svn commit: r430880 - in head/science/vmd: . files
David Naylor
dbn at FreeBSD.org
Sun Jan 8 17:36:17 UTC 2017
Author: dbn
Date: Sun Jan 8 17:36:15 2017
New Revision: 430880
URL: https://svnweb.freebsd.org/changeset/ports/430880
Log:
science/vmd: update to 1.9.3
- update MASTER_SITES to use upstream stride (the old - repackages - sources
were no longer working).
- take maintainership: although I don't use the software I am happy to respond
to PR's and check for updates periodically,
- add license information for each source:
- vmd: custom license that requires the user to explicitly download (and
accept the license before downloading). Mark the license as
auto-accept here as the present of the DISTFILE will indicate that
the license has been accepted
- tachyon: standard 3-clause BSD license :-)
- stride: almost BSD license, except only for academic use (i.e.
non-commersial) and a requirement to report bugs to the author.
Add a plain text copy of the license file to the port.
- add missing dependencies: gl, x11
- fix detection of python.
- simplify configure patch.
- update pkg-plist for changes in plugin versions.
Modified:
head/science/vmd/Makefile
head/science/vmd/distinfo
head/science/vmd/files/patch-configure
head/science/vmd/files/patch-lib_tachyon_unix_Make-arch
head/science/vmd/pkg-plist
Modified: head/science/vmd/Makefile
==============================================================================
--- head/science/vmd/Makefile Sun Jan 8 16:50:57 2017 (r430879)
+++ head/science/vmd/Makefile Sun Jan 8 17:36:15 2017 (r430880)
@@ -2,19 +2,22 @@
# $FreeBSD$
PORTNAME= vmd
-DISTVERSION= 1.9.1
-PORTREVISION= 5
+DISTVERSION= 1.9.3
CATEGORIES= science graphics python tcl tk
-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
+MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \
+ http://www.photonlimited.com/~johns/tachyon/files/0.99b6/:tachyon \
+ http://webclu.bio.wzw.tum.de/stride/:stride \
+ ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/:stride
DISTFILES= ${VMD_DIST} \
${TACHYON_DIST}:tachyon \
${STRIDE_DIST}:stride
-MAINTAINER= ports at FreeBSD.org
+MAINTAINER= dbn at FreeBSD.org
COMMENT= Molecular visualization program
+LICENSE= VMD BSD3CLAUSE STRIDE
+LICENSE_COMB= multi
+
BUILD_DEPENDS= makedepend:devel/makedepend \
${PYNUMERIC}
LIB_DEPENDS= libtcl85.so:lang/tcl85 \
@@ -23,18 +26,37 @@ LIB_DEPENDS= libtcl85.so:lang/tcl85 \
libnetcdf.so:science/netcdf
RUN_DEPENDS= ${PYNUMERIC}
+LICENSE_FILE_VMD= ${WRKSRC}/LICENSE
+LICENSE_PERMS_VMD= auto-accept
+LICENSE_NAME_VMD= Visaul Molecular Dynamics Software License Agreement
+LICENSE_DISTFILES_VMD= ${VMD_DIST}
+
+LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/lib/tachyon/Copyright
+LICENSE_DISTFILES_BSD3CLAUSE= ${TACHYON_DIST}
+
+LICENSE_TEXT_STRIDE= ${FILESDIR}/stride.txt
+LICENSE_PERMS_STRIDE= dist-mirror pkg-mirror auto-accept
+LICENSE_NAME_STRIDE= Stride Copyright Notice
+LICENSE_DISTFILES_STRIDE=${STRIDE_DIST}
+
USES= gmake perl5 python
+
USE_PERL5= build
-USE_GL= glu
-USE_GCC= any
+USE_GL= gl glu
+USE_XORG= x11
