
@@ -159,7 +159,7 @@ post-install:
tcl/libbiokit1.1/rmsd tcl/libbiokit1.1/percid \
tcl/phylotree1.2/upgmaclu tcl/stamp1.2/stamp \
tcl/bossconvert1.0/Topology \
- bin/catdcd5.1/catdcd bin/cionize1.0/cionize
+ bin/catdcd5.2/catdcd bin/cionize1.0/cionize
${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/${f}
.endfor
diff --git a/science/vmd/distinfo b/science/vmd/distinfo
index 5d42d032ddd2..1d36dd1916e4 100644
--- a/science/vmd/distinfo
+++ b/science/vmd/distinfo
@@ -1,6 +1,6 @@
-TIMESTAMP = 1482469862
-SHA256 (vmd-1.9.3.src.tar.gz) = 5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128
-SIZE (vmd-1.9.3.src.tar.gz) = 43981314
+TIMESTAMP = 1668527587
+SHA256 (vmd-1.9.4a57.src.tar.gz) = de278d0c5d969336d89068e0806fb50aaa0cb0f546ba985d840b279357860679
+SIZE (vmd-1.9.4a57.src.tar.gz) = 43155120
SHA256 (tachyon-0.99b6.tar.gz) = f4dcaf9c76a4f49310f56254390f9611c22e353947a1745a8c623e8bc8119b97
SIZE (tachyon-0.99b6.tar.gz) = 2981568
SHA256 (stride.tar.gz) = 51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a
diff --git a/science/vmd/files/patch-Make-arch b/science/vmd/files/patch-Make-arch
index fc680cffc2c7..adbec96b2b27 100644
--- a/science/vmd/files/patch-Make-arch
+++ b/science/vmd/files/patch-Make-arch
@@ -1,4 +1,4 @@
---- ../plugins/Make-arch.orig 2016-10-21 23:34:39.000000000 +0200
+--- ../plugins/Make-arch.orig 2016-10-21 23:34:39 UTC
+++ ../plugins/Make-arch
@@ -272,10 +272,8 @@
"CC = gcc" \
diff --git a/science/vmd/files/patch-Makefile b/science/vmd/files/patch-Makefile
index 53675de7524b..8088f99782f5 100644
--- a/science/vmd/files/patch-Makefile
+++ b/science/vmd/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig Sat Dec 6 04:20:58 2003
-+++ Makefile Wed Feb 2 21:30:13 2005
-@@ -86,10 +86,13 @@
+--- Makefile.orig 2022-04-27 06:21:11 UTC
++++ Makefile
+@@ -95,10 +95,13 @@ android.armv7a.text:
## FreeBSD builds
##
freebsd.mesa:
@@ -15,4 +15,4 @@
+ ./configure FREEBSDAMD64 OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON NETCDF
-
+ ##
diff --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure
index 33ca9e23ce8f..229aa6aead6b 100644
--- a/science/vmd/files/patch-configure
+++ b/science/vmd/files/patch-configure
@@ -1,4 +1,4 @@
---- configure.orig 2016-12-01 07:11:33 UTC
+--- configure.orig 2022-04-27 06:21:11 UTC
+++ configure
@@ -13,10 +13,10 @@
$install_name = "vmd";
@@ -13,7 +13,27 @@
# optionally override hard-coded defaults above with environment variables
-@@ -729,8 +729,8 @@ $tcl_include = "-I$stock_tcl_includ
+@@ -491,7 +491,7 @@ $arch_deletedir = "rm -rf";
+ $arch_echo = "echo";
+ $arch_tar = "tar";
+ $arch_compress = "compress";
+-$arch_gnucompress = "/usr/local/bin/gzip";
++$arch_gnucompress = "/usr/bin/gzip";
+ $arch_latex = "latex";
+ $arch_compilerc = $arch_echo;
+ $arch_rcflags = "No resource compiler required on this platform.";
+@@ -511,8 +511,8 @@ $arch_nvccflags = "-lineinfo --ptxas-options=-v " .
+ "-gencode arch=compute_70,code=sm_70 " .
+ "--ftz=true ";
+ # "-gencode arch=compute_75,code=sm_75 " .
