| Tags | Date | Developer | Last 200 Commit Logs |
|---|
| | 2024-04-22 | jasonks2 | 1 char typo in header area
* vnd/vnd_gui.tcl 1.28 (changed +2 -2)
|
| | 2024-03-07 | jasonks2 | Alignment Tool Part 1 is released! This feature includes 5 new functions that helps users select a population and align a morphological selection to any given input vector. Two new libraries, linear algebra (La) and Orient are added to the branch. Modifications to procedures ::NeuronVND::moveGraphs and ::NeuronVND::rotGraphs now allow a user to rotate and translate morphologies manually. This GUI tool can be accessed at the menubar under the tab “Analysis.
* vnd/vnd_gui.tcl 1.27 (changed +360 -24)
|
| | 2024-03-01 | johns | Applied old patch to allow VMD to accept pdbqt files from AutoDock that
have non-standard ENDBRANCH and ENDROOT records.
* molfile_plugin/src/readpdb.h 1.44 (changed +5 -1)
* molfile_plugin/src/pdbplugin.c 1.74 (changed +2 -2)
|
| | 2024-02-29 | jasonks2 | Fixed functionality for TreeView selector by adding a double click bind. Users can now double click a tree view element and have it pasted in the main entry box.
* vnd/vnd_gui.tcl 1.26 (changed +8 -2)
|
| | 2024-01-11 | gumbart | Added support for the quantum chemistry program Psi4, cranked version to 2.2
* fftk/pkgIndex.tcl 1.6 (changed +1 -1)
* fftk/fftk_guiProcs.tcl 1.50 (changed +13 -7)
* fftk/fftk_guiInterface.tcl 1.51 (changed +105 -83)
* fftk/fftk_SharedFcns.tcl 1.20 (changed +10 -7)
* fftk/fftk_QMPsi4.tcl 1.1 (added +2022 -0)
* fftk/fftk_QMORCA.tcl 1.5 (changed +13 -10)
* fftk/fftk_QMGaussian.tcl 1.4 (changed +14 -11)
* fftk/fftk_GeomOpt.tcl 1.12 (changed +9 -9)
* fftk/fftk_GenZMatrix.tcl 1.18 (changed +14 -14)
* fftk/fftk_GenDihScan.tcl 1.16 (changed +14 -15)
* fftk/fftk_GenBonded.tcl 1.21 (changed +17 -13)
* fftk/fftk_DihOpt.tcl 1.25 (changed +3 -1)
* fftk/fftk_Configuration.tcl 1.4 (changed +5 -1)
* fftk/fftk_ChargeOpt_ESP.tcl 1.3 (changed +13 -13)
* fftk/fftk_BuildPar.tcl 1.21 (changed +22 -1)
* fftk/fftk.tcl 1.17 (changed +4 -2)
* fftk/doc/index.html 1.22 (changed +2 -2)
* fftk/Makefile 1.10 (changed +2 -2)
|
| | 2023-12-14 | barryi | Added morpho_details query to cmd_query, to provide morpho coordinates (both original and moved) and per-node trans./rot. information to other procs. Aimed for now at principle axes and alignment work. See new procs: query_morpho_details_* and proto_calc_morph_* .
* vnd/vnd_read.tcl 1.40 (changed +144 -4)
|
| | 2023-11-02 | dgomes | Molefacture was not creating angles and dihedrals when a user decided not to use CGenFF.
* molefacture/molefacture_internals.tcl 1.58 (changed +2 -2)
|
| | 2023-11-02 | barryi | Morphology_line forced to width 1; progress bar working for drawing morpho styles see ::neuro::status_bar_processing_start; start of NWB file read
* vnd/vnd_read.tcl 1.38 (changed +88 -7)
Progress bars now "update" to update only Tk display (and not OpenGL). Removed tkcon printing workaround (which didn't work on Mac Tcl/TK 8.6)
* vnd/vnd_read.tcl 1.39 (changed +9 -15)
|
| | 2023-10-19 | barryi | Vnd_read.tcl: Per-node attribute reading, values queries, and searches are working. Searches can use comparators (lt,gt,eq) for doubles (i.e. numbers) and eq for string matches for strings (i.e. non-doubles), including wild-cards. NaNs are handled. See hash of dictionaries ::neuro::node_attrib_dictHash and procs ::neuro::hdf5_list_group_ns_attribs and ::neuro::sort_uniq_mixed_list. Geom searches (soma, morphology) now have eq, since soma x/y/z values listed in GUI browser. vnd_gui.tcl: Uses better sorting to display mixed number and non-number lists (calls ::neuro:::sort_uniq_mixed_list). Fixed bug with "existing selections" lists -- are again drawing data from correct field.
* vnd/vnd_read.tcl 1.37 (changed +152 -16)
* vnd/vnd_gui.tcl 1.25 (changed +6 -4)
|
| | 2023-10-16 | jasonks2 | Added new column to display non-virtual neurons present in each queryable selection. Added 1 menu entry for graphical Ruler to be initialized. Procs editted: createRepArgs, updateRepMenu, editRep, and delRep.
* vnd/vnd_gui.tcl 1.24 (changed +35 -11)
Added symbol for displaying ruler units in microns (greek mu). Checks toplevel gui for switching between angstroms (VMD) and microns (VND) units
* ruler/ruler.tcl 1.7 (changed +15 -3)
|
| | 2023-06-15 | mariano | Added raster plot analysis linked to spike activity
Initial version only colors by type, using same code as vnd_read
* vnd/vnd_gui.tcl 1.23 (changed +150 -13)
|
| | 2023-06-15 | barryi | Fixed bug with activity drawing - now draws requested material (e.g. Transparent)
* vnd/vnd_read.tcl 1.36 (changed +2 -1)
|
| | 2023-06-14 | jasonks2 | Added one proc, ::NeuronVND::loadAttributeData, which contains an attribute browser with double-click binds used to select and insert attribute names and values into the "Selected Neurons" entry field. Function is called in loadFiles region. Error is present in Linux and not on MacOS: attribute names don't appear when double clicked.
* vnd/vnd_gui.tcl 1.22 (changed +160 -5)
|
| | 2023-06-09 | mariano | Added code to proto_show_nodes variants to control GUI progress bar
* vnd/vnd_read.tcl 1.35 (changed +17 -5)
New movie making window
Fixed ffmpeg prompt errors
Revamped activity tab
New progess bar that triggers upon createRepArgs
Added new tabs for Jason's work
* vnd/vnd_gui.tcl 1.21 (changed +185 -93)
|
| | 2023-06-08 | barryi | Added "coordfile" procs for writing and reading special fle format for CrystalProteins 3D glass etching project. Fixed bugs when selecting numbering / named colors .
* vnd/vnd_read.tcl 1.29 (changed +132 -17)
Added proc for "exact" coordfile output (a proc for "exact" was not in previous commit). The small procedure change -- just just seting default_rad_scale 1 instead of 3 -- gives a more accurate represenation of swc data, but looks spindly onscreen. Really should implement both drect and exact styles as adjustable parameter -- these changes and parameter additions should in future be moved into standard onscreen morph drawing..
* vnd/vnd_read.tcl 1.32 (changed +56 -0)
Adjusted morphology draw style (proto_show_morph_moved_spheretube) so has same fixes / improvments as the special "coordfile" crystal-output rendering (proto_show_nodes_from_list_morpho_direct_ soma_coordfile).
* vnd/vnd_read.tcl 1.33 (changed +23 -16)
Extended coordfile format (for CrystalProteins 3D glass etching) to include
parent_is_soma and child_is_soma fields. Added improved/refined "direct" and
"exact" cooordfile writing procs -- best-loking for general corrdfile output is "direct"
(::neuro::proto_show_morph_moved_direct_soma_coordfile). Made fixes for morph
soma to use type instead of number field (etype vs en), which is proper use of
type field, and is also better since some .swc files break format rules and start with 0
instead of 1.
* vnd/vnd_read.tcl 1.31 (changed +319 -20)
Fixed bug-producing typo in cmd_query help
* vnd/vnd_read.tcl 1.34 (changed +0 -1)
Fixed coloring bug (work on laptop), suppressed some chatty status mesages during render. Starting in on work to make changes for Crystal Proteins glass etching of v1.