ONLY_FOR_ARCHS= i386 amd64
-RESTRICTED= License has restrictions
+CONFIGURE_ENV= PYTHON_INCLUDE_DIR=${PYTHON_INCLUDEDIR} \
+ PYTHON_LIBRARY_DIR=${PYTHON_LIBDIR} \
+ NUMPY_INCLUDE_DIR=${PYTHON_SITELIBDIR}/numpy/core/include \
+ NUMPY_LIBRARY_DIR=${PYTHON_SITELIBDIR}
+INSTALL_WRKSRC= ${WRKSRC}/src
VMD_DIST= ${PORTNAME}-${DISTVERSION}.src.tar.gz
-TACHYON_DIST= tachyon-0.99b2.tar.gz
-STRIDE_DIST= Stride_src.tar.Z
+TACHYON_DIST= tachyon-0.99b6.tar.gz
+STRIDE_DIST= stride.tar.gz
+STRIDE_DOC= stride.doc
.include <bsd.port.pre.mk>
@@ -58,7 +80,7 @@ IGNORE= license restrictions require man
.endif
do-extract:
- ${MKDIR} ${WRKDIR}
+ ${MKDIR} ${WRKDIR} ${WRKSRC}/lib/stride
${TAR} -xzf ${DISTDIR}/${VMD_DIST} -C ${WRKDIR}
${TAR} -xzf ${WRKSRC}/lib/surf/surf.tar.Z -C ${WRKSRC}/lib/surf
${TAR} -xzf ${DISTDIR}/${TACHYON_DIST} -C ${WRKSRC}/lib
@@ -68,10 +90,10 @@ post-patch:
${REINPLACE_CMD} \
-e "s|-ltk8.5|-ltk85|" \
-e "s|-ltcl8.5|-ltcl85|" \
- -e "s%\$$python_dir/lib_\$$config_arch%${PREFIX}%" \
- -e "s|python2.5|${PYTHON_VERSION}|" \
+ -e "s|-lpython2.5|-l${PYTHON_VERSION}${PYTHON_ABIVER}|" \
-e "s|%%PREFIX%%|${PREFIX}|g" \
-e "s|/usr/local|${LOCALBASE}|g" \
+ -e "s|-fno-for-scope||g" \
${WRKSRC}/configure
${REINPLACE_CMD} "s/\"gcc\"/\"${CC}\"/;s/\"g++\"/\"${CXX}\"/" \
${WRKSRC}/configure
@@ -85,18 +107,18 @@ post-patch:
${WRKSRC}/lib/stride/Makefile \
${WRKSRC}/lib/surf/Makefile \
${WRKSRC}/lib/tachyon/unix/Make-arch \
- ${WRKDIR}/plugins/cionize/mcudahacks/Makefile.specialbuilds \
${WRKDIR}/plugins/cionize/Makefile.specialbuilds \
${WRKDIR}/plugins/cionize/Makefile.mine \
${WRKDIR}/plugins/cionize/Makefile.testing \
${WRKDIR}/plugins/Make-arch \
${WRKDIR}/plugins/molfile_plugin/f77/Makefile
${REINPLACE_CMD} -E "s/(CXX[[:space:]]*=[[:space:]]*)g\+\+/\1${CXX}/" \
- ${WRKDIR}/plugins/cionize/Makefile.specialbuilds \
${WRKDIR}/plugins/fmtool/Makefile.specialbuilds \
${WRKDIR}/plugins/hesstrans/src/foo/Makefile \
${WRKDIR}/plugins/hesstrans/src/foo/nm_gnu.mak \
${WRKDIR}/plugins/Make-arch
+ ${REINPLACE_CMD} -e "s/return *;/return 0;/g" \
+ ${WRKSRC}/lib/surf/*.c
do-build:
${SETENV} ${MAKE_ENV} ${MAKE_CMD} bsd -C ${WRKSRC}/lib/tachyon/unix \
@@ -118,13 +140,12 @@ do-build:
&& ${MV} ${WRKSRC}/lib/stride/stride \
${WRKSRC}/lib/stride/stride_${VMD_ARCH}
-do-install:
- ${SETENV} ${MAKE_ENV} DESTDIR=${STAGEDIR} \
- ${MAKE_CMD} -C ${WRKSRC}/src install
+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/autopsf1.3/psfcheck.so tcl/hesstrans1.0/hesstrans.so \
- tcl/mutator1.4/libalchemify.so tcl/pmepot1.0/libpmepot.so \
+.for f in tcl/autopsf1.6/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/signalproc1.1/specden.so tcl/signalproc1.1/fftcmds.so \
tcl/signalproc1.1/sgsmooth.so tcl/volutil1.3/volutil \
@@ -133,7 +154,8 @@ do-install:
tcl/libbiokit1.1/structqr tcl/libbiokit1.1/qpair \
tcl/libbiokit1.1/rmsd tcl/libbiokit1.1/percid \
tcl/phylotree1.2/upgmaclu tcl/stamp1.2/stamp \
- bin/catdcd4.0/catdcd bin/cionize1.0/cionize
+ tcl/bossconvert1.0/Topology \
+ bin/catdcd5.1/catdcd bin/cionize1.0/cionize