+-$arch_gcc = "gcc";
+-$arch_gccpp = "g++";
++$arch_gcc = "cc";
++$arch_gccpp = "c++";
+ $arch_lex = "lex";
+ $arch_yacc = "yacc";
+ $arch_yflags = "-d";
+@@ -783,9 +783,10 @@ $tcl_include = "-I$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"; }
@@ -22,9 +42,11 @@
+$tcl_libs = "\${TCLLDFLAGS}";
+if ($config_tk) { $tcl_libs = "\${TKLDFLAGS} " . $tcl_libs; }
++
@tcl_cc = ();
@tcl_cu = ();
-@@ -1105,8 +1105,8 @@ if ($config_liboptix) {
+ @tcl_ccpp = ('ColorInfo.C',
+@@ -1353,8 +1354,8 @@ if ($config_liboptix) {
# This may be commented out if not required.
$libtachyon_defines = "-DVMDLIBTACHYON";
$libtachyon_dir = "$vmd_library_dir/tachyon";
@@ -35,7 +57,174 @@
$libtachyon_libs = "-ltachyon";
@libtachyon_cc = ();
@libtachyon_cu = ();
-@@ -3187,10 +3187,10 @@ DEFINES = $DEFINES
+@@ -1673,7 +1674,7 @@ if ($ENV{_CONDA_ROOT}) {
+ # $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
+ $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$vmd_library_dir/numpy/lib_$config_arch/include";
+ $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
+- $python_libs = "-lpython2.5 -lpthread";
++ $python_libs = "-lpython3.9 -lpthread";
+ }
+
+ $python_defines = "-DVMDPYTHON";
+@@ -2147,8 +2148,8 @@ if ($config_arch eq "ANDROIDARMV7A") {
+ $androidlibs = "-L/home/kvandivo/Proj/android-ndk-r8b/platforms/android-14/arch-arm/usr/lib -L/home/kvandivo/Proj/android-ndk-r8b/sources/cxx-stl/stlport/libs/armeabi-v7a/";
+ $androidsysroot = "--sysroot=/home/kvandivo/Proj/android-ndk-r8b/platforms/android-14/arch-arm";
+ $androidabi = "arm-linux-androideabi-";
+- $arch_cc = $androidbins . $androidabi . "gcc";
+- $arch_ccpp = $androidbins . $androidabi . "g++";
++ $arch_cc = $androidbins . $androidabi . "cc";
++ $arch_ccpp = $androidbins . $androidabi . "c++";
+ $arch_copts = "-Wall -Wno-unknown-pragmas -Wno-psabi -MMD -MP -fpic -ffunction-sections -funwind-tables -fstack-protector -D__ARM_ARCH_5__ -D__ARM_ARCH_5T__ -D__ARM_ARCH_5E__ -D__ARM_ARCH_5TE__ -march=armv7-a -msoft-float -mfpu=vfp -fno-exceptions -mthumb -Os -fomit-frame-pointer -fno-strict-aliasing -finline-limit=64 -Wa,--noexecstac";
+ $arch_opt_flag = "-Wall -Wno-unknown-pragmas -Wno-psabi -MMD -MP -fpic -ffunction-sections -funwind-tables -fstack-protector -D__ARM_ARCH_5__ -D__ARM_ARCH_5T__ -D__ARM_ARCH_5E__ -D__ARM_ARCH_5TE__ -march=armv7-a -msoft-float -mfpu=vfp -fno-exceptions -mthumb -Os -fomit-frame-pointer -fno-strict-aliasing -finline-limit=64 -Wa,--noexecstac";
+ $arch_copts = $androidincs;
+@@ -2220,7 +2221,7 @@ if ($config_arch eq "BLUEWATERS" ||
+ $arch_cc = "cc";
+ $arch_ccpp = "CC";
+ $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O6 -ffast-math";
+- $arch_opt_flag = "-m64 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math";
++ $arch_opt_flag = "-m64 -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math";
+ }
+
+ if ($config_mpi) {
+@@ -2321,15 +2322,15 @@ if ($config_arch eq "FREEBSD") {
+ $arch_lex = "flex";
+ $arch_yacc = "bison -b y -d "; # If standard yacc doesn't work
+
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
+ $arch_depend_flag = "-MM";
+ $arch_shld = "g++ -shared";
+ $arch_shlibname = "so";
+ $arch_shcppopts = "-fPIC";
+ $arch_shldopts = "-L/usr/local/lib";
+
+- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
++ $arch_opt_flag = "-m32 -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
+ $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3";
+
+ if ($config_static) {
+@@ -2377,8 +2378,8 @@ if ($config_arch eq "FREEBSDAMD64") {
+ $arch_lex = "flex";
+ $arch_yacc = "bison -b y -d "; # If standard yacc doesn't work
+
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
+ $arch_depend_flag = "-MM";
+ $arch_shld = "ld -shared";
+ $arch_shlibname = "so";
+@@ -2456,14 +2457,14 @@ if ($config_arch eq "LINUX") {
+ $arch_lopts .= "-i-static ";
+ } else {
+ # compling with GCC
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
+ $arch_depend_flag = "-MM";
+ $arch_shld = "g++ -shared";
+ $arch_shlibname = "so";
+ $arch_shcppopts = "-fPIC";
+ $arch_shldopts = "";
+- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
++ $arch_opt_flag = "-m32 -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
+ $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3";
+
+ if ($config_static) {
+@@ -2573,9 +2574,9 @@ if ($config_arch eq "LINUXAMD64") {
+ $arch_depend_flag = "-MM";
+ } else {