* vnd/vnd_read.tcl 1.28 (changed +16 -10)
Some fixes for for morph soma drawing.
* vnd/vnd_read.tcl 1.30 (changed +29 -14)
Width changes based on color. See morphology_draft_width_scale and morphology_width_scale. STL output has limited resolution (facets), may need to adopt conventional spheres until spheretube is fixed to use requested resolution, and STL output follows.
* vnd/vnd_read.tcl 1.27 (changed +40 -10)
|
| | 2023-05-17 | mariano | Removed an extra word left there since the last changes
* autopsf/autopsf.tcl 1.152 (changed +2 -2)
|
| | 2023-05-15 | mariano | Added explicit keyword to Freq option to provide forward compatibility with Gaussian 16
* fftk/fftk_QMGaussian.tcl 1.3 (changed +1 -1)
|
| | 2023-04-22 | johns | Added GROMACS tpr file reader plugin by Josh Vermaas
https://github.com/jvermaas/vmd-tprreader
The initial implementation has only been tested on single precision tpr files.
No alchemical changes were tested.
The files can't be made by a very old file generator.
GROMACS versions prior to 4.0 may be too old to load.
* molfile_plugin/src/tprplugin.h 1.1 (added +505 -0)
* molfile_plugin/src/tprplugin.C 1.1 (added +1139 -0)
* molfile_plugin/src/Gromacs.h 1.37 (changed +89 -2)
* molfile_plugin/Makefile 1.135 (changed +13 -4)
Updated to the latest colvars rev ffde432e48f88989d4d780e91dcd7dee19a94243
* cv_dashboard/cv_dashboard_main.tcl 1.10 (changed +1 -1)
|
| | 2023-04-21 | johns | Applied topotools bugfix update from Axel Kohlmeyer
* topotools/topotools.tcl 1.36 (changed +2 -2)
* topotools/topolammps.tcl 1.47 (changed +3 -3)
|
| | 2023-03-10 | mariano | Fixed bug with image rendering
* vnd/vnd_gui.tcl 1.20 (changed +2 -2)
|
| | 2023-03-09 | mariano | Added changes to compartment tab and created new movie control mode
* vnd/vnd_gui.tcl 1.19 (changed +192 -53)
|
| | 2023-03-08 | barryi | For vnd_read.tcl: Color scales now use VMD internal color scale methods. Added reading in user-defined attributes. Added: can do selection searching on user-defined attributes, including glob-style matching (*,?,\[ and \]) . Added: can query user-defined ("non-standard") and most required ("standard") node attributes. See query_node_list_attrib_values and the variable standard_node_attribs_queryable. Additions to cmd_query: non_standard_node_attribs, non_standard_node_attribs_by_fileset, node_list_attrib_values. Also: added special purpose movie making procs like: build_node_list . Need to update special-purpose-movie proc pop_name_extra_match_select list to use updated user-defined attributes directly. For vnd_gui.tcl: Fixed typo, added ::neuro:: to showError.
* vnd/vnd_read.tcl 1.26 (changed +527 -173)
* vnd/vnd_gui.tcl 1.18 (changed +2 -2)
|
| | 2022-12-15 | johns | Imported Colvars git rev 627e98d8b91901ae3a1a19a7522a290dc8fdd0e5
containing the latest updates from Giacomo and Jerome.
* cv_dashboard/cv_dashboard_main.tcl 1.9 (changed +16 -1)
* cv_dashboard/cv_dashboard_editor.tcl 1.4 (changed +2 -4)
* cv_dashboard/cv_dashboard.tcl 1.8 (changed +6 -5)
* cv_dashboard/README.md 1.4 (changed +4 -0)
|
| | 2022-11-24 | mariano | Added compartment page, similar to activity page
Extended render page, to include movie generation
Fixed some bugs regarding reset view
* vnd/vnd_gui.tcl 1.17 (changed +292 -47)
Added morphology_line style to cmd_mod_rep_node_fullsel
and removed the 'display resetview' from it.
Fixed a typo in show_compart_ranged
* vnd/vnd_read.tcl 1.25 (changed +5 -3)
|
| | 2022-11-06 | barryi | Fixes to properly read compartment segments assigned to each local node_id in a population. Start of procedures to find/display edge/synapse information during compartment activity display.
* vnd/vnd_read.tcl 1.24 (changed +169 -14)
|
| | 2022-11-02 | barryi | Added compartment-data related queries to cmd_query: compartment_data_min_max, compartment_time_ranges, compartment_var_names.
* vnd/vnd_read.tcl 1.23 (changed +86 -2)
Added procedures for loading, displaying, and animating compartment data.
Most relevant procs are: ::neuro::load_hdf5_compart_file, ::neuro::cmd_create_rep_compart_moment_selection_ranged, ::neuro::compart_animate_selection_render_ranged. For a future interactive slider/playnack controls, ::neuro::show_compart_moment_nodelist_ranged works with an existing molecule and existing sublist of globalNodeIdList.
* vnd/vnd_read.tcl 1.22 (changed +915 -24)
|
| | 2022-10-04 | johns | Applied Axel Kohlmeyer's patch to correct a typo in the signalproc plugin.
* signalproc/src/specden.c 1.2 (changed +17 -17)
Topotools plugin v1.9 from Axel Kohlmeyer
* topotools/topotools.tcl 1.35 (changed +27 -12)
* topotools/topolammps.tcl 1.46 (changed +398 -89)
* topotools/topogromacs.tcl 1.17 (changed +2 -1)
* topotools/pkgIndex.tcl 1.12 (changed +1 -1)
* topotools/doc/index.html 1.24 (changed +8 -8)
* topotools/Makefile 1.18 (changed +1 -1)
Updated with latest rev of qwikfold from Diego Gomes and Rafael Bernardi
* qwikfold/qwikfold_settings.tcl 1.2 (changed +36 -44)
* qwikfold/qwikfold_sanity_checks.tcl 1.2 (changed +4 -40)
* qwikfold/qwikfold_notebook.tcl 1.2 (changed +268 -89)
* qwikfold/qwikfold_menubar.tcl 1.2 (changed +5 -4)
* qwikfold/qwikfold_functions.tcl 1.2 (changed +82 -25)
* qwikfold/qwikfold.tcl 1.2 (changed +24 -22)
* qwikfold/pkgIndex.tcl 1.2 (changed +1 -1)
* qwikfold/Makefile 1.2 (changed +1 -1)
|
| | 2022-07-22 | mariano | Fixed color assigment in spike method
* vnd/vnd_read.tcl 1.21 (changed +5 -5)
Workaround to fix the different display origin between general reps and activity reps
* vnd/vnd_gui.tcl 1.16 (changed +5 -1)
|
| | 2022-07-22 | barryi | Changed spikeEnd in GUI from 1800 to 3000, to accomodate animation of datasets with bigger timestamps.
* vnd/vnd_gui.tcl 1.15 (changed +2 -2)
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| | 2022-07-21 | mariano | Added morphology_draft to spike and added larger spikewaittime
* vnd/vnd_gui.tcl 1.14 (changed +3 -3)
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| | 2022-07-21 | barryi | Now properly using VND global node id, instead of model population node_id, in show_spike_pop_moment_from_list.
* vnd/vnd_read.tcl 1.20 (changed +3 -1)
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| | 2022-07-20 | mariano | Removed scale by command from reset view and cmd_mod_rep_node_fullsel
* vnd/vnd_read.tcl 1.18 (changed +2 -2)
* vnd/vnd_gui.tcl 1.12 (changed +2 -2)
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| | 2022-07-20 | barryi | Removed more 'scale by' commands; they are no longer needed in general display procs now that bounds are working for reset view. Changed morphology-related style names -- Previously: morphology (displays disconnected spheres) and morpology_spheretubes (displays connected spheretubes) Now, respectively: morphology_draft (displays disconnected spheres) and morphology (displays connected spheretubes).
In GUI, changed value in representation style combobox to accomodate new morphology_draft name.
