diff options
| author | David Naylor <dbn@FreeBSD.org> | 2017-01-08 17:36:15 +0000 |
|---|---|---|
| committer | David Naylor <dbn@FreeBSD.org> | 2017-01-08 17:36:15 +0000 |
| commit | 153bb9688c6127c352a4acfd686e34b7f9ea99bd (patch) | |
| tree | 05702f8363eb28d0c8cf44b8cd2f210e2312d68d /science/vmd | |
| parent | eb2cee80bfc3d841e787091f14f624902bc6de8d (diff) | |
| download | ports-153bb9688c6127c352a4acfd686e34b7f9ea99bd.tar.gz ports-153bb9688c6127c352a4acfd686e34b7f9ea99bd.zip | |
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.
Notes
Notes:
svn path=/head/; revision=430880
Diffstat (limited to 'science/vmd')
| -rw-r--r-- | science/vmd/Makefile | 66 | ||||
| -rw-r--r-- | science/vmd/distinfo | 13 | ||||
| -rw-r--r-- | science/vmd/files/patch-configure | 83 | ||||
| -rw-r--r-- | science/vmd/files/patch-lib_tachyon_unix_Make-arch | 6 | ||||
| -rw-r--r-- | science/vmd/pkg-plist | 780 |
5 files changed, 520 insertions, 428 deletions
diff --git a/science/vmd/Makefile b/science/vmd/Makefile index 2ae9940b7a6e..6e5af3beaf59 100644 --- a/science/vmd/Makefile +++ b/science/vmd/Makefile @@ -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@FreeBSD.org +MAINTAINER= dbn@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 manual fetching of the distribution\ .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 diff --git a/science/vmd/distinfo b/science/vmd/distinfo index d86f624a7010..5d42d032ddd2 100644 --- a/science/vmd/distinfo +++ b/science/vmd/distinfo @@ -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 diff --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure index 0ce4ed2e20d9..6db1b98b3627 100644 --- a/science/vmd/files/patch-configure +++ b/science/vmd/files/patch-configure @@ -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!" diff --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch index aa8049780694..ef1aade136ff 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 -@@ -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" \ diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist index b725d1b0cc52..418f47aab794 100644 --- a/science/vmd/pkg-plist +++ b/science/vmd/pkg-plist @@ -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/mapplugin.so 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/parm7plugin.so 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/spiderplugin.so 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/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/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 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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 -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/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/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/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/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/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/biocoreutil.tcl 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 -lib/vmd/plugins/noarch/tcl/blast1.1/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.0/cggui.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.0/cgnetworking.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.0/cgtools.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.0/pkgIndex.tcl -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/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 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