+ # for compiling with g++:
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
+- $arch_opt_flag = "-m64 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
++ $arch_opt_flag = "-m64 -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math";
+ $arch_depend_flag = "-MM";
+ $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O6 -ffast-math";
+
+@@ -2680,8 +2681,8 @@ if ($config_arch eq "LINUXPPC64") {
+ print "No LP64 ABI on this platform currently.\n";
+ }
+
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
+ $arch_depend_flag = "-MM";
+ $arch_opt_flag = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math";
+ $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math";
+@@ -3056,8 +3057,8 @@ if ($config_arch eq "SUMMIT") {
+ # $arch_cppopts = "-D_H_ACCESS=1";
+ $arch_depend_flag = "-MM";
+ } elsif ($config_gcc) {
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
+ $arch_opt_flag = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8";
+ $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8";
+ $arch_depend_flag = "-MM";
+@@ -3131,8 +3132,8 @@ if ($config_arch eq "OPENPOWER" || $config_arch eq "SU
+ # $arch_cppopts = "-D_H_ACCESS=1";
+ $arch_depend_flag = "-MM";
+ } else {
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "cc";
++ $arch_ccpp = "c++";
+ $arch_opt_flag = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8";
+ $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8";
+ $arch_depend_flag = "-MM";
+@@ -3185,8 +3186,8 @@ if ($config_arch eq "SOLARIS2" || $config_arch eq "SOL
+ if ($config_lp64) {
+ print "GCC doesn't support LP64 ABI on this platform currently.\n";
+ }
+- $arch_ccpp = "g++";
+- $arch_cc = "gcc";
++ $arch_ccpp = "c++";
++ $arch_cc = "cc";
+ $arch_opt_flag = "-O";
+ $arch_copts = "-O";
+ $arch_debug_flag = "-g";
+@@ -3258,8 +3259,8 @@ if ($config_arch eq "SOLARISX86" || $config_arch eq "S
+ if ($config_lp64) {
+ die "No LP64 gcc for this platform currently.\n";
+ }
+- $arch_ccpp = "g++";
+- $arch_cc = "gcc";
++ $arch_ccpp = "c++";
++ $arch_cc = "cc";
+ # XXX gcc/g++ 2.95 and newer need -fpermissive since the X11 headers
+ # on Solaris (and other systems) are broken and still assume that missing
+ # types will default to int.... When they fix this in future revs of Solaris,
+@@ -3349,8 +3350,8 @@ if ($config_arch eq "WIN32") {
+ $arch_cppopts = "/TP";
+ $arch_coptout = "/Fo";
+ } else {
+- $arch_ccpp = "g++";
+- $arch_cc = "gcc";
++ $arch_ccpp = "c++";
++ $arch_cc = "cc";
+ $arch_opt_flag = "-O";
+ $arch_debug_flag = "-g";
+ $arch_depend_flag = "-M";
+@@ -3366,8 +3367,8 @@ if ($config_arch eq "WIN32") {
+
+
+ if ($config_arch eq "WIN64") {
+- $arch_ccpp = "g++";
+- $arch_cc = "gcc";
++ $arch_ccpp = "c++";
++ $arch_cc = "cc";
+ $arch_opt_flag = "-O";
+ $arch_debug_flag = "-g";
+ $arch_depend_flag = "-M";
+@@ -3721,10 +3722,10 @@ DEFINES = $DEFINES
# compiler and compiler directives
CC = $arch_cc
@@ -44,7 +233,7 @@
CCPP = $arch_ccpp
-CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CPPFLAGS = \${CXXFLAGS} $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-
- NVCC = $arch_nvcc
- NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
++CPPFLAGS = \${CXXFLAGS} $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ CPPAVXFLAGS = $arch_opt_flag $arch_cppopts -mavx -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ CPPAVX2FLAGS = $arch_opt_flag $arch_cppopts -mfma -mavx -mavx2 -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ CPPAVX512FLAGS = $arch_opt_flag $arch_cppopts -mavx512f -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
diff --git a/science/vmd/files/patch-lib_stride_Makefile b/science/vmd/files/patch-lib_stride_Makefile
index b9beb1655e68..8a07fd85789e 100644
--- a/science/vmd/files/patch-lib_stride_Makefile
+++ b/science/vmd/files/patch-lib_stride_Makefile
@@ -5,7 +5,7 @@
#CC = cc -O2 -fullwarn -TENV:large_GOT
#CC = cc -g -Wall
-CC = gcc -O2 # at least for SunOS
-+#CC = gcc -O2 # at least for SunOS
++#CC = cc -O2 # at least for SunOS
#CC = cc -g
#CC = cc -O2 -fullwarn
diff --git a/science/vmd/files/patch-surf_Makefile b/science/vmd/files/patch-lib_surf_Makefile
similarity index 73%
rename from science/vmd/files/patch-surf_Makefile
rename to science/vmd/files/patch-lib_surf_Makefile
index f8136f812ce7..a548100fa31f 100644
--- a/science/vmd/files/patch-surf_Makefile
+++ b/science/vmd/files/patch-lib_surf_Makefile
