| Tags | Date | Developer | Last 200 Commit Logs |
|---|
| | 2013-05-23 | johns | Applied Matt Harvey's patch to detect corrupt Gromacs XTC files and avoid
subsequently triggering SIGFPE on bad input files.
* molfile_plugin/src/Gromacs.h 1.32 (changed +12 -1)
Applied Toni Giorgino's patch to improve the PBCTools "writexst" with
more options, with associated documentation updates.
* pbctools/pbctools.tcl 1.17 (changed +2 -2)
* pbctools/pbcset.tcl 1.18 (changed +50 -9)
* pbctools/doc/pbctools.tex 1.6 (changed +71 -2)
|
| | 2013-05-22 | johns | New nmwiz plugin from Ahmet Bakan, which fixes a bug and improves
usability. Also eliminates extraneous whitespace
* nmwiz/nmwiz.tcl 1.15 (changed +490 -477)
Updated pbctools with version 2.7 from Olaf Lenz.
The new version adds a "writexst" routine contributed by Toni Giorgino,
and fully incorporates previous changes from the VMD CVS tree.
* pbctools/pbcwrap.tcl 1.17 (changed +1 -1)
* pbctools/pbcunwrap.tcl 1.15 (changed +1 -1)
* pbctools/pbctools.tcl 1.16 (changed +5 -1)
* pbctools/pbcset.tcl 1.17 (changed +37 -2)
* pbctools/pbcjoin.tcl 1.16 (changed +1 -1)
* pbctools/doc/index.html 1.15 (changed +428 -283)
* pbctools/NEWS 1.5 (changed +9 -3)
* pbctools/AUTHORS 1.3 (changed +1 -0)
|
| | 2013-05-17 | mayne | Added a case to writeExceptionZMats that accounts for N=O, e.g., oxime tautomers
* fftk/fftk_GenZMatrix.tcl 1.13 (changed +7 -7)
|
| | 2013-05-10 | mayne | Changed leading indent for custom code, and added colors data to pushtoVMD routines
* vmdprefs/vmdprefs.tcl 1.7 (changed +6 -3)
|
| | 2013-05-09 | johns | Updated parseFEP plugin with the latest code from Chris Chipot.
* parsefep/pkgIndex.tcl 1.7 (changed +1 -1)
* parsefep/parseFEP.tcl 1.12 (changed +1029 -1183)
* parsefep/Makefile 1.7 (changed +1 -1)
Updated version for the psfgen plugin I/O mod
* psfgen/Makefile.pluginio 1.2 (changed +1 -1)
|
| | 2013-05-03 | barryi | Added new method for density map cross correlation: specify set of selections. GUI allows choice of methods for specifying selection: set of selections, or contiguous secondary structure. Also: fixed reference frame bug in distance calc.
* timeline/timeline.tcl 1.93 (changed +248 -143)
In cross-correlation density map, turned off the weighted scaling. This feature might return soon as a user-specified option, so the minor work to collect data for this and do the calculation still happens, but the result is not used.
* timeline/timeline.tcl 1.94 (changed +5 -1)
|
| | 2013-05-02 | akohlmey | Correct typo in documentation. set version number to current version
* topotools/doc/index.html 1.17 (changed +3 -3)
|
| | 2013-04-30 | akohlmey | Add support for writing lammps data files with triclinic cells
* topotools/topolammps.tcl 1.38 (changed +25 -3)
|
| | 2013-04-25 | akohlmey | Add support for new Coeff section in LAMMPS data files
* topotools/topolammps.tcl 1.37 (changed +4 -1)
Consistently handle the case of passing an atom selection to topotools,
even if the atom selection is not up-to-date and thus cannot be recreated.
* topotools/topotools.tcl 1.25 (changed +20 -22)
* topotools/topocgcmm.tcl 1.7 (changed +2 -2)
|
| | 2013-04-19 | johns | Added a call to "mol dataflag" so that VMD considers guessed bonds to
be validated, so they will be written out if the user writes the
generated structure to a PSF file.
* topotools/topobonds.tcl 1.13 (changed +8 -1)
|
| | 2013-04-16 | johns | Fix typo in version
* colorscalebar/colorscalebar.tcl 1.25 (changed +3 -3)
|
| | 2013-04-15 | johns | Added CVS revision tag to head of source files
* nanotube/nanotube.tcl 1.16 (changed +3 -0)
* nanotube/gui.tcl 1.7 (changed +3 -0)
* nanotube/graphene.tcl 1.9 (changed +3 -0)
* aligntool/cealign.tcl 1.14 (changed +1 -4)
Added CVS tag to head of source files
* parsefep/parseFEP.tcl 1.11 (changed +1 -0)
* bendix/bendix.tcl 1.4 (changed +3 -1)
Added CVS tags to head of files
* phylotree/phylotree_widget.tcl 1.5 (changed +3 -0)
* phylotree/phylotree_nodeprops.tcl 1.4 (changed +3 -0)
* phylotree/phylotree_nexus.tcl 1.3 (changed +3 -0)
* phylotree/phylotree_newick.tcl 1.4 (changed +3 -0)
* phylotree/phylotree_matrixviewer.tcl 1.5 (changed +3 -0)
* phylotree/phylotree_je.tcl 1.3 (changed +3 -0)
* phylotree/phylotree_export.tcl 1.4 (changed +3 -0)
* phylotree/phylotree_data.tcl 1.5 (changed +3 -0)
* phylotree/phylotree_analysis.tcl 1.2 (changed +3 -0)
* phylotree/phylotree.tcl 1.5 (changed +3 -0)
* phylotree/cluster.tcl 1.2 (changed +3 -0)
Added CVS tags to head of source files
* viewchangerender/vcr_gui.tcl 1.13 (changed +2 -0)
* viewchangerender/vcr.tcl 1.14 (changed +2 -0)
* utilities/utilities.tcl 1.10 (changed +3 -1)
* trunctraj/trunctraj.tcl 1.2 (changed +3 -1)
* symmetrytool/symmetry.tcl 1.15 (changed +3 -0)
* ssrestraints/ssrestraints_stride.tcl 1.3 (changed +3 -0)
* ssrestraints/ssrestraints.tcl 1.15 (changed +2 -0)
* simpleedit/simpleedit.tcl 1.4 (changed +3 -0)
* signalproc/signalproc.tcl 1.2 (changed +3 -0)
* signalproc/fftpack.tcl 1.2 (changed +2 -0)
* signalproc/data_io_lib.tcl 1.3 (changed +3 -0)
* seqedit/seqedit_widget_statusbar.tcl 1.8 (changed +3 -0)
* seqedit/seqedit_widget_select.tcl 1.8 (changed +2 -0)
* seqedit/seqedit_widget_edit.tcl 1.4 (changed +3 -0)
* seqedit/seqedit_widget.tcl 1.17 (changed +2 -0)
* seqedit/seqedit.tcl 1.6 (changed +3 -0)
* seqedit/metric_similarity.tcl 1.3 (changed +3 -0)
* seqedit/metric_signatures.tcl 1.4 (changed +2 -0)
* seqedit/metric_percentid.tcl 1.5 (changed +2 -0)
* seqedit/metric_mutualinfo.tcl 1.4 (changed +2 -0)
* seqedit/metric_insertions.tcl 1.4 (changed +2 -0)
* seqedit/metric_entropy.tcl 1.3 (changed +3 -0)
* seqedit/metric_element.tcl 1.4 (changed +2 -0)
* seqedit/metric_conservation.tcl 1.4 (changed +2 -0)
* seqedit/consensus_builder.tcl 1.3 (changed +2 -0)