* vnd/vnd_read.tcl 1.19 (changed +12 -10)
* vnd/vnd_gui.tcl 1.13 (changed +2 -2)
|
| | 2022-07-19 | mariano | Fixes to GUI spacing, connectivity styles, and object draw
* vnd/vnd_gui.tcl 1.11 (changed +22 -15)
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| | 2022-07-19 | barryi | Changed soma-only drawing from spheretubes to traditional spheres. A workaround to allow proper bounds checking for display resevtview. It looks like VND/VMD is not currently accounting for spheretubes (at least multiple solo spheres with with drawtubes 0) in the MoleculeGraphics::find_bounds check.
* vnd/vnd_read.tcl 1.17 (changed +3 -1)
|
| | 2022-07-18 | barryi | Fixed bug that would read in a population N times if it had N groups. Was hard to notice visually, since led to creation of overlaid objects.
* vnd/vnd_read.tcl 1.16 (changed +3 -6)
|
| | 2022-07-14 | mariano | Added 'reset VND' option in File menu
for that I reshuffle some of the variable definitions into 'initialize' proc
Added new implementation of edit rep with new cmd_mod proc in vnd_read.tcl
Fixed some issues that came during the tutorial preparation
Added morphology_spheretube style
* vnd/vnd_gui.tcl 1.9 (changed +185 -102)
Added proc cmd_mod_rep_node_fullsel based on cmd_create...
that works with the GUI to edit reps and keep the same
mol id and rep id in nrepList
eventually we would want to replace this or collapse it
to the cmd_create, but the previous implementation for
edit rep had bugs in the rep order and this fixes that.
* vnd/vnd_read.tcl 1.15 (changed +67 -1)
Updated system query for num_neurons to num_neurons_non_virtual
* vnd/vnd_gui.tcl 1.10 (changed +2 -2)
|
| | 2022-07-13 | mariano | Fixed issue with lreplace in cmd_show_rep and cmd_hide_rep
original code was not updating the variable 'shown' in nrepList
cause issues with the save/load visualization state
* vnd/vnd_read.tcl 1.14 (changed +4 -3)
|
| | 2022-07-13 | barryi | Added ability to control if a new nrep includes virtuals (neurons with model_type == "virtual", set from their type). Also added whole-system queries num_neurons_non_virtual, num_nodes_non_virtual (synonyms). Details: When cmd_create_rep_node_fullsel is called, if the namespace-wide variable ::neuro::display_virtuals_at_creation is True, the rep will contain the virtuals. If False, the rep will not contain the virtuals. The nRepList entry for this nrep will contain num_neurons that reflects whether virtuals are included. A new flag has been added to each nRepList entry: displayed_virtuals_at_creation. For edge nreps, virtuals for source/target are for now always included, and displayed_virtuals_at_creation is always True,
* vnd/vnd_read.tcl 1.13 (changed +100 -33)
|
| | 2022-07-11 | barryi | Fixed bug: had failed to load system if no morphologies directory was defined. Not defining morphologies_dir is acceptable in SONATA for systems with no morphologies.
* vnd/vnd_read.tcl 1.12 (changed +7 -2)
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| | 2022-07-06 | barryi | Fixed bug that showed giant soma for morphology_spherertube. Corrected single-element morphology section list assignemnt, so that section ID starts -- properrly, by SWC format -- at 1 instead of 0. Works with checks elsewhere that expect 1.
* vnd/vnd_read.tcl 1.11 (changed +9 -5)
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| | 2022-07-05 | johns | Added Axel Kohlmeyer's plugin for YAML format LAMMPS dump files.
* molfile_plugin/Makefile 1.134 (changed +13 -4)
Added Axel Kohlmeyer's plugin for YAML format LAMMPS dumps
* molfile_plugin/src/lammpsyamlplugin.c 1.1 (added +1702 -0)
Added Axel Kohlmeyer's plugin for YAML formatted LAMMPS dump files.
* molfile_plugin/doc/lammpsyamlplugin.html 1.1 (added +101 -0)
* molfile_plugin/doc/lammpsplugin.html 1.8 (changed +81 -57)
* molfile_plugin/doc/index.html 1.61 (changed +1 -0)
Bug fix from Axel.
* molfile_plugin/src/lammpsplugin.c 1.51 (changed +29 -25)
Imported Axel Kohlmeyer's latest LAMMPS plugin.
* molfile_plugin/src/lammpsplugin.c 1.50 (changed +157 -125)
Updated blast minor version after Sam Knight's Tk GUI revision.
* blast/pkgIndex.tcl 1.4 (changed +1 -1)
* blast/blast_resultviewer.tcl 1.9 (changed +2 -2)
* blast/blast.tcl 1.9 (changed +2 -2)
* blast/Makefile 1.4 (changed +1 -1)
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| | 2022-07-04 | johns | Sam Knight's rewrite of the APBSRun Tk GUI to eliminate conflicting uses
of the "pack" and "grid" layout managers, which had been (illegally) mixed.
The new implementation uses only grid, and is therefore compatible Tcl/Tk
8.6.x versions that no longer tolerate mixing of layout managers.
* apbsrun/apbsrun.tcl 1.138 (changed +364 -343)
Sam Knight's rewrite of the RMSD Tk GUI to eliminate conflicting uses
of the "pack" and "grid" layout managers, which had been (illegally) mixed.
The new implementation uses only grid, and is therefore compatible Tcl/Tk
8.6.x versions that no longer tolerate mixing of layout managers.
* rmsd/rmsd.tcl 1.8 (changed +95 -50)
Sam Knight's rewrite of the RMSDTT Tk GUI to eliminate conflicting uses
of the "pack" and "grid" layout managers, which had been (illegally) mixed.
The new implementation uses only grid, and is therefore compatible Tcl/Tk
8.6.x versions that no longer tolerate mixing of layout managers.
* rmsdtt/rmsdtt.tcl 1.9 (changed +246 -147)
Sam Knight's rewrite of the RMSDVT Tk GUI to eliminate conflicting uses
of the "pack" and "grid" layout managers, which had been (illegally) mixed.
The new implementation uses only grid, and is therefore compatible Tcl/Tk
8.6.x versions that no longer tolerate mixing of layout managers.
* rmsdvt/rmsdvt-gui.tcl 1.7 (changed +229 -221)
Sam Knight's rewritten BLAST result viewer Tk GUI eliminates conflicting uses
of the "pack" and "grid" layout managers, which had been (illegally) mixed.
The new implementation uses only grid, and is therefore compatible Tcl/Tk
8.6.x versions that no longer tolerate mixing of layout managers.
* blast/blast_resultviewer.tcl 1.8 (changed +112 -99)
Second revision of Sam's Tk GUI rewrite using "grid" to more closely
match a few of the original "pack" based widget layouts.
* rmsdtt/rmsdtt.tcl 1.10 (changed +13 -10)
Updated apbsrun minor version after Sam Knight's Tk GUI revision.
* apbsrun/pkgIndex.tcl 1.7 (changed +1 -1)
* apbsrun/doc/index.html 1.26 (changed +1 -1)
* apbsrun/apbsrun.tcl 1.139 (changed +2 -2)
* apbsrun/Makefile 1.9 (changed +1 -1)
Updated rmsd tool minor version after Sam Knight's Tk GUI revision.
* rmsd/rmsd.tcl 1.9 (changed +2 -2)
* rmsd/pkgIndex.tcl 1.2 (changed +1 -1)
* rmsd/doc/index.html 1.3 (changed +1 -1)
* rmsd/Makefile 1.5 (changed +1 -1)
Updated rmsdtt minor version after Sam Knight's Tk GUI revision.
* rmsdtt/rmsdtt.tcl 1.11 (changed +4 -4)
* rmsdtt/pkgIndex.tcl 1.4 (changed +1 -1)
* rmsdtt/Makefile 1.3 (changed +1 -1)
Updated rmsdvt minor version after Sam Knight's Tk GUI revision.