@@ -1,6 +1,6 @@
---- lib/surf/Makefile.orig Fri Mar 25 17:52:40 2005
-+++ lib/surf/Makefile Fri Mar 25 17:50:20 2005
-@@ -6,7 +6,7 @@
+--- lib/surf/Makefile.orig 2022-11-15 15:32:58 UTC
++++ lib/surf/Makefile
+@@ -6,7 +6,7 @@ INCLUDE = -I.
LINCLUDE = -lm
OPT_CFLAGS = -O2 $(FLAGS) $(INCLUDE)
#CFLAGS = -g $(FLAGS) $(INCLUDE)
diff --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch
index ef1aade136ff..56b2f0a699c7 100644
--- a/science/vmd/files/patch-lib_tachyon_unix_Make-arch
+++ b/science/vmd/files/patch-lib_tachyon_unix_Make-arch
@@ -1,11 +1,265 @@
--- lib/tachyon/unix/Make-arch.orig 2013-04-21 19:09:28 UTC
+++ lib/tachyon/unix/Make-arch
-@@ -1103,7 +1103,7 @@ bsd:
+@@ -134,7 +134,7 @@ android-armv7a-thr:
+ linux-carma-thr:
+ $(MAKE) all \
+ "ARCH = linux-carma-thr" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -mfpu=vfpv3-d16 -ffast-math -fomit-frame-pointer -fno-strict-aliasing -O3 -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -145,7 +145,7 @@ linux-carma-thr:
+ linux-carma-thr-fast:
+ $(MAKE) all \
+ "ARCH = linux-carma-thr-fast" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -fexpensive-optimizations -funsafe-math-optimizations -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -mfpu=vfpv3 -ffast-math -fomit-frame-pointer -fno-strict-aliasing -O3 -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -156,7 +156,7 @@ linux-carma-thr-fast:
+ linux-carma-thr-neon:
+ $(MAKE) all \
+ "ARCH = linux-carma-thr-neon" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -fexpensive-optimizations -funsafe-math-optimizations -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -mfpu=neon -ffast-math -fomit-frame-pointer -fno-strict-aliasing -O3 -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -174,7 +174,7 @@ linux-carma-thr-neon:
+ linux-carma-softfp-thr:
+ $(MAKE) all \
+ "ARCH = linux-carma-softfp-thr" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -msoft-float -mfpu=vfpv3-d16 -ffast-math -fomit-frame-pointer -fno-strict-aliasing -finline-limit=64 -Wa,--noexecstack -O -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -611,7 +611,7 @@ solaris-thr:
+ solaris-pthreads-gcc:
+ $(MAKE) all \
+ "ARCH = solaris-pthreads-gcc" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -D_REENTRANT -DSunOS $(MISCFLAGS) $(THREADSFLAGS) -DUSEPOSIXTHREADS" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -791,7 +791,7 @@ solaris-apcc-ultra-thr:
+ solaris-gcc-thr:
+ $(MAKE) all \
+ "ARCH = solaris-gcc-thr" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -ansi -Wall -pedantic -O4 -mv8 -msupersparc -DSunOS $(MISCFLAGS) $(THREADSFLAGS) -D_REENTRANT" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -801,7 +801,7 @@ solaris-gcc-thr:
+ solaris-gcc-thr-x11:
+ $(MAKE) all \
+ "ARCH = solaris-gcc-thr-x11" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -ansi -Wall -pedantic -O4 -mv8 -msupersparc $(X11INC) -DSunOS $(MISCFLAGS) $(THREADSFLAGS) -D_REENTRANT -DUSEX11" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1086,7 +1086,7 @@ macosx-x86-thr-ogl:
+ beos:
+ $(MAKE) all \
+ "ARCH = beos" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -O3 -fomit-frame-pointer -ffast-math $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1102,8 +1102,8 @@ beos:
+ bsd:
$(MAKE) all \
"ARCH = bsd" \
- "CC = gcc" \
+- "CC = gcc" \
- "CFLAGS = -O3 -fomit-frame-pointer -ffast-math -DBsd $(MISCFLAGS)" \
++ "CC = cc" \
+ "CFLAGS += -O3 -fomit-frame-pointer -ffast-math -DBsd $(MISCFLAGS)" \
"AR = ar" \
"ARFLAGS = r" \
"STRIP = strip" \
+@@ -1113,7 +1113,7 @@ bsd:
+ bsd-sparc:
+ $(MAKE) all \
+ "ARCH = bsd-sparc" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -mv8 -msupersparc -O3 -fomit-frame-pointer -ffast-math -DBsd $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1128,7 +1128,7 @@ bsd-sparc:
+ win32:
+ $(MAKE) all \
+ "ARCH = win32" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -mpentium -Wall -O3 -fomit-frame-pointer -ffast-math -DWIN32 $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1139,7 +1139,7 @@ win32:
+ win32-mpi:
+ $(MAKE) all \
+ "ARCH = win32-mpi" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -mpentium -Wall -O3 -fomit-frame-pointer -ffast-math -DWIN32 $(MISCFLAGS) -I'/Program files/MPIPro/INCLUDE' $(MPIFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1155,7 +1155,7 @@ win32-mpi:
+ linux:
+ $(MAKE) all \