* seqedit/clustalw_preferences.tcl 1.5 (changed +3 -0)
* seqdata/seqdata_vmd.tcl 1.10 (changed +3 -0)
* seqdata/seqdata_temperature.tcl 1.4 (changed +2 -0)
* seqdata/seqdata_taxonomy.tcl 1.4 (changed +3 -0)
* seqdata/seqdata_swissprot.tcl 1.4 (changed +3 -0)
* seqdata/seqdata_scop.tcl 1.5 (changed +3 -0)
* seqdata/seqdata_pir.tcl 1.3 (changed +3 -0)
* seqdata/seqdata_pdb.tcl 1.4 (changed +3 -0)
* seqdata/seqdata_genbank.tcl 1.4 (changed +3 -0)
* seqdata/seqdata_fasta.tcl 1.8 (changed +3 -0)
* seqdata/seqdata_astral.tcl 1.3 (changed +3 -1)
* seqdata/seqdata_aln.tcl 1.4 (changed +3 -1)
* seqdata/seqdata.tcl 1.13 (changed +3 -0)
* saltbr/saltbr.tcl 1.7 (changed +2 -0)
* ruler/ruler.tcl 1.6 (changed +2 -0)
* rnaview/rnaview.tcl 1.5 (changed +2 -0)
* rmsdvt/rmsdvt.tcl 1.4 (changed +2 -0)
* rmsdvt/rmsdvt-gui.tcl 1.5 (changed +2 -0)
* rmsdvt/modal.tcl 1.2 (changed +5 -1)
* rmsdtt/rmsdtt.tcl 1.8 (changed +3 -1)
* remote/remote.tcl 1.15 (changed +2 -0)
* readcharmmpar/readcharmmpar.tcl 1.18 (changed +2 -0)
* psipred/psipred.tcl 1.4 (changed +3 -0)
* propka/propka.tcl 1.5 (changed +1 -0)
* plumed/templates_list_v2_autogen.tcl 1.2 (changed +3 -0)
* plumed/templates_list_v1.tcl 1.2 (changed +4 -0)
* plotter/plotter.tcl 1.2 (changed +3 -1)
* pbctools/pbcgui.tcl 1.4 (changed +2 -0)
* paratool/paratool_topology.tcl 1.29 (changed +4 -1)
* paratool/paratool_refinement.tcl 1.13 (changed +2 -0)
* paratool/paratool_potscan.tcl 1.22 (changed +4 -0)
* paratool/paratool_parameters.tcl 1.40 (changed +2 -0)
* paratool/paratool_hessian.tcl 1.11 (changed +4 -0)
* paratool/paratool_energies.tcl 1.18 (changed +4 -1)
* paratool/paratool_components.tcl 1.34 (changed +2 -0)
* optimization/optimization.tcl 1.14 (changed +5 -2)
* nmwiz/nmwiz.tcl 1.14 (changed +2 -0)
* networkview/networkViewGui.tcl 1.5 (changed +3 -0)
* networkview/networkView.tcl 1.6 (changed +3 -0)
* networkview/networkSetup.tcl 1.4 (changed +3 -0)
* networkview/communityNetwork.tcl 1.5 (changed +3 -0)
* networkview/adjacencyMatrix.tcl 1.4 (changed +3 -0)
* namdserver/namdserver.tcl 1.9 (changed +2 -0)
* namdgui/namdgui_tclforces.tcl 1.6 (changed +4 -0)
* namdgui/namdgui.tcl 1.37 (changed +2 -1)
* mutator/mutator_gui.tcl 1.8 (changed +5 -3)
* mutator/mutator.tcl 1.15 (changed +3 -1)
* multiseqdialog/wait_dialog.tcl 1.4 (changed +3 -0)
* multiseqdialog/scrolledframe.tcl 1.3 (changed +3 -0)
* multiseqdialog/multiseqdialog.tcl 1.12 (changed +3 -0)
* multiseqdialog/download_updates.tcl 1.6 (changed +3 -0)
* moltoptools/moltoptools.tcl 1.3 (changed +4 -0)
* jmvexport/jmvexport.tcl 1.4 (changed +3 -1)
* irspecgui/irspecgui.tcl 1.17 (changed +2 -0)
* intersurf/nicostuf.tcl 1.2 (changed +4 -0)
* intersurf/intersurf_gui.tcl 1.3 (changed +3 -0)
* intersurf/color_func.tcl 1.3 (changed +3 -0)
* inorganicbuilder/inorganicbuilder.tcl 1.46 (changed +2 -1)
* idatm/idatm.tcl 1.17 (changed +4 -0)
* hesstrans/hessTest.tcl 1.3 (changed +3 -0)
* heatmapper/heatmapper.tcl 1.5 (changed +2 -0)
* hbonds/hbonds.tcl 1.9 (changed +3 -0)
* gofrgui/gofrgui.tcl 1.13 (changed +2 -0)
* fftk/fftk_distort.tcl 1.2 (changed +4 -0)
* extendedpdb/extendedpdb.tcl 1.3 (changed +2 -0)
* dowser/dowser_gui.tcl 1.9 (changed +2 -0)
* dowser/dowser.tcl 1.9 (changed +3 -0)
* dipwatch/dipwatch.tcl 1.5 (changed +2 -0)
* dataimport/dataimport.tcl 1.4 (changed +2 -0)
* cluster/cluster.tcl 1.4 (changed +3 -0)
* clustalw/mafft.tcl 1.5 (changed +3 -1)
* clustalw/clustalw.tcl 1.7 (changed +3 -1)
* clonerep/clonerep.tcl 1.13 (changed +2 -0)
* cispeptide/cispeptide_gui.tcl 1.5 (changed +2 -0)
* cispeptide/cispeptide.tcl 1.19 (changed +2 -0)
* chirality/chirality_gui.tcl 1.5 (changed +2 -0)
* chirality/chirality.tcl 1.24 (changed +2 -0)
* cgtools/cgtools.tcl 1.18 (changed +3 -1)
* cgtools/cgnetworking.tcl 1.23 (changed +2 -0)
* bossconvert/bossconvert.tcl 1.2 (changed +3 -0)
* blast/blast_resultviewer.tcl 1.6 (changed +3 -1)
* blast/blast.tcl 1.7 (changed +3 -1)
* biocore/biocoreHelper.tcl 1.4 (changed +3 -1)
* biocore/biocore.tcl 1.22 (changed +3 -1)
* bignum/bignum.tcl 1.4 (changed +3 -0)
Added CVS tags to the head of source files
* volutil/volutil.tcl 1.3 (changed +2 -0)
* volmapgui/volmapgui.tcl 1.23 (changed +2 -0)
* vmdtkcon/vmdtkcon.tcl 1.11 (changed +3 -0)
* vmdtkcon/tkcon-modified.tcl 1.10 (changed +3 -1)
* stamp/stamp.tcl 1.4 (changed +3 -0)
* multimolanim/multimolanim.tcl 1.4 (changed +2 -0)
* libbiokit/metric.tcl 1.4 (changed +2 -0)
* libbiokit/libbiokit_profcombine.tcl 1.3 (changed +2 -0)
* libbiokit/libbiokit_entropy.tcl 1.3 (changed +2 -0)
* libbiokit/libbiokit.tcl 1.7 (changed +3 -1)
Added CVS tas to the head of source files
* multiseq/select_nrset.tcl 1.5 (changed +3 -1)
* multiseq/plot.tcl 1.6 (changed +3 -0)
* multiseq/phylotree_options.tcl 1.7 (changed +3 -0)
* multiseq/multiseq.tcl 1.35 (changed +2 -0)
* multiseq/import_options.tcl 1.8 (changed +3 -1)
* multiseq/export_options.tcl 1.6 (changed +3 -0)
* multiseq/colormap_vmd.tcl 1.6 (changed +2 -0)
Cranked version for recent vmdcon bug fix
* ilstools/pkgIndex.tcl 1.6 (changed +1 -1)
* ilstools/ilstools.tcl 1.16 (changed +2 -2)
* ilstools/Makefile 1.7 (changed +1 -1)
Cranked version number for recent vmdcon bug fix
* zoomseq/zoomseq.tcl 1.23 (changed +2 -2)
* zoomseq/pkgIndex.tcl 1.4 (changed +1 -1)
* zoomseq/Makefile 1.6 (changed +1 -1)
* vmddebug/vmddebug.tcl 1.3 (changed +2 -2)
* vmddebug/pkgIndex.tcl 1.2 (changed +2 -2)
* vmddebug/debugatomsel.tcl 1.3 (changed +2 -2)
* vmddebug/Makefile 1.2 (changed +1 -1)
* solvate/solvate.tcl 1.58 (changed +2 -2)
* solvate/pkgIndex.tcl 1.6 (changed +1 -1)
* solvate/Makefile 1.11 (changed +1 -1)
* clonerep/pkgIndex.tcl 1.4 (changed +1 -1)
* clonerep/clonerep.tcl 1.12 (changed +1 -1)
* clonerep/Makefile 1.4 (changed +1 -1)
Cranked version number of colorscalebar for recent bug fix to vmdcon.