${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/${f}
.endfor
Modified: head/science/vmd/distinfo
==============================================================================
--- head/science/vmd/distinfo Sun Jan 8 16:50:57 2017 (r430879)
+++ head/science/vmd/distinfo Sun Jan 8 17:36:15 2017 (r430880)
@@ -1,6 +1,7 @@
-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
+TIMESTAMP = 1482469862
+SHA256 (vmd-1.9.3.src.tar.gz) = 5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128
+SIZE (vmd-1.9.3.src.tar.gz) = 43981314
+SHA256 (tachyon-0.99b6.tar.gz) = f4dcaf9c76a4f49310f56254390f9611c22e353947a1745a8c623e8bc8119b97
+SIZE (tachyon-0.99b6.tar.gz) = 2981568
+SHA256 (stride.tar.gz) = 51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a
+SIZE (stride.tar.gz) = 318997
Modified: head/science/vmd/files/patch-configure
==============================================================================
--- head/science/vmd/files/patch-configure Sun Jan 8 16:50:57 2017 (r430879)
+++ head/science/vmd/files/patch-configure Sun Jan 8 17:36:15 2017 (r430880)
@@ -1,19 +1,19 @@
---- configure.orig 2012-02-02 16:53:54.000000000 +0900
-+++ configure 2014-08-28 16:42:38.000000000 +0900
+--- configure.orig 2016-12-01 07:11:33 UTC
++++ configure
@@ -13,10 +13,10 @@
$install_name = "vmd";
# Directory where VMD startup script is installed, should be in users' paths.
-$install_bin_dir="/usr/local/bin";
-+$install_bin_dir="%%PREFIX%%/bin";
++$install_bin_dir="\${DESTDIR}%%PREFIX%%/bin";
# Directory where VMD files and executables are installed
-$install_library_dir="/usr/local/lib/$install_name";
-+$install_library_dir="%%PREFIX%%/lib/$install_name";
++$install_library_dir="\${DESTDIR}%%PREFIX%%/lib/$install_name";
# optionally override hard-coded defaults above with environment variables
-@@ -788,8 +788,8 @@
+@@ -1105,8 +1105,8 @@ if ($config_liboptix) {
# This may be commented out if not required.
$libtachyon_defines = "-DVMDLIBTACHYON";
$libtachyon_dir = "$vmd_library_dir/tachyon";
@@ -24,12 +24,12 @@
$libtachyon_libs = "-ltachyon";
@libtachyon_cc = ();
@libtachyon_cu = ();
-@@ -2942,10 +2942,10 @@
+@@ -3187,10 +3187,10 @@ DEFINES = $DEFINES
# compiler and compiler directives
CC = $arch_cc
-CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CFLAGS += $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
++CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
CCPP = $arch_ccpp
-CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
@@ -37,72 +37,3 @@
NVCC = $arch_nvcc
NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-@@ -2997,38 +2997,38 @@
- \$(COMPILERC) \$(RCFLAGS)
-
- install:
-- if [ ! -d "$install_library_dir" ]; then \\
-- \$(MAKEDIR) "$install_library_dir" ; \\
-+ if [ ! -d "\${DESTDIR}$install_library_dir" ]; then \\
-+ \$(MAKEDIR) "\${DESTDIR}$install_library_dir" ; \\
- fi ; \\
-- if [ ! -d "$install_bin_dir" ]; then \\
-- \$(MAKEDIR) "$install_bin_dir" ; \\
-+ if [ ! -d "\${DESTDIR}$install_bin_dir" ]; then \\
-+ \$(MAKEDIR) "\${DESTDIR}$install_bin_dir" ; \\
- fi ; \\