+ "ARCH = linux" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m32 -Wall -O3 -g -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1167,7 +1167,7 @@ linux:
+ linux-profile:
+ $(MAKE) all \
+ "ARCH = linux-profile" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m32 -Wall -O3 -g -pg -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1179,7 +1179,7 @@ linux-profile:
+ linux-debug:
+ $(MAKE) all \
+ "ARCH = linux-debug" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m32 -Wall -g -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1191,7 +1191,7 @@ linux-debug:
+ linux-64:
+ $(MAKE) all \
+ "ARCH = linux-64" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m64 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1203,7 +1203,7 @@ linux-64:
+ linux-64-debug:
+ $(MAKE) all \
+ "ARCH = linux-64-debug" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m64 -Wall -O -g -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1216,7 +1216,7 @@ linux-64-debug:
+ linux-64-thr:
+ $(MAKE) all \
+ "ARCH = linux-64-thr" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m64 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(THREADSFLAGS) -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1240,7 +1240,7 @@ linux-icc-64-thr:
+ linux-64-openmp:
+ $(MAKE) all \
+ "ARCH = linux-64-openmp" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m64 -Wall -O3 -fopenmp -fomit-frame-pointer -ffast-math -DLinux -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1277,7 +1277,7 @@ linux-mic-thr:
+ linux-p4:
+ $(MAKE) all \
+ "ARCH = linux-p4" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -mcpu=i686 -march=i686 -funroll-loops -fexpensive-optimizations -malign-double -fschedule-insns2 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1315,7 +1315,7 @@ linux-p4-icc-thr:
+ linux-athlon:
+ $(MAKE) all \
+ "ARCH = linux-athlon" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -mcpu=athlon -march=athlon -funroll-loops -fexpensive-optimizations -malign-double -fschedule-insns2 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1326,7 +1326,7 @@ linux-athlon:
+ linux-athlon-thr:
+ $(MAKE) all \
+ "ARCH = linux-athlon-thr" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -mcpu=athlon -march=athlon -funroll-loops -fexpensive-optimizations -malign-double -fschedule-insns2 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(THREADSFLAGS) -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1363,7 +1363,7 @@ linux-athlon-pgcc:
+ linux-thr:
+ $(MAKE) all \
+ "ARCH = linux-thr" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m32 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(THREADSFLAGS) -D_REENTRANT $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1422,7 +1422,7 @@ linux-icc-thr-ogl:
+ linux-beowulf-mpi-ogl:
+ $(MAKE) all \
+ "ARCH = linux-beowulf-mpi" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m32 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS) $(MPIFLAGS) -DUSEOPENGL $(LINUX_GLX_INCS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1434,7 +1434,7 @@ linux-beowulf-mpi-ogl:
+ linux-beowulf-mpi:
+ $(MAKE) all \
+ "ARCH = linux-beowulf-mpi" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -m32 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS) $(MPIFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1551,7 +1551,7 @@ linux-lam-thr:
+ linux-ipaq:
+ $(MAKE) all \
+ "ARCH = linux-ipaq" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1563,7 +1563,7 @@ linux-ipaq:
+ linux-ppc:
+ $(MAKE) all \
+ "ARCH = linux-ppc" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1575,7 +1575,7 @@ linux-ppc:
+ linux-ps2:
+ $(MAKE) all \
+ "ARCH = linux-ps2" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
+@@ -1587,7 +1587,7 @@ linux-ps2:
+ linux-alpha:
+ $(MAKE) all \
+ "ARCH = linux-alpha" \
+- "CC = gcc" \
++ "CC = cc" \
+ "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \
+ "AR = ar" \
+ "ARFLAGS = r" \
diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist
index 46a5ba2c0aab..023779be50ae 100644
--- a/science/vmd/pkg-plist
+++ b/science/vmd/pkg-plist
@@ -5,9 +5,10 @@ lib/vmd/Announcement
lib/vmd/LICENSE
lib/vmd/README
lib/vmd/doc/ug.pdf
-lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd5.1/catdcd
+lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd5.2/catdcd
lib/vmd/plugins/%%VMD_ARCH%%/bin/cionize1.0/cionize