* colorscalebar/pkgIndex.tcl 1.5 (changed +1 -1)
* colorscalebar/Makefile 1.5 (changed +1 -1)
Cranked version of pbctools for recent vmdcon bug fix
* pbctools/pkgIndex.tcl 1.9 (changed +2 -2)
* pbctools/pbcwrap.tcl 1.16 (changed +2 -2)
* pbctools/pbcunwrap.tcl 1.14 (changed +2 -2)
* pbctools/pbctools.tcl 1.15 (changed +2 -2)
* pbctools/pbcset.tcl 1.16 (changed +2 -2)
* pbctools/pbcjoin.tcl 1.15 (changed +2 -2)
* pbctools/pbcgui.tcl 1.3 (changed +2 -2)
* pbctools/pbcbox.tcl 1.16 (changed +2 -2)
* pbctools/Makefile 1.9 (changed +1 -1)
|
| | 2013-04-15 | akohlmey | Replace incorrect "vmdcon -error" with "vmdcon -err"
* zoomseq/zoomseq.tcl 1.22 (changed +3 -3)
* vmddebug/vmddebug.tcl 1.2 (changed +2 -2)
* topotools/topovarxyz.tcl 1.4 (changed +7 -7)
* topotools/topoutils.tcl 1.12 (changed +11 -11)
* topotools/topotools.tcl 1.24 (changed +23 -23)
* topotools/topolammps.tcl 1.36 (changed +26 -26)
* topotools/topoimpropers.tcl 1.9 (changed +4 -4)
* topotools/topogromacs.tcl 1.6 (changed +2 -2)
* topotools/topodihedrals.tcl 1.9 (changed +3 -3)
* topotools/topocgcmm.tcl 1.6 (changed +5 -5)
* topotools/topobonds.tcl 1.12 (changed +5 -5)
* topotools/topoatoms.tcl 1.14 (changed +4 -4)
* topotools/topoangles.tcl 1.10 (changed +3 -3)
* solvate/solvate.tcl 1.57 (changed +8 -8)
* pbctools/pbcset.tcl 1.15 (changed +3 -3)
* pbctools/pbcjoin.tcl 1.14 (changed +4 -4)
* pbctools/pbcbox.tcl 1.15 (changed +2 -2)
* nanotube/nanotube.tcl 1.14 (changed +7 -7)
* nanotube/gui.tcl 1.5 (changed +1 -1)
* nanotube/graphene.tcl 1.7 (changed +6 -6)
* ilstools/ilstools.tcl 1.15 (changed +2 -2)
* colorscalebar/colorscalebar.tcl 1.24 (changed +2 -2)
* clonerep/clonerep.tcl 1.11 (changed +3 -3)
Teach nanotube/graphene sheet builder to build boron nitride systems.
step version number to 1.5
* nanotube/pkgIndex.tcl 1.6 (changed +1 -1)
* nanotube/nanotube.tcl 1.15 (changed +38 -8)
* nanotube/gui.tcl 1.6 (changed +20 -8)
* nanotube/graphene.tcl 1.8 (changed +41 -12)
* nanotube/doc/index.html 1.6 (changed +29 -14)
* nanotube/Makefile 1.6 (changed +1 -1)
|
| | 2013-04-13 | johns | Eliminate compiler warning about format conversion specifier and parameter
* molfile_plugin/src/pbeqplugin.C 1.6 (changed +3 -3)
Eliminate unusual parameter passing idiom that created bogus
warnings about uninitialized variables in the calling code.
* molfile_plugin/src/qmplugin.h 1.20 (changed +5 -4)
Eliminated the old code path that was intolerant of AMBER generated edm files
* molfile_plugin/src/edmplugin.C 1.33 (changed +5 -35)
Eliminated uninitialized variable warning
* molfile_plugin/src/crdplugin.c 1.39 (changed +5 -3)
Eliminated unused local variable and fixed an uninitialized idlist pointer
variable.
* molfile_plugin/src/lammpsplugin.c 1.43 (changed +4 -3)
Eliminated unused variable
* molfile_plugin/src/mdfplugin.C 1.20 (changed +2 -3)
* molfile_plugin/src/jsplugin.c 1.59 (changed +1 -3)
Eliminated unused variables
* molfile_plugin/src/spiderplugin.C 1.16 (changed +3 -3)
* molfile_plugin/src/moldenplugin.c 1.37 (changed +1 -2)
Fixed a typo in the call to Tcl_GetStringResult().
* molfile_plugin/src/webpdbplugin.c 1.53 (changed +3 -3)
Fixed an uninitialized local variable issue.
* molfile_plugin/src/offplugin.C 1.3 (changed +3 -2)
Fixed uninitialized variable
* hesstrans/src/hesstrans.C 1.5 (changed +1 -1)
Force initialization of bitsizeint[] to avoid compiler warnings.
* molfile_plugin/src/Gromacs.h 1.31 (changed +5 -1)
Force initialization of bszmask to eliminate compiler warnings about
potentially uninitialized data.
* molfile_plugin/src/jsplugin.c 1.58 (changed +3 -3)
Move initialization of j to avoid problems with error handling jump code
* molfile_plugin/src/offplugin.C 1.4 (changed +1 -1)
Updated gamessplugin and moldenplugin to use the new version of
the init_qmdata() helper routine which has been modified to avoid
bogus generation of compiler warnings about uninitialized parameters.
* molfile_plugin/src/moldenplugin.c 1.36 (changed +3 -3)
* molfile_plugin/src/gamessplugin.c 1.209 (changed +3 -3)
Write explicit pointer test to avoid compiler warnings
* psfgen/src/tcl_psfgen.c 1.56 (changed +1 -1)
|
| | 2013-04-12 | kvandivo | Fixed a typo that raphael pointed out with counting the suboptimal
path scaling
* networkview/suboptimalPaths.tcl 1.5 (changed +3 -3)
|
| | 2013-04-11 | johns | Applied Roberto Guerra's patch to fix a problem with the interpretation of
the cell vectors in cases that must be rotated.
* molfile_plugin/src/xsfplugin.C 1.18 (changed +5 -5)
|
| | 2013-04-11 | akohlmey | Fix bug in handling triclinic cells with negative tilt factors
* molfile_plugin/src/lammpsplugin.c 1.42 (changed +60 -43)
|
| | 2013-04-10 | barryi | In interSel dialog box, added dimming/inactication for the label/entryfields corresponding to unchecked selection method radiobuttons. Also tweaked labels.