-- if [ ! -d "$install_library_dir"/doc ]; then \\
-- \$(MAKEDIR) "$install_library_dir"/doc; \\
-+ if [ ! -d "\${DESTDIR}$install_library_dir"/doc ]; then \\
-+ \$(MAKEDIR) "\${DESTDIR}$install_library_dir"/doc; \\
- fi
-- -\$(COPY) ../Announcement "$install_library_dir"
-- -\$(COPY) ../README "$install_library_dir"
-- -\$(COPY) ../LICENSE "$install_library_dir"
-- -\$(COPY) $vmd_doc_dir/ug.pdf "$install_library_dir"/doc
-- if [ -f $install_library_dir/$config_progname ]; then \\
-- \$(MOVE) "$install_library_dir/$config_progname" "$install_library_dir/OLD_$config_progname" ; \$(DELETE) "$install_library_dir/OLD_$config_progname" ; fi
-- -\$(COPY) ../$config_arch/$config_progname "$install_library_dir"
-+ -\$(COPY) ../Announcement "\${DESTDIR}$install_library_dir"
-+ -\$(COPY) ../README "\${DESTDIR}$install_library_dir"
-+ -\$(COPY) ../LICENSE "\${DESTDIR}$install_library_dir"
-+ -\$(COPY) $vmd_doc_dir/ug.pdf "\${DESTDIR}$install_library_dir"/doc
-+ if [ -f \${DESTDIR}$install_library_dir/$config_progname ]; then \\
-+ \$(MOVE) "\${DESTDIR}$install_library_dir/$config_progname" "\${DESTDIR}$install_library_dir/OLD_$config_progname" ; \$(DELETE) "\${DESTDIR}$install_library_dir/OLD_$config_progname" ; fi
-+ -\$(COPY) ../$config_arch/$config_progname "\${DESTDIR}$install_library_dir"
- if [ -d "../lib/redistrib/lib_$config_arch" ]; then \\
- \$(CD) ../lib/redistrib/lib_$config_arch; \$(TAR) -cf - ./* | \\
-- (cd "$install_library_dir" ; \$(TAR) -xf -) \\
-+ (cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -) \\
- fi ;
-- -\$(COPY) @vmd_other_exe "$install_library_dir"
-+ -\$(COPY) @vmd_other_exe "\${DESTDIR}$install_library_dir"
- -\$(CD) ..; \$(TAR) -cf - scripts | \\
-- (cd "$install_library_dir" ; \$(TAR) -xf -)
-+ (cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
- -\$(CD) $vmd_library_dir; \$(TAR) -cf - scripts | \\
-- (cd "$install_library_dir" ; \$(TAR) -xf -)
-+ (cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
- -\$(CD) ..; \$(TAR) -cf - python | \\
-- (cd "$install_library_dir"/scripts ; \$(TAR) -xf -)
-+ (cd "\${DESTDIR}$install_library_dir"/scripts ; \$(TAR) -xf -)
- -\$(CD) ..; \$(TAR) -cf - plugins | \\
-- (cd "$install_library_dir" ; \$(TAR) -xf -)
-+ (cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
- -\$(CD) ..; \$(TAR) -cf - shaders | \\
-- (cd "$install_library_dir" ; \$(TAR) -xf -)
-- -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
-+ (cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
-+ -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "\${DESTDIR}$install_library_dir"
- \$(CD) $vmd_bin_dir ; \\
- if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
- if [ ! -x "/bin/csh" ]; then \\
-@@ -3044,7 +3044,7 @@
- cat $vmd_bin_csh >> run_vmd_tmp ; \\
- fi ; \\
- chmod +x run_vmd_tmp ; \\
-- \$(COPY) run_vmd_tmp "$install_bin_dir"/$install_name ; \\
-+ \$(COPY) run_vmd_tmp "\${DESTDIR}$install_bin_dir"/$install_name ; \\
- \$(DELETE) run_vmd_tmp
- \$(ECHO) Make sure "$install_bin_dir"/$install_name is in your path.
- \$(ECHO) "VMD installation complete. Enjoy!"