* rmsdvt/rmsdvt.tcl 1.5 (changed +3 -3)
* rmsdvt/rmsdvt-gui.tcl 1.8 (changed +3 -3)
* rmsdvt/pkgIndex.tcl 1.2 (changed +1 -1)
* rmsdvt/Makefile 1.2 (changed +1 -1)
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| | 2022-06-29 | mariano | Added "Stop rotation"
* vnd/vnd_gui.tcl 1.8 (changed +2 -1)
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| | 2022-06-09 | barryi | Added ability to use spheretubes for morphology drawing, so morphologies don't appear as disconnected groups of spheres at close inspection. For now, uses special style morphology_spheretube for node and spike animation cmd_create commands. Drawing spheretubes for now as lower-performance pairs of points and over-drawing; in future should draw as complete sections (chains of connected points, between bifurcations and end points.
* vnd/vnd_read.tcl 1.10 (changed +167 -1)
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| | 2022-05-28 | mariano | New activity tab with animation controls
for play, pause, step, speed and window
* vnd/vnd_gui.tcl 1.7 (changed +260 -22)
* vnd/playback.gif 1.1 (added +7 -0)
* vnd/play.gif 1.1 (added +7 -0)
* vnd/pause.gif 1.1 (added +8 -0)
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| | 2022-05-20 | mariano | Changed pack to grid to fix issue with newer tcl
* dipwatch/dipwatch.tcl 1.7 (changed +27 -13)
|
| | 2022-05-05 | barryi | Loading and displaying spike time series for populations is added. load_hdf5_edge_file_pair , cmd_show_spike_pop_seqeunce_from_fullsel, and show_spike_pop_moment_from_list are relevant procs for loading, showing a fixed animation onscreen with parameters, and showing a "moment" of the series.The moments are the basis for current fixed onscreen animation but can be used for interactive animation, movie making, and similar. The zoomscale parameter for cmd_show_spike_pop_seqeunce_from_fullsel is a hack - should be replaced with good control of scaling when drawing multiple molecs (nreps). Also: reading virtual attribute for nodes.
* vnd/vnd_read.tcl 1.9 (changed +199 -47)
|
| | 2022-04-27 | johns | Added additional safety checks in psfgen topo_mol_get_atom() to prevent
psfgen from attempting to dereference residue atomArray[]->name strings
for NULL atoms. The same safety checks are used in similar loops
elsewhere, so hopefully Joao's "NEWPSFGEN" code will behave correctly
with fallthrough after the residue atom loop terminates.
* psfgen/src/topo_mol.c 1.70 (changed +5 -2)
Force-clear psfgen context/handle data structures during allocations,
by using calloc() rather than malloc.
* psfgen/src/tcl_psfgen.c 1.93 (changed +6 -4)
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| | 2022-04-26 | johns | Add NETCDFDYNAMIC flag for all Mac builds.
* build.csh 1.149 (changed +2 -0)
Updated the MacOS X plugin builds to build against libnetcdf.dylib
* build.csh 1.148 (changed +6 -4)
|
| | 2022-04-25 | mariano | Initial version of connectivity GUI
Replaced createRepArgs code to avoid issue with '-' in selections
* vnd/vnd_gui.tcl 1.6 (changed +97 -40)
|
| | 2022-04-25 | johns | Added example colvars scripts organized as single file script collections
* cv_dashboard/templates/other.colvars 1.1 (added +25 -0)
* cv_dashboard/templates/component.colvars 1.1 (added +242 -0)
* cv_dashboard/templates/colvar.colvars 1.1 (added +149 -0)
* cv_dashboard/templates/bias.colvars 1.1 (added +143 -0)
Deleted
* cv_dashboard/templates/other/moving_frame_of_reference.in 1.3 (removed +0 -25)
Remove old template files
* cv_dashboard/templates/colvar/extended-Lagrangian_colvar.in 1.2 (removed +0 -36)
* cv_dashboard/templates/colvar/colvar_with_many_parameters.in 1.2 (removed +0 -37)
* cv_dashboard/templates/colvar/colvar_with_analysis.in 1.2 (removed +0 -38)
* cv_dashboard/templates/colvar/basic_colvar.in 1.2 (removed +0 -20)
* cv_dashboard/templates/colvar/DBC_ligand_RMSD.in 1.3 (removed +0 -33)
Removed old templates.
* cv_dashboard/templates/component/tilt.in 1.2 (removed +0 -13)
* cv_dashboard/templates/component/spinAngle.in 1.2 (removed +0 -13)
* cv_dashboard/templates/component/selfCoordNum.in 1.2 (removed +0 -11)
* cv_dashboard/templates/component/rmsd.in 1.2 (removed +0 -12)
* cv_dashboard/templates/component/orientation.in 1.3 (removed +0 -20)
* cv_dashboard/templates/component/mapTotal.in 1.2 (removed +0 -11)
* cv_dashboard/templates/component/inertia.in 1.2 (removed +0 -11)
* cv_dashboard/templates/component/hbond.in 1.2 (removed +0 -11)
* cv_dashboard/templates/component/gyration.in 1.2 (removed +0 -11)
* cv_dashboard/templates/component/groupCoord.in 1.2 (removed +0 -15)
* cv_dashboard/templates/component/distancedir.in 1.2 (removed +0 -13)
* cv_dashboard/templates/component/distanceZ.in 1.2 (removed +0 -16)
* cv_dashboard/templates/component/distanceXY.in 1.2 (removed +0 -16)
* cv_dashboard/templates/component/distanceVec.in 1.2 (removed +0 -14)
* cv_dashboard/templates/component/distancePairs.in 1.2 (removed +0 -14)
* cv_dashboard/templates/component/distanceInv.in 1.2 (removed +0 -15)
* cv_dashboard/templates/component/distance.in 1.2 (removed +0 -13)
* cv_dashboard/templates/component/dipoleMagnitude.in 1.2 (removed +0 -10)
* cv_dashboard/templates/component/dipoleAngle.in 1.2 (removed +0 -16)
* cv_dashboard/templates/component/dihedralPC.in 1.2 (removed +0 -12)
* cv_dashboard/templates/component/dihedral.in 1.2 (removed +0 -19)
* cv_dashboard/templates/component/coordNum.in 1.2 (removed +0 -20)
* cv_dashboard/templates/component/angle.in 1.2 (removed +0 -17)
Updated to latest colvars template structure
* cv_dashboard/cv_dashboard.tcl 1.7 (changed +1 -1)
|
| | 2022-04-21 | barryi | Edge rendering now includes morphology target (efferent) information for swc files (later add source (afferent) swc info if this is ever used by files). To display, use one of the following new edge style of cmd_create_rep_source_target_edges_fullsel: simple_edge_swc, source_sphere_swc, target_sphere_swc, source_target_sphere_swc.
* vnd/vnd_read.tcl 1.8 (changed +139 -36)
|
| | 2022-04-15 | johns | Updated to colvars main 948003965f79c7266e5e7da39156cf8f1b4c59fe
* cv_dashboard/pkgIndex.tcl 1.3 (changed +1 -1)
* cv_dashboard/cv_dashboard_settings.tcl 1.2 (changed +51 -41)
* cv_dashboard/cv_dashboard_plots.tcl 1.3 (changed +245 -17)
* cv_dashboard/cv_dashboard_main.tcl 1.8 (changed +712 -209)
* cv_dashboard/cv_dashboard_editor.tcl 1.3 (changed +517 -96)
* cv_dashboard/cv_dashboard.tcl 1.6 (changed +357 -65)
* cv_dashboard/README.md 1.3 (changed +24 -42)
* cv_dashboard/Makefile 1.5 (changed +1 -1)
|
| | 2022-03-29 | barryi | Added piecewise file reading, using for edge files. Now can read large files like v1 without crashing. See new procs hdf5_piecewise_dataset and hdf5_simple_dataset_range. Also: turned off some list sorting not currently needed; now handling "indicies" edge subgroup spelling variant the same as special, optional "indices" edge subgroups -- which for now remains ignoring these subgroups.
* vnd/vnd_read.tcl 1.7 (changed +112 -6)
|
| | 2022-03-28 | barryi | Made edge searching faster (4.04x speedup for a layer 4 model test). Now creates globalEdgeDataList and does a round of list-based searching. Also made help message for queries more polite.