* timeline/timeline.tcl 1.92 (changed +17 -7)
|
| | 2013-04-10 | akohlmey | Rework GUI to consistently use the grid layout manager
trace internal molid variable with a function to en-/disable widgets if molid is not valid to avoid error conditions on bad user interactions
* gofrgui/gofrgui.tcl 1.11 (changed +168 -206)
Rework GUI to only use grid layout manager
handle en-/disable of widgets more consistently
* irspecgui/irspecgui.tcl 1.16 (changed +167 -179)
Step version number
* gofrgui/doc/index.html 1.10 (changed +1 -1)
Trigger EnDisable when all molecules are deleted
* gofrgui/gofrgui.tcl 1.12 (changed +3 -1)
Update version and homepage URL
* irspecgui/doc/index.html 1.9 (changed +2 -2)
|
| | 2013-04-08 | barryi | Expanded dialog box to control expanded selection types for interSel. Also: tweaks for list parse error box messages, some rearranging of old-prefixed dialog box variables, intention is that these (and non old-prefixed) are in the same state as previous checkin,.
* timeline/timeline.tcl 1.90 (changed +237 -92)
Fixed bug in dialog variable for RMSF.
* timeline/timeline.tcl 1.91 (changed +2 -2)
|
| | 2013-04-03 | kvandivo | Revised residue based coarse graining so it does not check to see whether
or not a PSF is included (since it isn't necessary) and tweaked the RBCG
code to not attempt to use segment ID information in the atomselects if
it hasn't been set.
* cgtools/pkgIndex.tcl 1.11 (changed +3 -3)
* cgtools/doc/index.html 1.24 (changed +3 -1)
* cgtools/cgtools.tcl 1.17 (changed +14 -3)
* cgtools/cgnetworking.tcl 1.22 (changed +1 -1)
* cgtools/cggui.tcl 1.36 (changed +4 -22)
* cgtools/Makefile 1.6 (changed +1 -1)
|
| | 2013-04-03 | barryi | Added copyUser to GUI, copies data values for whole trajectory to user field (or user2 / user3 / user4 as selected), so can be graphically displayed, easily seen by Tcl procs, etc.. Works for all cases (per-residue and free selections); has copy after all calcs. option. Also, fixed some general bugs on menu dialog box reset values.
* timeline/timeline.tcl 1.89 (changed +165 -5)
|
| | 2013-04-02 | mayne | Modified chargeOpt to remove dependency on PSFGen
* fftk/fftk_ChargeOpt.tcl 1.20 (changed +89 -23)
|
| | 2013-03-28 | mayne | ChargeOpt "Guess" button first clears the treeview box before refilling with guessed atoms
* fftk/fftk_guiProcs.tcl 1.25 (changed +3 -1)
Modified regex for reading Mulliken charges with hydrogens summed into heavy atoms to account for changes in Gaussian log syntax
* qmtool/qmtool_readwrite.tcl 1.53 (changed +2 -2)
|
| | 2013-03-14 | kvandivo | Beefed up some commented out debugging statements and couple of other
unimportant changes that make debugging a bit easier
* remote/remote.tcl 1.14 (changed +5 -4)
Doc updates to more closely match current reality
* remote/doc/index.html 1.20 (changed +155 -70)
* remote/doc/getip.html 1.1 (added +6 -0)
Minor code cleanup, added some currently inactive debugging statements
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/VMDMobile.java 1.24 (changed +6 -5)
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/UDPServer.java 1.5 (changed +3 -2)
More doc tweaks in anticipation of release
* remote/doc/twoFingers_resized.png 1.2 (changed +114 -309)
* remote/doc/pluginMain.png 1.2 (changed +18 -15)
* remote/doc/index.html 1.21 (changed +6 -10)
|
| | 2013-03-04 | johns | CARMA builds require Tcl/Tk 8.6.0 for stability, so I'm going to leave
them hard-coded to use 8.6.0 in the makefile for the time being.
* Make-arch 1.83 (changed +3 -3)
Eliminated various compiler-generated safety checks and increased
default optimizations for Tegra for the CARMA builds.
* Make-arch 1.84 (changed +3 -3)
|
| | 2013-02-28 | johns | Updated gofrgui plugin with changes to comment out the old Tk "pack" commands
that remained from the original implementation. Tk 8.6.0 no longer allows
"pack" and "grid" commands to manage the same objects (or for one to "supercede"
management by the other). Needs further testing.
* gofrgui/pkgIndex.tcl 1.4 (changed +1 -1)
* gofrgui/gofrgui.tcl 1.10 (changed +53 -40)
* gofrgui/Makefile 1.4 (changed +1 -1)
Updated irspecgui plugin with changes to comment out the old Tk "pack" commands
that remained from the original implementation. Tk 8.6.0 no longer allows
"pack" and "grid" commands to manage the same objects (or for one to "supercede"
management by the other). Needs further testing.
* irspecgui/pkgIndex.tcl 1.4 (changed +1 -1)
* irspecgui/irspecgui.tcl 1.15 (changed +47 -37)
* irspecgui/Makefile 1.6 (changed +1 -1)
|
| | 2013-02-27 | johns | Added README files from Bendix distribution.
* bendix/doc/README.txt 1.1 (added +72 -0)
* bendix/doc/README.html 1.1 (added +173 -0)
Updated to version 1.1 of the Bendix plugin by Caroline Dahl.
* bendix/pkgIndex.tcl 1.2 (changed +1 -1)
* bendix/doc/GUI-tips.gif 1.2 (changed binary)
* bendix/bendix.tcl 1.3 (changed +2214 -982)
* bendix/Makefile 1.3 (changed +1 -1)
|
| | 2013-02-26 | johns | Added new molfile plugin constants MOLFILE_DIRECTIO_MIN_BLOCK_SIZE
and MOLFILE_DIRECTIO_MAX_BLOCK_SIZE which set compile-time limits on
the range of disk block and memory page sizes that VMD can support for
direct I/O that bypasses the kernel buffer cache.
* include/molfile_plugin.h 1.105 (changed +16 -1)
Updated jsplugin to use the new MOLFILE_DIRECTIO_MIN_BLOCK_SIZE
and MOLFILE_DIRECTIO_MAX_BLOCK_SIZE compile-time constants that define
the range of disk block and memory page sizes that VMD can support for
direct I/O calls that bypass the kernel buffer cache.
* molfile_plugin/src/jsplugin.c 1.57 (changed +19 -9)
Updated to the latest version 1.7 of the parseFEP plugin by
Peng Liu and Chris Chipot.
* parsefep/pkgIndex.tcl 1.6 (changed +1 -1)
* parsefep/parseFEP.tcl 1.10 (changed +104 -86)
* parsefep/Makefile 1.6 (changed +1 -1)
|
| | 2013-02-26 | gumbart | Changed my affiliation
* fftk/fftk_SharedFcns.tcl 1.6 (changed +3 -3)
* fftk/fftk.tcl 1.9 (changed +3 -3)
|
| | 2013-02-25 | johns | Added missing namespace for ::util::quatinterpmatrices call.
* viewchangerender/vcr.tcl 1.13 (changed +1 -1)
Applied Josh's update to fix a closing brace, and change the quatarc routine
so it always interpolates rotations along the shortest path.
* utilities/utilities.tcl 1.9 (changed +10 -1)
|
| | 2013-02-22 | kvandivo | Set the intial mode to move when the plugin window is opened
* remote/remote.tcl 1.13 (changed +11 -1)
|
| | 2013-02-22 | barryi | Native contact error checks and progress bar. Fixed formatting for displayed values for free selections. More robust parsing of selection lists for native contact and inter-sel contacts, with error alert boxes.