lib/vmd/plugins/%%VMD_ARCH%%/molfile/abinitplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/amiraplugin.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
@@ -79,9 +80,9 @@ 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/autopsf1.6/autopsf.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/psfcheck.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.8/autopsf.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.8/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.8/psfcheck.so
lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/Topology
lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/bossconvert.tcl
lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/imprlist
@@ -131,9 +132,9 @@ 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/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/ug.pdf
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen2.0/libpsfgen.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen2.0/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen2.0/ug.pdf
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
@@ -187,9 +188,9 @@ 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/autoionize1.4/autoionize.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.4/autoionizegui.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.4/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.5/autoionize.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.5/autoionizegui.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.5/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk.tcl
lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_gui.tcl
lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_procs.tcl
@@ -219,6 +220,8 @@ lib/vmd/plugins/noarch/tcl/bendix1.1/GUI-tips.gif
lib/vmd/plugins/noarch/tcl/bendix1.1/Monsieur_Bendix_smaller_still.gif
lib/vmd/plugins/noarch/tcl/bendix1.1/bendix.tcl
lib/vmd/plugins/noarch/tcl/bendix1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/bfeestimator1.0/bfee.tcl
+lib/vmd/plugins/noarch/tcl/bfeestimator1.0/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
@@ -233,28 +236,44 @@ lib/vmd/plugins/noarch/tcl/biocore1.1/unlocked.gif
lib/vmd/plugins/noarch/tcl/blast1.11/blast.tcl
lib/vmd/plugins/noarch/tcl/blast1.11/blast_resultviewer.tcl
lib/vmd/plugins/noarch/tcl/blast1.11/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/cgtools1.2/cggui.tcl
-lib/vmd/plugins/noarch/tcl/cgtools1.2/cgnetworking.tcl
-lib/vmd/plugins/noarch/tcl/cgtools1.2/cgtools.tcl
-lib/vmd/plugins/noarch/tcl/cgtools1.2/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/cgtools1.2/protein.cgc
-lib/vmd/plugins/noarch/tcl/cgtools1.2/rbcg-2007.par
-lib/vmd/plugins/noarch/tcl/cgtools1.2/rbcg-2007.top
-lib/vmd/plugins/noarch/tcl/cgtools1.2/water.cgc
-lib/vmd/plugins/noarch/tcl/chirality1.2/chirality.tcl
-lib/vmd/plugins/noarch/tcl/chirality1.2/chirality_gui.tcl
-lib/vmd/plugins/noarch/tcl/chirality1.2/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/cispeptide1.3/cispeptide.tcl
-lib/vmd/plugins/noarch/tcl/cispeptide1.3/cispeptide_gui.tcl
-lib/vmd/plugins/noarch/tcl/cispeptide1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgenffcaller1.0/cgenffcaller.tcl
+lib/vmd/plugins/noarch/tcl/cgenffcaller1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.3/cggui.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.3/cgnetworking.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.3/cgtools.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.3/protein.cgc
+lib/vmd/plugins/noarch/tcl/cgtools1.3/rbcg-2007.par
+lib/vmd/plugins/noarch/tcl/cgtools1.3/rbcg-2007.top
+lib/vmd/plugins/noarch/tcl/cgtools1.3/water.cgc
+lib/vmd/plugins/noarch/tcl/chirality1.4/chirality.tcl
+lib/vmd/plugins/noarch/tcl/chirality1.4/chirality_gui.tcl
+lib/vmd/plugins/noarch/tcl/chirality1.4/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cispeptide1.4/cispeptide.tcl
+lib/vmd/plugins/noarch/tcl/cispeptide1.4/cispeptide_gui.tcl
+lib/vmd/plugins/noarch/tcl/cispeptide1.4/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl
lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/clonerep1.3/clonerep.tcl
-lib/vmd/plugins/noarch/tcl/clonerep1.3/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/colorscalebar1.4/colorscalebar.tcl