* vnd/vnd_read.tcl 1.6 (changed +67 -18)
|
| | 2022-03-25 | mariano | Initial version of tree view with button to create example rep containing one selection
* vnd/vnd_gui.tcl 1.4 (changed +81 -27)
Replaced call to cmd_create_rep for cmd_create_rep_node_fullsel
that allows more complex selection syntax and adjusted the tree view
example rep creation to include the full selection
* vnd/vnd_gui.tcl 1.5 (changed +5 -18)
|
| | 2022-03-24 | barryi | Added full selection strings (logic and parenthesis) and edge searches. Can a) make a nodes rep from one full selection string b) make an edges (connections) rep from two node selection strings. See new procs cmd_create_rep_node_fullsel, cmd_create_rep_source_target_edges_fullsel. Edge source is in edges_source_nodes_target_nodes . Parser uses tokenize_sel_string and shunting_yard and some utility stack and queue procs. Also, extented some selections so == takes a list of numbers.
* vnd/vnd_read.tcl 1.5 (changed +632 -67)
|
| | 2022-03-01 | mariano | Added tree view GUI to information section
works with current cmd_query commands
missing functionality of 'Query' and
possible automatic rep generation with
toggle button
* vnd/vnd_gui.tcl 1.3 (changed +47 -13)
|
| | 2022-03-01 | barryi | Fixed a variable change that had broken several _select functions. Also, fixed an incorrect response to some kinds of error in selection string when creating rep based on a selection: no longer attempts to draw nonexistent node -1.
* vnd/vnd_read.tcl 1.4 (changed +40 -31)
|
| | 2022-02-27 | barryi | Added several queries to ::neuro::cmd_query, including node_types_in_group FILESET POPULATION GROUP. Fixed an error that was resetting globalEdgeIdCount for each pop read in. Fixed bugs with node vs edge variables.
* vnd/vnd_read.tcl 1.3 (changed +167 -84)
|
| | 2022-02-17 | barryi | Now reading in edges (i.e. neuron connections). Current default is to not read edges, since large (GB-scale) edge files can cause memory problems and crashes. To load edges: when calling cmd_load_model_config_file, set reading_edges param to True. Added cartesian Boolean property to nodes, True for nodes with any x,y,z coords. There are no longer skipped groups when loading. See ::neuro::initVars for new namespace variables edge(), globalEdgeIdList, edge_pop_hash, and more. Can now do simple straight-cylinder edge drawing with ::neuro::proto_show_edges_from_list. Need to add edge-oriented (less vitally, cartesian-status-oriented) query and selection commands.
* vnd/vnd_read.tcl 1.2 (changed +689 -201)
|
| | 2022-02-16 | mariano | Unified createRepArgs procs and revamped syntax for args
Fixed multiple bugs with Representations table
Improved updateRepMenu, editRep and delRep
* vnd/vnd_gui.tcl 1.2 (changed +103 -105)
|
| | 2022-02-13 | gumbart | Fixed small bug I introduced when sel2 isn't present.
* hbonds/hbonds.tcl 1.11 (changed +4 -2)
|
| | 2022-02-09 | johns | Added vnd to the build.
* Makefile 1.150 (changed +2 -1)
|
| | 2022-02-08 | johns | Added "vnd" (a neuroscience visualization GUI and associated
back-end data parsing, selection, and storage code) to the plugin tree.
* vnd/vnd_read.tcl 1.1 (added +3590 -0)
* vnd/vnd_gui.tcl 1.1 (added +1117 -0)
* vnd/pkgIndex.tcl 1.1 (added +16 -0)
* vnd/Makefile 1.1 (added +22 -0)
Added placeholder doc
* vnd/doc/index.html 1.1 (added +13 -0)
|
| | 2022-01-20 | mariano | First fix for pack/grid issue with TCL8.6
in the calculation menu
* timeline/timeline.tcl 1.101 (changed +17 -17)
|
| | 2021-12-12 | johns | Added qwikfold to the build
* Makefile 1.149 (changed +2 -1)
|
| | 2021-12-10 | johns | Updated plumed plugin to version 2.8
* plumed/vmdplumed.tcl 1.12 (changed +22 -21)
* plumed/templates_list_vmdcv.tcl 1.3 (changed +1 -1)
* plumed/templates_list_v2.tcl 1.4 (changed +245 -122)
* plumed/templates_list_v1.tcl 1.8 (changed +1 -1)
* plumed/pkgIndex.tcl 1.9 (changed +1 -1)
* plumed/Makefile 1.10 (changed +1 -1)
Updated to Plumed plugin version 2.8
* plumed/doc/INSTALL-PLUMED-FIRST.md 1.3 (changed +25 -12)
* plumed/doc/ChangeLog 1.5 (changed +4 -0)
* plumed/doc/CITATION.md 1.2 (changed +6 -4)
|
| | 2021-12-03 | mariano | Changed pack calls to grid
* multiseq/stamp_options.tcl 1.7 (changed +20 -11)
* multiseq/select_residues.tcl 1.7 (changed +17 -9)
* multiseq/select_contactshell.tcl 1.6 (changed +15 -8)
* multiseq/plot.tcl 1.7 (changed +17 -10)
* multiseq/phylotree_options.tcl 1.8 (changed +13 -7)
* multiseq/multiseq.tcl 1.39 (changed +31 -15)
* multiseq/import_options.tcl 1.9 (changed +17 -9)
* multiseq/get_input.tcl 1.6 (changed +11 -6)
* multiseq/find.tcl 1.6 (changed +15 -8)
* multiseq/export_options.tcl 1.7 (changed +15 -8)
|
| | 2021-12-03 | johns | Added QwikFold 0.7 to the tree for the time being.
* qwikfold/qwikfold_settings.tcl 1.1 (added +307 -0)
* qwikfold/qwikfold_sanity_checks.tcl 1.1 (added +181 -0)
* qwikfold/qwikfold_notebook.tcl 1.1 (added +142 -0)
* qwikfold/qwikfold_menubar.tcl 1.1 (added +28 -0)
* qwikfold/qwikfold_functions.tcl 1.1 (added +623 -0)
* qwikfold/qwikfold.tcl 1.1 (added +135 -0)
* qwikfold/python/pae.py 1.1 (added +22 -0)
* qwikfold/python/lddt.py 1.1 (added +22 -0)
* qwikfold/python/distogram.py 1.1 (added +22 -0)
* qwikfold/python/coverage.py 1.1 (added +41 -0)
* qwikfold/python/convert.py 1.1 (added +13 -0)
* qwikfold/python/contact.py 1.1 (added +24 -0)
* qwikfold/pkgIndex.tcl 1.1 (added +21 -0)
* qwikfold/patches/run_alphafold.py.patch 1.1 (added +38 -0)
* qwikfold/patches/residue_constants.py.patch 1.1 (added +21 -0)
* qwikfold/patches/amber_minimize.py.patch 1.1 (added +25 -0)
* qwikfold/examples/ubiquitin.fasta 1.1 (added +7 -0)
* qwikfold/examples/dimer.fasta 1.1 (added +9 -0)
* qwikfold/examples/adhesin.fasta 1.1 (added +19 -0)
* qwikfold/examples/T1050.fasta 1.1 (added +7 -0)
* qwikfold/examples/20ala.fasta 1.1 (added +8 -0)
* qwikfold/examples/10ala.fasta 1.1 (added +8 -0)
* qwikfold/doc/index.html 1.1 (added +241 -0)
* qwikfold/Makefile 1.1 (added +22 -0)
Sync with colvars git version 6d97a4339092d4f04f0dee0bf91c66cafc3bc406
* cv_dashboard/cv_dashboard_main.tcl 1.7 (changed +2 -2)
* cv_dashboard/cv_dashboard_display.tcl 1.3 (changed +2 -2)
|
| | 2021-12-02 | johns | Updated list of environment variables.