Modified: head/science/vmd/files/patch-lib_tachyon_unix_Make-arch
==============================================================================
--- head/science/vmd/files/patch-lib_tachyon_unix_Make-arch Sun Jan 8 16:50:57 2017 (r430879)
+++ head/science/vmd/files/patch-lib_tachyon_unix_Make-arch Sun Jan 8 17:36:15 2017 (r430880)
@@ -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
-@@ -989,7 +989,7 @@
+--- lib/tachyon/unix/Make-arch.orig 2013-04-21 19:09:28 UTC
++++ lib/tachyon/unix/Make-arch
+@@ -1103,7 +1103,7 @@ bsd:
$(MAKE) all \
"ARCH = bsd" \
"CC = gcc" \
Modified: head/science/vmd/pkg-plist
==============================================================================
--- head/science/vmd/pkg-plist Sun Jan 8 16:50:57 2017 (r430879)
+++ head/science/vmd/pkg-plist Sun Jan 8 17:36:15 2017 (r430880)
@@ -5,7 +5,7 @@ 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/catdcd5.1/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
@@ -42,6 +42,7 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/map
lib/vmd/plugins/%%VMD_ARCH%%/molfile/mdfplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/mol2plugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/moldenplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/molemeshplugin.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
@@ -49,8 +50,10 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/par
lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/pbeqplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbxplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/phiplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/pltplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/plyplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/pqrplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/psfplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/raster3dplugin.so
@@ -60,6 +63,7 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/spi
lib/vmd/plugins/%%VMD_ARCH%%/molfile/stlplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/tinkerplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/uhbdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vasp5xdatcarplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspchgcarplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspoutcarplugin.so
lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspparchgplugin.so
@@ -67,77 +71,66 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/vas
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/vtkplugin.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/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/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/bossconvert1.0/Topology
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/bossconvert.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/imprlist
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/oplsaa.par
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/oplsaa.sb
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/pkgIndex.tcl
lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/cionize.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/pkgIndex.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/clustalw1.1/clustalw_help
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/pkgIndex.tcl
lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.so
lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/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
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+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit_entropy.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit_profcombine.tcl
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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/seqqr
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/structqr
lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/tcl_libbiokit.so
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-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
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+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mafft1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/libalchemify.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/mutator.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/mutator_gui.tcl
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lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/pkgIndex.tcl
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-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/phylotree1.2/phylotree_data.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_export.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_je.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_matrixviewer.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_newick.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_nexus.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_nodeprops.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_widget.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/pkgIndex.tcl
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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
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-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/psfgen1.6/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
@@ -145,16 +138,39 @@ lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview
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/CVS/Entries
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Repository
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Root
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/rnaview1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/data_io_lib.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftcmds.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftpack.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/sgsmooth.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/signalproc.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/specden.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/dssp.directories
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pdb.directories
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pkgIndex.tcl
+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/stamp.tcl
lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/volutil
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
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/alascan.tcl
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/alascan_analysis.tcl
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/fep.tcl
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/apbsrun1.3/apbsrun.tcl
lib/vmd/plugins/noarch/tcl/apbsrun1.3/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/apbsrun1.3/radii.dat
@@ -168,9 +184,38 @@ lib/vmd/plugins/noarch/tcl/autoimd1.7/au
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/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/bdtk1.0/bdtk.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_gui.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_procs.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/CVS/Entries
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/CVS/Repository
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/CVS/Root
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/interactions.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/ions.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/membrane.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/CVS/Entries
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/CVS/Repository
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/CVS/Root
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/extend114_chl-chl.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/extend114_pot-chl.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/extend114_pot-pot.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/graphene_cla.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/graphene_pot.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/CVS/Entries
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/CVS/Repository
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/CVS/Root
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape1.gif
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape1.shp
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape2.gif
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape2.shp
+lib/vmd/plugins/noarch/tcl/bdtk1.0/pkgIndex.tcl
+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/bignum1.0/bignum.tcl
lib/vmd/plugins/noarch/tcl/bignum1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/biocore1.1/biocore.tcl
@@ -182,29 +227,29 @@ lib/vmd/plugins/noarch/tcl/biocore1.1/bi
lib/vmd/plugins/noarch/tcl/biocore1.1/locked.gif