-lib/vmd/plugins/noarch/tcl/colorscalebar1.4/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.4/clonerep.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.4/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar3.0/colorscalebar.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar3.0/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/cv_dashboard1.5/cv_dashboard.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/cv_dashboard_display.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/cv_dashboard_editor.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/cv_dashboard_main.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/cv_dashboard_plots.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/cv_dashboard_settings.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/CVS/Entries
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/CVS/Repository
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/CVS/Root
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/bias.colvars
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/colvar.colvars
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/component.colvars
+lib/vmd/plugins/noarch/tcl/cv_dashboard1.5/templates/other.colvars
lib/vmd/plugins/noarch/tcl/dataimport1.0/dataimport.tcl
lib/vmd/plugins/noarch/tcl/dataimport1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/demomaster1.0/demomaster.tcl
@@ -269,28 +288,32 @@ 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/fftk1.1/fftk.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_BondAngleOpt.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_BuildPar.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_ChargeOpt.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_DihOpt.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenBonded.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenDihScan.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenZMatrix.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GeomOpt.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_SharedFcns.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_distort.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_guiInterface.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_guiProcs.tcl
-lib/vmd/plugins/noarch/tcl/fftk1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_BondAngleOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_BuildPar.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_ChargeOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_ChargeOpt_ESP.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_Configuration.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_DihOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_GenBonded.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_GenDihScan.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_GenZMatrix.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_GeomOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_QMGaussian.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_QMORCA.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_SharedFcns.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_distort.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_guiInterface.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/fftk_guiProcs.tcl
+lib/vmd/plugins/noarch/tcl/fftk2.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/gofrgui1.3/gofrgui.tcl
lib/vmd/plugins/noarch/tcl/gofrgui1.3/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/heatmapper1.1/heatmapper.tcl
-lib/vmd/plugins/noarch/tcl/heatmapper1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/idatm0.1/idatm.tcl
-lib/vmd/plugins/noarch/tcl/idatm0.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/hbonds1.3/hbonds.tcl
+lib/vmd/plugins/noarch/tcl/hbonds1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/heatmapper1.2/heatmapper.tcl
+lib/vmd/plugins/noarch/tcl/heatmapper1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/idatm0.2/idatm.tcl
+lib/vmd/plugins/noarch/tcl/idatm0.2/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/ilstools1.5/acetylene.xyz
lib/vmd/plugins/noarch/tcl/ilstools1.5/carbondioxide.xyz
lib/vmd/plugins/noarch/tcl/ilstools1.5/carbonmonoxide.xyz
@@ -306,6 +329,9 @@ lib/vmd/plugins/noarch/tcl/ilstools1.5/oxygen.xyz
lib/vmd/plugins/noarch/tcl/ilstools1.5/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/infobutton1.0/info.gif
+lib/vmd/plugins/noarch/tcl/infobutton1.0/infobutton.tcl