* doc/plg_compiling.dox 1.8 (changed +15 -2)
|
| | 2021-11-19 | mariano | Changes pack to grid geometry manager to be compatible with plugins
that use multiplot embed in new TCL 8.6
Checked plugins that use 'multiplot embed':
QwikMD, QMtool, FFTK and MDFF
Only QwikMD and QMtool required fixes
* multiplot/multiplot.tcl 1.44 (changed +8 -8)
Fixed multiplot embed column order
* qwikmd/qwikmd.tcl 1.85 (changed +3 -3)
Fixed pack/grid issue when calling multiplot embed
* qmtool/qmtool_analysis.tcl 1.13 (changed +10 -5)
|
| | 2021-11-17 | mariano | Added error check for empty molecule in element combobox selection
* molefacture/molefacture_gui.tcl 1.76 (changed +9 -1)
|
| | 2021-10-07 | johns | Updated to Colvars version 1f1c3c32dcd2cf9fba9457514ce63bf284271fa9
* cv_dashboard/templates/other/moving_frame_of_reference.in 1.2 (changed +2 -2)
* cv_dashboard/templates/component/orientation.in 1.2 (changed +2 -2)
* cv_dashboard/templates/colvar/DBC_ligand_RMSD.in 1.2 (changed +4 -4)
* cv_dashboard/cv_dashboard_main.tcl 1.6 (changed +65 -4)
* cv_dashboard/cv_dashboard_display.tcl 1.2 (changed +1 -1)
* cv_dashboard/cv_dashboard.tcl 1.5 (changed +7 -0)
* cv_dashboard/Makefile 1.4 (changed +1 -1)
|
| | 2021-09-21 | jim | Fix readmol for billion-atom systems.
* psfgen/src/topo_mol_pluginio.c 1.62 (changed +18 -18)
|
| | 2021-09-16 | johns | Applied JC Gumbart's patch to correct the hbond analysis plugin to
correctly handle cases where segnames aren't set, and to handle cases
where multiple chains occur across selections.
* hbonds/pkgIndex.tcl 1.4 (changed +1 -1)
* hbonds/hbonds.tcl 1.10 (changed +33 -14)
* hbonds/Makefile 1.4 (changed +1 -1)
|
| | 2021-08-26 | johns | Applied Michael Quevillon's patch to make tinker structure parsing work
with or without box information lines, using the same scheme we use in the
timestep parsing code.
* molfile_plugin/src/tinkerplugin.c 1.16 (changed +19 -10)
|
| | 2021-07-18 | gumbart | Fixed bug when LP section is present but empty in PSF file
* fftk/fftk_SharedFcns.tcl 1.19 (changed +6 -2)
|
| | 2021-04-07 | mariano | Added independent editplot GUI, called from a new 'edit' menubar button
Minor changes to plot's namespace variables to accomodate for added
functionality in plot customization (e.g. titlefontsize)
Added prototype proc to draw grid lines
* multiplot/multiplot.tcl 1.42 (changed +696 -46)
|
| | 2021-03-10 | johns | Ensure that the PsfAtom constructors clear all of the string fields
completely prior to using them.
* autopsf/src/psfatom.C 1.15 (changed +14 -5)
Prevent ouf-of-bounds write of NUL string termination character
if the length of inres is longer than the capacity of the resname
string buffer. By clearing with memset first, we guarantee that the
string will be terminated. This is a likely cause of some of the
crash/hang behaviors recently observed with autopsf.
* autopsf/src/psfres.h 1.9 (changed +1 -5)
Wholesale cleanup of bad code formatting caused by the use of tabs
* autopsf/src/psftypelist.h 1.2 (changed +15 -18)
* autopsf/src/psftypelist.C 1.3 (changed +18 -15)
* autopsf/src/psftype.h 1.2 (changed +20 -27)
* autopsf/src/psftype.C 1.4 (changed +51 -44)
* autopsf/src/psfreslist.h 1.4 (changed +18 -21)
* autopsf/src/psfreslist.C 1.6 (changed +18 -15)
* autopsf/src/psfres.h 1.8 (changed +42 -51)
* autopsf/src/psfres.C 1.9 (changed +57 -43)
* autopsf/src/psfcheck.C 1.25 (changed +280 -268)
* autopsf/src/psfbond.h 1.2 (changed +17 -23)
* autopsf/src/psfbond.C 1.3 (changed +24 -23)
* autopsf/src/psfatomlist.h 1.4 (changed +0 -2)
* autopsf/src/psfatomlist.C 1.3 (changed +17 -17)
* autopsf/src/psfatom.h 1.10 (changed +23 -36)
* autopsf/src/psfatom.C 1.14 (changed +57 -57)
|
| | 2021-03-08 | johns | Corrected typo in tablelist distribution macros
* tablelist/Makefile 1.5 (changed +1 -1)
|
| | 2021-03-06 | johns | Synced with colvars git master.
* cv_dashboard/cv_dashboard_main.tcl 1.5 (changed +4 -4)
|
| | 2021-01-29 | dhardy | Fix compile issue on MacOSX
Clang complained about missing prototype for newhandle_msg_ex().
* psfgen/src/tcl_psfgen.c 1.92 (changed +2 -1)
|
| | 2021-01-28 | johns | Updated to Tcl/Tk tablelist package version 6.11
* tablelist/tablelist_tile.tcl 1.2 (changed +3 -4)
* tablelist/tablelistCommon.tcl 1.1 (added +107 -0)
* tablelist/tablelist.tcl 1.2 (changed +3 -4)
* tablelist/scripts/utils/scaleutilMisc.tcl 1.1 (added +712 -0)
* tablelist/scripts/utils/scaleutil.tcl 1.1 (added +422 -0)
* tablelist/scripts/utils/pkgIndex.tcl 1.1 (added +16 -0)
* tablelist/scripts/utils/mwutil.tcl 1.1 (added +657 -0)
* tablelist/scripts/tclIndex 1.2 (changed +331 -168)
* tablelist/scripts/tablelistWidget.tcl 1.2 (changed +3562 -1196)
* tablelist/scripts/tablelistUtil.tcl 1.2 (changed +2017 -625)
* tablelist/scripts/tablelistThemes.tcl 1.2 (changed +716 -365)
* tablelist/scripts/tablelistSort.tcl 1.2 (changed +56 -40)
* tablelist/scripts/tablelistMove.tcl 1.2 (changed +53 -88)
* tablelist/scripts/tablelistImages.tcl 1.2 (changed +2337 -1448)
* tablelist/scripts/tablelistEdit.tcl 1.2 (changed +512 -354)
* tablelist/scripts/tablelistConfig.tcl 1.2 (changed +621 -337)
* tablelist/scripts/tablelistBind.tcl 1.2 (changed +1424 -372)
* tablelist/scripts/repair.tcl 1.2 (changed +1 -1)
* tablelist/pkgIndex.tcl 1.2 (changed +9 -10)
* tablelist/doc/yuyo.png 1.1 (added +11 -0)
* tablelist/doc/winxpSilver.png 1.2 (changed binary)
* tablelist/doc/winxpOlive.png 1.2 (changed binary)
* tablelist/doc/winxpBlue.png 1.2 (changed binary)
* tablelist/doc/winnative.png 1.2 (changed binary)
* tablelist/doc/win7Classic.png 1.2 (changed binary)
* tablelist/doc/win7Aero.png 1.2 (changed binary)
* tablelist/doc/win10.png 1.1 (added +10 -0)
* tablelist/doc/white200.png 1.1 (added +15 -0)
* tablelist/doc/white175.png 1.1 (added +16 -0)
* tablelist/doc/white150.png 1.1 (added +12 -0)
* tablelist/doc/white125.png 1.1 (added +13 -0)
* tablelist/doc/white100.png 1.1 (added +12 -0)
* tablelist/doc/vistaClassic.png 1.2 (changed binary)
* tablelist/doc/vistaAero.png 1.2 (changed binary)
* tablelist/doc/ubuntuMate.png 1.1 (added +10 -0)
* tablelist/doc/ubuntu3.png 1.1 (added +15 -0)
* tablelist/doc/ubuntu2.png 1.1 (added +13 -0)
* tablelist/doc/tileWidgets.png 1.2 (changed binary)
* tablelist/doc/tablelistWidget.html 1.2 (changed +3855 -1494)
* tablelist/doc/tablelistTkCore.html 1.2 (changed +20 -5)
* tablelist/doc/tablelistTile.html 1.2 (changed +43 -18)
* tablelist/doc/tablelistThemes.html 1.2 (changed +64 -20)