* timeline/timeline.tcl 1.88 (changed +64 -14)
|
| | 2013-02-21 | petefred | Make autopsf case sensitive by default -- as JC points out, this is in
line with the pdb spec
* autopsf/autopsf.tcl 1.123 (changed +25 -4)
|
| | 2013-02-19 | johns | Applied a fix for correct handling of negative resids that show up in
PDB files where DNA helices come together. By quoting the resid string
we prevent an internal autopsf-constructed atom selection string
from being mistakenly parsed as if it was a badly formatted regex or
numeric value, and it works as intended. Patch provided by Josh Vermaas.
* autopsf/pkgIndex.tcl 1.8 (changed +1 -1)
* autopsf/autopsf.tcl 1.122 (changed +11 -3)
* autopsf/Makefile 1.18 (changed +1 -1)
|
| | 2013-02-07 | johns | Eliminated direct use of the Tcl interpreter result field in favor of
calling Tcl_GetStringResult(), as required by Tcl 8.6.x
* molfile_plugin/src/webpdbplugin.c 1.52 (changed +3 -3)
Updated plugin build flags for CARMA
* build.csh 1.106 (changed +3 -3)
Use Tcl 8.5 for CARMA builds too
* Make-arch 1.82 (changed +1 -1)
|
| | 2013-02-06 | kvandivo | Added new screen to choose a VMD machine to connect to. Revised menus
accordingly. Last 10 servers are now stored. Also moved network traffic
off of UI thread to keep Android 3+ happy.
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/VMDMobile.java 1.23 (changed +214 -61)
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/ServerChooser.java 1.2 (changed +220 -10)
* remote/mobileapps/android/VMDMobile/res/values/strings.xml 1.13 (changed +6 -3)
* remote/mobileapps/android/VMDMobile/res/menu/menu.xml 1.4 (changed +15 -6)
* remote/mobileapps/android/VMDMobile/res/layout/touchpad.xml 1.3 (changed +2 -2)
* remote/mobileapps/android/VMDMobile/res/layout/serverchooser.xml 1.2 (changed +17 -0)
* remote/mobileapps/android/VMDMobile/res/layout/mainpreferences.xml 1.10 (changed +0 -24)
* remote/mobileapps/android/VMDMobile/res/layout/addnewserverinformation.xml 1.1 (added +70 -0)
* remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_goto.png 1.3 (added +7 -9)
* remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_goto.png 1.3 (added +0 -0)
* remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_goto.png 1.3 (added +3 -8)
Added option to delete temporary snapshot files, used if only one mobile
device is getting the snapshot (and not multiple devices)
* remote/remote.tcl 1.12 (changed +56 -32)
* remote/pkgIndex.tcl 1.6 (changed +1 -1)
* remote/Makefile 1.8 (changed +1 -1)
Bumped android app version number, added xml declaration of ServerChooser
activity, bumped minimum sdk version to 10 (corresponds to android 2.3.4)
and added request for wifi_multicast permission, which lets the app
warn the user that they need to turn wifi on for proper usage.
* remote/mobileapps/android/VMDMobile/AndroidManifest.xml 1.8 (changed +8 -3)
Moved network traffic off of main thread into AsyncTask (needed for
Android 3+, since it is more picky about running things on UI thread)
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/SnapshotView.java 1.4 (changed +30 -8)
|
| | 2013-02-06 | johns | Added build flags for the SECO/NVIDIA CARMA board
* Make-arch 1.80 (changed +16 -0)
Added build flags for the SECO/NVIDIA CARMA boards
* build.csh 1.105 (changed +11 -1)
Fix package require typo
* viewchangerender/vcr.tcl 1.12 (changed +1 -1)
Updated CARMA build flags to enable shared libs and improve optimization
* Make-arch 1.81 (changed +3 -3)
|
| | 2013-02-04 | johns | Replaced the previous rev of moldenplugin with an alternative
version by Alexey Titov, which is a patched version
(unforunately based on an earlier rev) that has been
extensively exercised by the Terachem developers. This version cures
some problems that were still not fixed by our previous rev, so we'll use
Alexey's version until we can reconcile the changes in this version with the
other updates contained in the most recent previous version by Jan Saam.
* molfile_plugin/src/moldenplugin.c 1.35 (changed +146 -135)
|
| | 2013-01-30 | kvandivo | Minor changes to var scope, comments.
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/UDPServer.java 1.4 (changed +3 -1)
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/MultiTouchPad.java 1.6 (changed +1 -1)
* remote/mobileapps/android/VMDMobile/src/edu/uiuc/ks/vmdmobile/MainPreferences.java 1.2 (changed +2 -1)
|
| | 2013-01-29 | johns | Fix typo in Josh's last name
* utilities/utilities.tcl 1.8 (changed +1 -1)
Updated version number of mutator plugin per JC's recent bug fix.
* mutator/pkgIndex.tcl 1.8 (changed +1 -1)
* mutator/mutator.tcl 1.14 (changed +1 -1)
* mutator/Makefile 1.9 (changed +1 -1)
|
| | 2013-01-24 | johns | Added Tcl routines for conversion between matrix and quaternion
rotation representations, and performining quaternion based interpolation
between two rotation matrices.
* utilities/utilities.tcl 1.7 (changed +90 -1)
* utilities/pkgIndex.tcl 1.2 (changed +1 -1)
* utilities/Makefile 1.2 (changed +1 -1)
Updated viewchangerender plugin with improved quaternion-based rotation
interpolation code.
* viewchangerender/vcr_gui.tcl 1.12 (changed +1 -1)
* viewchangerender/vcr.tcl 1.11 (changed +11 -4)
* viewchangerender/pkgIndex.tcl 1.3 (changed +2 -2)
* viewchangerender/Makefile 1.4 (changed +1 -1)
|
| | 2013-01-24 | gumbart | Bug fix for segments without resid specified
* mutator/mutator.tcl 1.13 (changed +28 -19)
|
| | 2013-01-17 | johns | Updated the plumed Makefile and added another updated rev from
Toni Giorgino that improves widget packing.
* plumed/vmdplumed.tcl 1.6 (changed +26 -23)
* plumed/Makefile 1.4 (changed +2 -1)
|
| | 2013-01-16 | kvandivo | Fixed a minor grammatical error
* cgtools/doc/index.html 1.23 (changed +1 -1)
|
| | 2013-01-12 | johns | Updated with Brian Bennion's latest molemeshplugin.
* molfile_plugin/src/molemeshplugin.C 1.2 (changed +10 -5)
|
| | 2013-01-11 | kvandivo | Added in ability to multiply suboptimal path counts by a scaling factor
(defaults to 1) which rafael needed for his work.
* networkview/suboptimalPaths.tcl 1.4 (changed +13 -10)
* networkview/pkgIndex.tcl 1.4 (changed +1 -1)
* networkview/networkViewGui.tcl 1.4 (changed +13 -3)
* networkview/networkView.tcl 1.5 (changed +2 -2)
* networkview/networkSetup.tcl 1.3 (changed +2 -2)
* networkview/communityNetwork.tcl 1.4 (changed +2 -2)
* networkview/adjacencyMatrix.tcl 1.3 (changed +2 -2)
* networkview/Makefile 1.4 (changed +1 -1)
|
| | 2013-01-09 | mayne | Fixed bug in which glog parser pulled RHF energies instead of MP2
* fftk/fftk_DihOpt.tcl 1.12 (changed +10 -3)
|
| | 2013-01-09 | johns | Latest version of plumed plugin from Toni Giorgino. Tagged as
version "1.9" rather than "1.901" for the time being.