lib/vmd/plugins/noarch/tcl/biocore1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/biocore1.1/unlocked.gif
-lib/vmd/plugins/noarch/tcl/blast1.1/blast.tcl
-lib/vmd/plugins/noarch/tcl/blast1.1/blast_resultviewer.tcl
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-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
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-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/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/cliptool1.0/cliptool.tcl
lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl
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-lib/vmd/plugins/noarch/tcl/colorscalebar1.3/colorscalebar.tcl
-lib/vmd/plugins/noarch/tcl/colorscalebar1.3/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/contactmap1.1/contactmap.tcl
lib/vmd/plugins/noarch/tcl/contactmap1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/dataimport1.0/dataimport.tcl
@@ -221,40 +266,41 @@ lib/vmd/plugins/noarch/tcl/exectool1.2/j
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
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-lib/vmd/plugins/noarch/tcl/fftk1.0/fftk_guiInterface.tcl
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-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
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-lib/vmd/plugins/noarch/tcl/gofrgui1.2/gofrgui.tcl
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+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
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lib/vmd/plugins/noarch/tcl/hbonds1.2/hbonds.tcl
lib/vmd/plugins/noarch/tcl/hbonds1.2/pkgIndex.tcl
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lib/vmd/plugins/noarch/tcl/idatm0.1/idatm.tcl
lib/vmd/plugins/noarch/tcl/idatm0.1/pkgIndex.tcl
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+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/convert_xbgf_to_frags.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/amino.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/butyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/carboxyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/carboxylate.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/chloride.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/cycloheptane.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/cyclooctane.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/epoxide.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/formyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/frag.mdb
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/furan_1C.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/furan_2C.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/hydroxyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/indole.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/methyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/methyl.pdb
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/nitrile.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/nitro.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/phenyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/phospho.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/tbutyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/thiol.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/thiophene_1C.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/thiophene_2C.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/vinyl.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/A.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/C.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/G.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/T.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/U.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/dna_backbone.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/dna_dihedrals.gif
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/rna_backbone.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/rna_backbone_added.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_builder.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_edit.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_geometry.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_gui.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_internals.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_state.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/moltoptools0.1/moltoptools.tcl
lib/vmd/plugins/noarch/tcl/moltoptools0.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/multimolanim1.0/multimolanim.tcl
lib/vmd/plugins/noarch/tcl/multimolanim1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/multiplot1.6/multiplot.tcl
-lib/vmd/plugins/noarch/tcl/multiplot1.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/multiplot1.7/multiplot.tcl
+lib/vmd/plugins/noarch/tcl/multiplot1.7/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/multiseq2.1/colormap_vmd.tcl
lib/vmd/plugins/noarch/tcl/multiseq2.1/export_options.tcl
lib/vmd/plugins/noarch/tcl/multiseq2.1/find.tcl
@@ -440,36 +489,36 @@ lib/vmd/plugins/noarch/tcl/multiseqdialo
lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/scrolledframe.tcl
lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/wait_dialog.tcl
-lib/vmd/plugins/noarch/tcl/multitext1.0/multitext.tcl
-lib/vmd/plugins/noarch/tcl/multitext1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/multitext1.1/multitext.tcl
+lib/vmd/plugins/noarch/tcl/multitext1.1/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/namdenergy1.4/namdenergy.tcl
lib/vmd/plugins/noarch/tcl/namdenergy1.4/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/namdgui1.3/namdgui.tcl
lib/vmd/plugins/noarch/tcl/namdgui1.3/namdgui_tclforces.tcl
lib/vmd/plugins/noarch/tcl/namdgui1.3/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/namdplot1.1/namdplot.tcl
-lib/vmd/plugins/noarch/tcl/namdplot1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/namdplot1.2/namdplot.tcl
+lib/vmd/plugins/noarch/tcl/namdplot1.2/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/namdserver1.1/namdserver.tcl
lib/vmd/plugins/noarch/tcl/namdserver1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/nanotube.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/graphene.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/gui.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/graphene.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/gui.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/nanotube.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/navfly1.0/navfly.tcl
lib/vmd/plugins/noarch/tcl/navfly1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/navigate1.0/navigate.tcl
lib/vmd/plugins/noarch/tcl/navigate1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/suboptimalPaths.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/adjacencyMatrix.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/networkSetup.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/communityNetwork.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/networkViewGui.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/networkView.tcl
-lib/vmd/plugins/noarch/tcl/nmwiz1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/nmwiz1.0/nmwiz.tcl
-lib/vmd/plugins/noarch/tcl/optimization1.1/optimization.tcl
-lib/vmd/plugins/noarch/tcl/optimization1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/adjacencyMatrix.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/communityNetwork.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/networkSetup.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/networkView.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/networkViewGui.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/suboptimalPaths.tcl
+lib/vmd/plugins/noarch/tcl/nmwiz1.2/nmwiz.tcl
+lib/vmd/plugins/noarch/tcl/nmwiz1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/optimization1.3/optimization.tcl
+lib/vmd/plugins/noarch/tcl/optimization1.3/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/palettetool1.0/palettetool.tcl
lib/vmd/plugins/noarch/tcl/palettetool1.0/pkgIndex.tcl
lib/vmd/plugins/noarch/tcl/paratool1.5/paratool.tcl
@@ -489,20 +538,23 @@ lib/vmd/plugins/noarch/tcl/paratool1.5/p
lib/vmd/plugins/noarch/tcl/paratool1.5/paratool_tmcomplex.tcl
lib/vmd/plugins/noarch/tcl/paratool1.5/paratool_topology.tcl
lib/vmd/plugins/noarch/tcl/paratool1.5/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/parsefep1.5/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/parsefep1.5/parseFEP.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcbox.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcgui.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcjoin.tcl
*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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