* tablelist/doc/tablelistMentry.html 1.2 (changed +30 -21)
* tablelist/doc/tablelistIwidgets.html 1.2 (changed +24 -8)
* tablelist/doc/tablelistCtext.html 1.2 (changed +10 -6)
* tablelist/doc/tablelistCombobox.html 1.2 (changed +11 -2)
* tablelist/doc/tablelistColSort.html 1.2 (changed +7 -2)
* tablelist/doc/tablelistBinding.html 1.2 (changed +89 -16)
* tablelist/doc/tablelistBWidget.html 1.2 (changed +14 -3)
* tablelist/doc/tablelist.html 1.2 (changed +768 -438)
* tablelist/doc/stylesheet.css 1.2 (changed +12 -3)
* tablelist/doc/styles.png 1.2 (changed binary)
* tablelist/doc/scrollbars.png 1.1 (added +18 -0)
* tablelist/doc/radiance.png 1.2 (changed binary)
* tablelist/doc/plastique.png 1.2 (changed binary)
* tablelist/doc/plastik.png 1.2 (changed binary)
* tablelist/doc/plain200.png 1.1 (added +19 -0)
* tablelist/doc/plain175.png 1.1 (added +15 -0)
* tablelist/doc/plain150.png 1.1 (added +11 -0)
* tablelist/doc/plain125.png 1.1 (added +12 -0)
* tablelist/doc/plain100.png 1.1 (added +10 -0)
* tablelist/doc/phase.png 1.2 (changed binary)
* tablelist/doc/oxygen2.png 1.2 (changed binary)
* tablelist/doc/oxygen1.png 1.2 (changed binary)
* tablelist/doc/newWave.png 1.2 (changed binary)
* tablelist/doc/mint2.png 1.1 (added +9 -0)
* tablelist/doc/mint.png 1.2 (changed binary)
* tablelist/doc/menta.png 1.1 (added +14 -0)
* tablelist/doc/mate.png 1.2 (changed binary)
* tablelist/doc/klearlooks.png 1.2 (changed binary)
* tablelist/doc/index.html 1.2 (changed +7 -6)
* tablelist/doc/embeddedWindows_tile.png 1.2 (changed binary)
* tablelist/doc/embeddedWindows.png 1.2 (changed binary)
* tablelist/doc/dustSand.png 1.2 (changed binary)
* tablelist/doc/dust.png 1.2 (changed binary)
* tablelist/doc/dirViewer.png 1.2 (changed binary)
* tablelist/doc/config.png 1.2 (changed binary)
* tablelist/doc/classic200.png 1.1 (added +15 -0)
* tablelist/doc/classic175.png 1.1 (added +12 -0)
* tablelist/doc/classic150.png 1.1 (added +14 -0)
* tablelist/doc/classic125.png 1.1 (added +12 -0)
* tablelist/doc/classic100.png 1.1 (added +13 -0)
* tablelist/doc/bwidget.png 1.2 (changed binary)
* tablelist/doc/browseTree.png 1.2 (changed binary)
* tablelist/doc/browse.png 1.2 (changed binary)
* tablelist/doc/blueMenta.png 1.1 (added +11 -0)
* tablelist/doc/bicolor200.png 1.1 (added +12 -0)
* tablelist/doc/bicolor175.png 1.1 (added +12 -0)
* tablelist/doc/bicolor150.png 1.1 (added +12 -0)
* tablelist/doc/bicolor125.png 1.1 (added +11 -0)
* tablelist/doc/bicolor100.png 1.1 (added +8 -0)
* tablelist/doc/baghira.png 1.2 (changed binary)
* tablelist/doc/arrowStyles_vista.png 1.1 (added +30 -0)
* tablelist/doc/arrowStyles.png 1.2 (changed binary)
* tablelist/doc/arc.png 1.1 (added +12 -0)
* tablelist/doc/aqua.png 1.2 (changed binary)
* tablelist/doc/ambiance.png 1.2 (changed binary)
* tablelist/doc/adwaita.png 1.2 (changed binary)
* tablelist/demos/unchecked200.gif 1.1 (added +7 -0)
* tablelist/demos/unchecked175.gif 1.1 (added +7 -0)
* tablelist/demos/unchecked150.gif 1.1 (added +6 -0)
* tablelist/demos/unchecked125.gif 1.1 (added +6 -0)
* tablelist/demos/unchecked100.gif 1.1 (added +6 -0)
* tablelist/demos/tileWidgets.tcl 1.2 (changed +23 -15)
* tablelist/demos/styles_tile.tcl 1.2 (changed +17 -17)
* tablelist/demos/styles.tcl 1.2 (changed +19 -19)
* tablelist/demos/option_tile.tcl 1.2 (changed +24 -24)
* tablelist/demos/option.tcl 1.2 (changed +10 -11)
* tablelist/demos/openFolder200.gif 1.1 (added +7 -0)
* tablelist/demos/openFolder175.gif 1.1 (added +7 -0)
* tablelist/demos/openFolder150.gif 1.1 (added +8 -0)
* tablelist/demos/openFolder125.gif 1.1 (added +8 -0)
* tablelist/demos/openFolder100.gif 1.1 (added +7 -0)
* tablelist/demos/openAction200.gif 1.1 (added +8 -0)
* tablelist/demos/openAction175.gif 1.1 (added +7 -0)
* tablelist/demos/openAction150.gif 1.1 (added +7 -0)
* tablelist/demos/openAction125.gif 1.1 (added +8 -0)
* tablelist/demos/openAction100.gif 1.1 (added +7 -0)
* tablelist/demos/miscWidgets_tile.tcl 1.2 (changed +12 -14)
* tablelist/demos/miscWidgets.tcl 1.2 (changed +12 -14)
* tablelist/demos/leaf200.xbm 1.1 (added +17 -0)
* tablelist/demos/leaf175.xbm 1.1 (added +16 -0)
* tablelist/demos/leaf150.xbm 1.1 (added +13 -0)
* tablelist/demos/leaf125.xbm 1.1 (added +12 -0)
* tablelist/demos/leaf100.xbm 1.1 (added +11 -0)
* tablelist/demos/iwidgets_tile.tcl 1.2 (changed +18 -16)
* tablelist/demos/iwidgets.tcl 1.2 (changed +18 -16)
* tablelist/demos/images.tcl 1.2 (changed +19 -11)
* tablelist/demos/file200.gif 1.1 (added +7 -0)
* tablelist/demos/file175.gif 1.1 (added +8 -0)
* tablelist/demos/file150.gif 1.1 (added +7 -0)
* tablelist/demos/file125.gif 1.1 (added +7 -0)
* tablelist/demos/file100.gif 1.1 (added +8 -0)
* tablelist/demos/embeddedWindows_tile.tcl 1.2 (changed +59 -25)
* tablelist/demos/embeddedWindows.tcl 1.2 (changed +39 -22)
* tablelist/demos/dirViewer_tile.tcl 1.2 (changed +34 -19)
* tablelist/demos/dirViewer.tcl 1.2 (changed +28 -19)
* tablelist/demos/config_tile.tcl 1.2 (changed +36 -31)
* tablelist/demos/config.tcl 1.2 (changed +18 -19)
* tablelist/demos/comp200.xbm 1.1 (added +17 -0)
* tablelist/demos/comp175.xbm 1.1 (added +16 -0)
* tablelist/demos/comp150.xbm 1.1 (added +13 -0)
* tablelist/demos/comp125.xbm 1.1 (added +12 -0)
* tablelist/demos/comp100.xbm 1.1 (added +11 -0)
* tablelist/demos/clsdFolder200.gif 1.1 (added +7 -0)
* tablelist/demos/clsdFolder175.gif 1.1 (added +7 -0)
* tablelist/demos/clsdFolder150.gif 1.1 (added +8 -0)
* tablelist/demos/clsdFolder125.gif 1.1 (added +8 -0)
* tablelist/demos/clsdFolder100.gif 1.1 (added +7 -0)
* tablelist/demos/checked200.gif 1.1 (added +7 -0)
* tablelist/demos/checked175.gif 1.1 (added +6 -0)
* tablelist/demos/checked150.gif 1.1 (added +6 -0)
* tablelist/demos/checked125.gif 1.1 (added +6 -0)
* tablelist/demos/checked100.gif 1.1 (added +6 -0)
* tablelist/demos/bwidget_tile.tcl 1.2 (changed +11 -13)
* tablelist/demos/bwidget.tcl 1.2 (changed +11 -13)
* tablelist/demos/browse_tile.tcl 1.2 (changed +24 -17)
* tablelist/demos/browseTree_tile.tcl 1.2 (changed +33 -18)
* tablelist/demos/browseTree.tcl 1.2 (changed +28 -18)
* tablelist/demos/browse.tcl 1.2 (changed +18 -17)
* tablelist/README.txt 1.2 (changed +21 -17)
* tablelist/Makefile 1.4 (changed +8 -2)
* tablelist/Makefile 1.3 (changed +1 -1)
* tablelist/COPYRIGHT.txt 1.2 (changed +2 -2)
* tablelist/CHANGES.txt 1.2 (changed +613 -5)
|
| | 2021-01-26 | johns | Corrected an atom selection leak and incremented the cgtools version to 1.3.