* plumed/vmdplumed.tcl 1.5 (changed +936 -450)
* plumed/templates_list_v2_autogen.tcl 1.1 (added +211 -0)
* plumed/templates_list_v1.tcl 1.1 (added +40 -0)
* plumed/pkgIndex.tcl 1.3 (changed +1 -1)
* plumed/doc/README 1.1 (added +211 -0)
* plumed/Makefile 1.3 (changed +1 -1)
* plumed/ChangeLog 1.1 (added +37 -0)
New version of the VTF plugin requires Tcl linkage to allow extra data
fields to be exposed to Tcl.
* molfile_plugin/Makefile 1.120 (changed +17 -17)
Updated multiplot callbacks to provide 5 params, needed by nmwiz plugin
* multiplot/pkgIndex.tcl 1.8 (changed +1 -1)
* multiplot/multiplot.tcl 1.39 (changed +5 -5)
* multiplot/Makefile 1.8 (changed +1 -1)
Updated nmwiz plugin by Ahmet Bakan.
* nmwiz/nmwiz.tcl 1.13 (changed +654 -159)
Updated version of VTF plugin from Olaf
* molfile_plugin/src/vtfplugin.c 1.15 (changed +596 -285)
Updates to heatmapper plugin contributed by Ahmet Bakan. The new version
adds support for callbacks, and fixes a bug where heatmapper was doing
overly aggressive deletion of Tk images which could interfere with other
plugins.
* heatmapper/pkgIndex.tcl 1.2 (changed +1 -1)
* heatmapper/heatmapper.tcl 1.4 (changed +55 -19)
* heatmapper/Makefile 1.2 (changed +1 -1)
|
| | 2013-01-08 | kvandivo | Changed name of market to store
* remote/doc/index.html 1.19 (changed +4 -3)
|
| | 2013-01-04 | barryi | Native contact calculation added, output is fraction of native contacts for each selection, 0.0 to 1.0. Monitors key atoms (keyAtomSelString), e.g. CA for proteins. 0.0 to 1.0. The reference frame always 1.0 for every selection.
In GUI, user can set cutoff distance, set of multiple From selections, the To selection, and reference frame.
* timeline/timeline.tcl 1.87 (changed +179 -138)
|
| | 2013-01-02 | mayne | Fixed "item blue" bug when loading theme file
* vmdprefs/vmdprefs.tcl 1.6 (changed +3 -3)
|
| | 2012-12-20 | mayne | Added MP2 single point calc for incorporating MP2-level dipole into charge optimization
* fftk/fftk_guiInterface.tcl 1.25 (changed +21 -11)
* fftk/fftk_GenZMatrix.tcl 1.12 (changed +35 -12)
* fftk/fftk_ChargeOpt.tcl 1.19 (changed +25 -13)
|
| | 2012-12-20 | johns | Added molemeshplugin to the build, and sorted the individual plugins into
alphabetical order to improve readability of the makefile and to make it
easier to locate things. Added comments regarding several of the plugins
that have dependencies on other libraries, and/or that are not to be
built on certain platforms (e.g. Android).
* molfile_plugin/Makefile 1.119 (changed +305 -267)
|
| | 2012-12-18 | johns | Added Brian Bennion's molemesh plugin for reading mesh files generated by
the MOLE 2.0 program (mole.upol.cz).
* molfile_plugin/src/molemeshplugin.C 1.1 (added +331 -0)
|
| | 2012-12-07 | barryi | Added ability to work with coarse grained systems, via keyAtomSelString. Currently works with Martini force field (backbone atom BAS). Simple to extend to other coarse grained systems. Code for native contact (with side chains) in, needs some tweaking for normalizing, not exposed to user via GUI yet.
* timeline/timeline.tcl 1.85 (changed +277 -22)
Now can extend atom types recognized for coarse grain atoms with a line in .vmdrc. For instance set ::timeLineSettingExtraKeyAtoms "name AGH" .
* timeline/timeline.tcl 1.86 (changed +6 -2)
|
| | 2012-11-21 | mayne | Upon launch tries to load a vmdrc file from $env(HOME); added a vmdprefs format check to the theme file reader; fixed bug with custom code parsing
* vmdprefs/vmdprefs.tcl 1.5 (changed +49 -14)
|
| | 2012-11-20 | mayne | Added fftk_distort.tcl to the Makefile
* fftk/Makefile 1.2 (changed +2 -1)
|
| | 2012-11-18 | mayne | Allow user to specify vmdrc path; allow user to activate/deactivate portions of the theme file
* vmdprefs/vmdprefs.tcl 1.4 (changed +385 -104)
|
| | 2012-11-17 | mayne | Prompt users before overwriting bak files; vmdrc does not try to load graphic related elements when running in text mode
* vmdprefs/vmdprefs.tcl 1.3 (changed +124 -101)
|
| | 2012-11-15 | mayne | Fixed typo in variable name related to guessing bonded input
* fftk/fftk_guiProcs.tcl 1.24 (changed +2 -2)
|
| | 2012-11-12 | mayne | Retype/recharge cmpd+wat combined structure
* fftk/fftk_ChargeOpt.tcl 1.18 (changed +4 -2)
|
| | 2012-11-09 | mayne | Fixed error in if/then statements pertaining to guessing initial optBonded input
* fftk/fftk_guiProcs.tcl 1.23 (changed +3 -3)
|
| | 2012-11-01 | mayne | Add distortion code
* fftk/fftk_distort.tcl 1.1 (added +488 -0)
Added gui element to read the final obj value from baopt
* fftk/fftk_guiProcs.tcl 1.22 (changed +7 -2)
* fftk/fftk_guiInterface.tcl 1.24 (changed +21 -3)
* fftk/fftk_BondAngleOpt.tcl 1.8 (changed +3 -2)
Modified fftk.tcl to source the new fftk_distort.tcl file
* fftk/fftk.tcl 1.8 (changed +2 -1)
|
| | 2012-10-31 | mayne | Protect against psf and/or namdbin filenames with spaces
* fftk/fftk_DihOpt.tcl 1.11 (changed +3 -3)
* fftk/fftk_BondAngleOpt.tcl 1.7 (changed +3 -3)
|
| | 2012-10-29 | johns | Added draft of char's new atom fields.
* include/molfile_plugin.h 1.104 (changed +19 -2)
|
| | 2012-10-23 | mayne | Fixed minor bug with colp autoscale
* fftk/fftk_ChargeOpt.tcl 1.17 (changed +2 -2)
Updated to add some functionality to ffTK
* utilities/utilities.tcl 1.6 (changed +86 -23)
Updates to bond/angle optimization
* fftk/fftk_guiProcs.tcl 1.21 (changed +106 -58)
* fftk/fftk_guiInterface.tcl 1.23 (changed +7 -33)
* fftk/fftk_BondAngleOpt.tcl 1.6 (changed +133 -223)
|
| | 2012-10-19 | johns | Fixed GUI typos caught by Josh Vermaas
* autoionize/autoionizegui.tcl 1.11 (changed +3 -3)
|
| | 2012-10-18 | mayne | Re(?)committing fixes to GenZMatrix to allow for more general ACC/DON assignments
* fftk/fftk_GenZMatrix.tcl 1.11 (changed +500 -329)
|
| | 2012-10-17 | kvandivo | Latest changes from ZLS group with tweaks
* networkview/suboptimalPaths.tcl 1.3 (changed +2 -2)
* networkview/pkgIndex.tcl 1.3 (changed +1 -1)
* networkview/networkViewGui.tcl 1.3 (changed +25 -6)
* networkview/networkView.tcl 1.4 (changed +90 -13)
* networkview/networkSetup.tcl 1.2 (changed +86 -82)
* networkview/communityNetwork.tcl 1.3 (changed +2 -2)
* networkview/adjacencyMatrix.tcl 1.2 (changed +2 -1)
* networkview/Makefile 1.3 (changed +1 -1)
|
| | 2012-10-17 | johns | Fix link to error image.