+lib/vmd/plugins/noarch/tcl/infobutton1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/inorganicbuilder.tcl
lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Entries
lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Repository
@@ -330,18 +356,28 @@ lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.top
lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/irspecgui1.3/irspecgui.tcl
lib/vmd/plugins/noarch/tcl/irspecgui1.3/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_check.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_correlation.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_gui.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_map.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_setup.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_sim.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_template.namd
-lib/vmd/plugins/noarch/tcl/mdff0.5/mdff_tmp.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/xmdff_phenix.tcl
-lib/vmd/plugins/noarch/tcl/mdff0.5/xmdff_template.namd
+lib/vmd/plugins/noarch/tcl/json1.0/json.tcl
+lib/vmd/plugins/noarch/tcl/json1.0/json_write.tcl
+lib/vmd/plugins/noarch/tcl/json1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/README_REMDFF.txt
+lib/vmd/plugins/noarch/tcl/mdff0.6/load-mdff-results.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_check.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_correlation.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_gui.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_map.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_setup.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_sim.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_template.namd
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdff_tmp.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/mdffgui_balloon.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/remdff_template.namd
+lib/vmd/plugins/noarch/tcl/mdff0.6/replica-mdff.namd
+lib/vmd/plugins/noarch/tcl/mdff0.6/resetmaps.sh
+lib/vmd/plugins/noarch/tcl/mdff0.6/show_replicas_mdff.vmd
+lib/vmd/plugins/noarch/tcl/mdff0.6/xmdff_phenix.tcl
+lib/vmd/plugins/noarch/tcl/mdff0.6/xmdff_template.namd
lib/vmd/plugins/noarch/tcl/membrane1.2/membrane.tcl
lib/vmd/plugins/noarch/tcl/membrane1.2/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/membrane1.2/popc36_box.pdb
@@ -353,140 +389,203 @@ lib/vmd/plugins/noarch/tcl/membrane1.2/pope36_box.psf
lib/vmd/plugins/noarch/tcl/membrane1.2/pope_box.pdb
lib/vmd/plugins/noarch/tcl/membrane1.2/pope_box.psf
lib/vmd/plugins/noarch/tcl/membrane1.2/top_all27_prot_lipid.inp
+lib/vmd/plugins/noarch/tcl/membranemixer1.0/membranemixer.tcl
+lib/vmd/plugins/noarch/tcl/membranemixer1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/mergestructs1.1/mergestructs.tcl
lib/vmd/plugins/noarch/tcl/mergestructs1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/ATOMTYPE_OPLS.DEF
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/CVS/Entries
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/CVS/Repository
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/CVS/Root
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/ALA.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/ARG.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/ASN.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/ASP.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/CVS/Entries
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/CVS/Repository
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/CVS/Root
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/CYS.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/GLN.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/GLU.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/GLY-end.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/GLY.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/HIS.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/HSE.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/ILE.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/LEU.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/LYS.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/MET.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/PHE.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/PRO.mfrag
-lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/amino_acids/SER.mfrag
*** 679 LINES SKIPPED ***