* parsefep/doc/index.html 1.4 (changed +1 -1)
Updated ParseFEP docs with latest files from Chris Chipot.
* parsefep/doc/index.html 1.3 (changed +72 -40)
* parsefep/doc/error.gif 1.1 (added binary)
|
| | 2012-10-14 | johns | Pull dtrplugin out of the android builds for the time being until we get
past implementation Android NDK STL implementation limitations.
* molfile_plugin/Makefile 1.118 (changed +7 -7)
|
| | 2012-10-02 | mayne | Update todo
* fftk/TODO.txt 1.7 (changed +1 -6)
|
| | 2012-10-02 | johns | Added Android on ARM V7A to the standard plugin compiles
* build.csh 1.104 (changed +3 -0)
Prevent the DESRES maeffplugin from being compiled when cross-compiling
for Android on ARM V7A targets, due to problems with the Android NDK
cross-development toolchain for Linux.
* molfile_plugin/Makefile 1.115 (changed +27 -4)
Remove test code
* molfile_plugin/Makefile 1.117 (changed +1 -2)
Removed test code.
* molfile_plugin/Makefile 1.116 (changed +1 -2)
|
| | 2012-09-28 | johns | Added Android plugin build config and various macros for the Android NDK
cross compilation directory paths etc.
* Make-arch 1.79 (changed +24 -0)
Make dtrplugin compile on android..
* molfile_plugin/src/dtrplugin.cxx 1.23 (changed +2 -2)
Updated Tom Bishop's contact info
* vdna/doc/index.html 1.8 (changed +3 -3)
|
| | 2012-09-24 | mayne | Added additional sanity check for dihedral input
* fftk/fftk_DihOpt.tcl 1.10 (changed +8 -5)
Changed wording on dih viz checkbutton
* fftk/fftk_guiProcs.tcl 1.20 (changed +2 -2)
Fixed bug when multiple spaces were used for dihedral type definition when runing dih opt
* fftk/fftk_guiProcs.tcl 1.19 (changed +7 -3)
|
| | 2012-09-22 | mayne | Added ability to plot points on dihedral fitting plots
* fftk/fftk_guiProcs.tcl 1.18 (changed +19 -1)
|
| | 2012-09-21 | mayne | Added plot axes adjustment controls to dihedral fitting plots
* fftk/fftk_guiProcs.tcl 1.17 (changed +124 -10)
Fixed issue setting initial values for dih optimizer when lock phase was turned on
* fftk/fftk_DihOpt.tcl 1.9 (changed +81 -35)
Removed ability to manually set/modify equilibrium value when scanning dih values; it is no longer supported in G09RevC
* fftk/fftk_guiProcs.tcl 1.16 (changed +4 -13)
* fftk/fftk_guiInterface.tcl 1.22 (changed +28 -39)
* fftk/fftk_GenDihScan.tcl 1.8 (changed +5 -7)
|
| | 2012-09-19 | mayne | Added development version of bond/angle optimization, although the tab is hidden until some problems are fixed
* fftk/fftk_guiProcs.tcl 1.15 (changed +85 -25)
* fftk/fftk_guiInterface.tcl 1.21 (changed +306 -106)
* fftk/fftk_SharedFcns.tcl 1.5 (changed +108 -1)
* fftk/fftk_GeomOpt.tcl 1.8 (changed +1 -1)
* fftk/fftk_GenZMatrix.tcl 1.9 (changed +329 -522)
* fftk/fftk_GenDihScan.tcl 1.6 (changed +1 -1)
* fftk/fftk_GenBonded.tcl 1.12 (changed +86 -103)
* fftk/fftk_DihOpt.tcl 1.8 (changed +1 -1)
* fftk/fftk_ChargeOpt.tcl 1.16 (changed +9 -3)
* fftk/fftk_BuildPar.tcl 1.6 (changed +1 -1)
* fftk/fftk_BondAngleOpt.tcl 1.5 (changed +1470 -447)
* fftk/fftk.tcl 1.7 (changed +2 -2)
Cleaned up the to do list
* fftk/TODO.txt 1.6 (changed +12 -160)
Completely rewritten GenZMatrix routines to allow for ACC and/or DON positions for any molecule (including diatomic and linear)
* fftk/fftk_GenZMatrix.tcl 1.8 (changed +522 -329)
Modified default Gaussian Route sections to force printing of 'input orientation'
* fftk/fftk_GeomOpt.tcl 1.9 (changed +2 -2)
* fftk/fftk_GenZMatrix.tcl 1.10 (changed +2 -2)
* fftk/fftk_GenDihScan.tcl 1.7 (changed +2 -2)
|
| | 2012-08-28 | johns | Updated with latest rev of the normal modes wizard from Ahmet Bakan.
* nmwiz/nmwiz.tcl 1.12 (changed +34 -15)
Updated with the latest version of the parseFEP code from Peng Liu.
* parsefep/parseFEP.tcl 1.9 (changed +6 -5)
|
| | 2012-08-24 | jim | Fallback in case kernel does not implement readv.
* molfile_plugin/src/fastio.h 1.26 (changed +12 -7)
|
| | 2012-08-23 | mayne | Changed row expansion/contraction from button bar to notebook
* vmdprefs/vmdprefs.tcl 1.2 (changed +3 -3)
|
| | 2012-08-22 | kvandivo | Updates written on the Mac
* remote/mobileapps/android/VMDMobile/README 1.3 (changed +33 -1)
|
| | 2012-08-21 | johns | Added Bendix doc images
* bendix/doc/Monsieur_Bendix_smaller_still.gif 1.1 (added binary)
* bendix/doc/GUI-tips.gif 1.1 (added binary)
Added Chris Mayne's VMD preferences plugin
* vmdprefs/vmdprefs.tcl 1.1 (added +3620 -0)
* vmdprefs/pkgIndex.tcl 1.1 (added +16 -0)
* vmdprefs/Makefile 1.1 (added +23 -0)
Added new vmdprefs plugin to the build
* Makefile 1.134 (changed +2 -1)
Added placeholder docs
* vmdprefs/doc/index.html 1.1 (added +12 -0)
|
| | 2012-08-10 | barryi | Added globl cross-correlation coefficient for second structures, and associated GUI. Seems to work, only tested on Macintosh so far.
* timeline/timeline.tcl 1.84 (changed +433 -31)
|
| | 2012-08-05 | barryi | Inter-selection-set contacts count works. User enters VMD/tcl-compatible list of selection strings, gets the set of Choose(n,2) combinations of two selections that result, with contacts between the two selections graphed vs. time (user sets cutoff). Progress bar updates with each pair of selections. Also, general improvement to text label display for all free-selction sets (notably, the long labels typical for InterSelContact)
* timeline/timeline.tcl 1.83 (changed +253 -10)
|
| | 2012-08-02 | johns | Made the PSF plugin allow NAMD-tagged PSF files to use a space delimited
bond record format since NAMD accepts that variation. Changed the PSF
informational messages to clearly indicate when it has found a NAMD-format
PSF file, as opposed to one of the Charmm variants.
* molfile_plugin/src/psfplugin.c 1.74 (changed +62 -46)
|
| | 2012-08-01 | johns | Applied Caroline Dahl's latest fixes for Bendix.
* bendix/bendix.tcl 1.2 (changed +193 -71)
|
| | 2012-07-30 | johns | Changed .gro parsing code to use fixed field widths to address problems
with files that had no spaces between the coordinate fields.
* molfile_plugin/src/gromacsplugin.C 1.47 (changed +3 -3)
* molfile_plugin/src/Gromacs.h 1.30 (changed +25 -10)
Copy bendix help images into distribution for the time being.
* bendix/Makefile 1.2 (changed +1 -1)
Misc cleanup of stray tabs
* molfile_plugin/src/Gromacs.h 1.28 (changed +37 -33)
Misc cleanup of tabbing etc.
* molfile_plugin/src/Gromacs.h 1.29 (changed +78 -74)
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| | 2012-07-27 | johns | Further nmwiz updates from Ahmet Bakan.
* nmwiz/nmwiz.tcl 1.11 (changed +96 -58)
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| | 2012-07-25 | mayne | Added screencasts section
* fftk/doc/index.html 1.4 (changed +24 -0)
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| | 2012-07-24 | johns | Latest version of normal mode wizard plugin from Ahmet Bakan.
* nmwiz/nmwiz.tcl 1.10 (changed +107 -20)
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| | 2012-07-19 | johns | Added the Bendix plugin for helix geometry analysis and visualization,
by Anna Caroline E. Dahl, Matthieu Chavent, and Mark S. P. Sansom.
Paper DOI: http://dx.doi.org/10.1093/bioinformatics/bts357
* bendix/pkgIndex.tcl 1.1 (added +16 -0)
* bendix/bendix.tcl 1.1 (added +4946 -0)
* bendix/Makefile 1.1 (added +23 -0)
Added the Bendix plugin to the build.
* Makefile 1.133 (changed +2 -1)
Cranked version number of plumed plugin in the make distrib target
* plumed/Makefile 1.2 (changed +1 -1)
Updated Toni Giorgino's VMD plumed plugin with the latest version.
* plumed/vmdplumed.tcl 1.4 (changed +480 -263)
* plumed/pkgIndex.tcl 1.2 (changed +1 -1)
Updated the molden plugin with the latest version which fixes various
limitations that had previously caused problems for Terachem users.
I still need to reconcile this change set against overlapping
changes contributed by Alexey Titov, where applicable.
* molfile_plugin/src/qmplugin.h 1.19 (changed +6 -2)
* molfile_plugin/src/moldenplugin.c 1.34 (changed +132 -96)
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| | 2012-07-18 | barryi | Added popup percent-progress bar with cancel button (users can observe, halt long calculations); all Calculate items update the progress bar. All Calculate items now obey frame range limits (firstAnalysisFrame, lastAnalysisFrame). Data set filtering now happens via a copy buffer (no file write/read cycle for the user or internally); a "Filter Data..." menu items has been added to the GUI to set paramaters and run the filtering.
* timeline/timeline.tcl 1.82 (changed +798 -70)
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| | 2012-07-17 | gumbart | Added MP2 scale factor for frequencies
* qmtool/qmtool_readwrite.tcl 1.52 (changed +6 -1)
* qmtool/qmtool.tcl 1.48 (changed +2 -1)
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| | 2012-07-03 | jim | Provide some feedback when ignoring guessed coordinates due to angle < 45 deg.
* psfgen/src/topo_mol.c 1.22 (changed +3 -0)
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| | 2012-05-29 | johns | Updated with the latest version from Peng Liu.
* parsefep/pkgIndex.tcl 1.5 (changed +1 -1)
* parsefep/parseFEP.tcl 1.8 (changed +495 -218)
* parsefep/Makefile 1.5 (changed +1 -1)
Updated with the latest version of NMWiz from Ahmet Bakan.
* nmwiz/pkgIndex.tcl 1.4 (changed +1 -1)
* nmwiz/nmwiz.tcl 1.9 (changed +228 -66)
* nmwiz/doc/nmwiz_prody.png 1.3 (changed binary)
* nmwiz/doc/nmwiz_multiplot.png 1.2 (changed binary)
* nmwiz/doc/nmwiz_main.png 1.3 (changed binary)
* nmwiz/doc/nmwiz_gui.png 1.2 (changed binary)
* nmwiz/doc/nmwiz_frommolecule.png 1.2 (changed binary)
* nmwiz/doc/nmwiz_comparison.png 1.2 (changed binary)
* nmwiz/doc/index.html 1.4 (changed +16 -7)
* nmwiz/Makefile 1.4 (changed +1 -1)
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| | 2012-05-27 | akohlmey | Upgrade rst7plugin to support reading and writing box and velocity information.
* molfile_plugin/src/rst7plugin.c 1.19 (changed +131 -43)
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| | 2012-05-25 | barryi | Primitive filtering function added (writeDataFiltered), command line only (writeDataFiltered). No GUI yet, needs to work without requiring save to file.
Color scales extended: now has Black->White, White->Black, RGB, BGR (avail via GUI). Associated GUI bug fixed (as correct intial radiobutton menu selection for highlight color and colorscale name)
printPicRedraw added for experimental remote send (to attached touch
devices) of Timeline printout. Relies on Unix commands to reformat picture.
Only command-line interface.
* timeline/timeline.tcl 1.81 (changed +638 -20)
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| | 2012-05-22 | mayne | Added checks for fwd and rev bond/angle defintions when calculating bonded parameters
* fftk/fftk_GenBonded.tcl 1.11 (changed +45 -24)
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| | 2012-05-17 | mayne | Added proc to reset Gaussian values to defaults, both in init and in gui, for all instances; modified default wat int route from RHF to HF - gaussian can determine R or U
* fftk/fftk_guiInterface.tcl 1.20 (changed +4 -26)
* fftk/fftk_GeomOpt.tcl 1.7 (changed +26 -6)
* fftk/fftk_GenZMatrix.tcl 1.7 (changed +26 -6)
* fftk/fftk_GenDihScan.tcl 1.5 (changed +26 -6)
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| | 2012-05-15 | mayne | Fixed Calc Bonded to properly assign force constants to internal coordinates
* qmtool/qmtool_readwrite.tcl 1.51 (changed +7 -3)
* fftk/fftk_guiInterface.tcl 1.19 (changed +52 -33)
* fftk/fftk_GenBonded.tcl 1.9 (changed +79 -9)
Fixed order of statments in GenBonded fftk LOG file
* fftk/fftk_GenBonded.tcl 1.10 (changed +3 -2)
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| | 2012-05-15 | gumbart | Fixed dipole angle weighting in objective function
* fftk/fftk_ChargeOpt.tcl 1.15 (changed +5 -3)
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| | 2012-05-14 | mayne | Corrected testreb to testrev in buildpar
* fftk/fftk_BuildPar.tcl 1.5 (changed +2 -2)
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| | 2012-04-25 | mayne | Fixed plot color variable in colp
* fftk/fftk_ChargeOpt.tcl 1.14 (changed +3 -3)
Write charge optimization debugging file to same dir as the log file
* fftk/fftk_ChargeOpt.tcl 1.13 (changed +2 -2)
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| | 2012-04-24 | mayne | Fixed kmax -> refineKmax in refine proc for dihedral optimization
* fftk/fftk_DihOpt.tcl 1.7 (changed +11 -11)
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| | 2012-04-18 | mayne | Changed QME-MME to MME-QME reported in chargeopt log file
* fftk/fftk_ChargeOpt.tcl 1.12 (changed +2 -2)
Fixed problem loading LOG files from previous charge opt runs; data was loading into the wrong column in results box
* fftk/fftk_guiProcs.tcl 1.14 (changed +2 -2)
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| | 2012-04-16 | mayne | Fixed gridding issue with Dipole Weight when mode is set to SA in charge opt
* fftk/fftk_guiInterface.tcl 1.18 (changed +4 -2)
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