* cgtools/pkgIndex.tcl 1.12 (changed +3 -3)
* cgtools/cgtools.tcl 1.19 (changed +5 -3)
* cgtools/cgnetworking.tcl 1.24 (changed +2 -2)
* cgtools/cggui.tcl 1.37 (changed +4 -4)
* cgtools/Makefile 1.7 (changed +1 -1)
|
| | 2020-12-22 | johns | Added dependency on win32molfilelibs for the win32bin targets to prevent
a race condition with building the libmolfile_plugin.a dependency that
the standalone binaries expect to link against.
* Makefile 1.148 (changed +2 -2)
|
| | 2020-12-21 | johns | Added latest colvar templates from git master
* cv_dashboard/templates/component/tilt.in 1.1 (added +13 -0)
* cv_dashboard/templates/component/spinAngle.in 1.1 (added +13 -0)
* cv_dashboard/templates/component/selfCoordNum.in 1.1 (added +11 -0)
* cv_dashboard/templates/component/rmsd.in 1.1 (added +12 -0)
* cv_dashboard/templates/component/orientation.in 1.1 (added +20 -0)
* cv_dashboard/templates/component/mapTotal.in 1.1 (added +11 -0)
* cv_dashboard/templates/component/inertia.in 1.1 (added +11 -0)
* cv_dashboard/templates/component/hbond.in 1.1 (added +11 -0)
* cv_dashboard/templates/component/gyration.in 1.1 (added +11 -0)
* cv_dashboard/templates/component/groupCoord.in 1.1 (added +15 -0)
* cv_dashboard/templates/component/distancedir.in 1.1 (added +13 -0)
* cv_dashboard/templates/component/distanceZ.in 1.1 (added +16 -0)
* cv_dashboard/templates/component/distanceXY.in 1.1 (added +16 -0)
* cv_dashboard/templates/component/distanceVec.in 1.1 (added +14 -0)
* cv_dashboard/templates/component/distancePairs.in 1.1 (added +14 -0)
* cv_dashboard/templates/component/distanceInv.in 1.1 (added +15 -0)
* cv_dashboard/templates/component/distance.in 1.1 (added +13 -0)
* cv_dashboard/templates/component/dipoleMagnitude.in 1.1 (added +10 -0)
* cv_dashboard/templates/component/dipoleAngle.in 1.1 (added +16 -0)
* cv_dashboard/templates/component/dihedralPC.in 1.1 (added +12 -0)
* cv_dashboard/templates/component/dihedral.in 1.1 (added +19 -0)
* cv_dashboard/templates/component/coordNum.in 1.1 (added +20 -0)
* cv_dashboard/templates/component/angle.in 1.1 (added +17 -0)
Added latest colvar templates from git master.
* cv_dashboard/templates/colvar/extended-Lagrangian_colvar.in 1.1 (added +36 -0)
* cv_dashboard/templates/colvar/colvar_with_many_parameters.in 1.1 (added +37 -0)
* cv_dashboard/templates/colvar/colvar_with_analysis.in 1.1 (added +38 -0)
* cv_dashboard/templates/colvar/basic_colvar.in 1.1 (added +20 -0)
* cv_dashboard/templates/colvar/DBC_ligand_RMSD.in 1.1 (added +33 -0)
Added latest colvar templatest from git master
* cv_dashboard/templates/other/moving_frame_of_reference.in 1.1 (added +25 -0)
Updated cv_dashboard from the latest git master.
* cv_dashboard/cv_dashboard_main.tcl 1.4 (changed +6 -1)
* cv_dashboard/cv_dashboard.tcl 1.4 (changed +6 -3)
* cv_dashboard/README.md 1.2 (changed +7 -1)
|
| | 2020-12-17 | johns | Prevent failure of stat() on multi-gigabyte trajectory files from
causing the DCD open method to return a fatal error when compiled
on 64-bit Windows platforms.
* molfile_plugin/src/dcdplugin.c 1.88 (changed +4 -2)
|
| | 2020-12-14 | mariano | Fixed bug for FFTK usage
* qmtool/qmtool.tcl 1.51 (changed +2 -2)
|
| | 2020-12-14 | johns | Corrected inconsistent cv_dashboard version numbers.
* cv_dashboard/pkgIndex.tcl 1.2 (changed +1 -1)
* cv_dashboard/Makefile 1.3 (changed +1 -1)
Eliminated image file duplications caused by case-insensitive filesystems.
* fftk/doc/ffTK-sample.png 1.2 (removed +0 -3081)
* fftk/doc/ffTK-sample-med.png 1.2 (removed +0 -328)
Prevent the use of parallel make for WIN32 and WIN64 targets until we resolve
some dependencies that appear to trigger an output race among make workers
with particular build targets.
* build.csh 1.147 (changed +2 -2)
Updated image files from 2015 version that had camel case, which
causes problems on case-insensitive filesystems.
* fftk/doc/fftk-sample.png 1.2 (changed binary)
* fftk/doc/fftk-sample-med.png 1.2 (changed binary)
Use lower case image filename to prevent issues on
case-insensitive filesystems
* fftk/doc/index.html 1.21 (changed +1 -1)
|
| | 2020-12-13 | johns | Added build config for MacOS X hosts with ARM64 CPU architecture.
* build.csh 1.145 (changed +18 -0)
* Make-arch 1.95 (changed +18 -0)
Fix missing function prototype in rnaview
* rnaview/src/xml2ps.c 1.2 (changed +1 -1)
Tweak for MacOS X on ARM64
* build.csh 1.146 (changed +1 -1)
|
| | 2020-12-03 | johns | Psfgen file format tag logic correction from Josh Vermaas.
* psfgen/src/topo_mol_output.c 1.47 (changed +4 -5)
|
| | 2020-11-24 | mariano | Fixed bug with FFTK atomname Ow
The bug originated from a fix that I
implemented to qmtool, regarding
two-letter atomnames.
In the original version they were
being recognize by the first letter
For example, Chlorine (Cl) were considered
as Carbon (C).
* qmtool/qmtool_readwrite.tcl 1.62 (changed +3 -1)
|
| | 2020-11-01 | johns | Implemented changes from Josh Vermaas to address incorrect parsing of
some combinations of AMBER restart files, e.g. as written by AMBER 18.
The new code should now properly parse restart files that either have
velocities or do not, and that either have timestamp information, or not.
All four of those combinations have been tested successfully with the
new code, and a little bit of further code cleanup and commenting
has been done since the new logic is a little more complex.
* molfile_plugin/src/rst7plugin.c 1.22 (changed +45 -18)
Updated the cv_dashboard plugin from the git master tagged as "vmd-1.9.4a49".
* cv_dashboard/cv_dashboard_settings.tcl 1.1 (added +168 -0)
* cv_dashboard/cv_dashboard_plots.tcl 1.2 (changed +13 -11)
* cv_dashboard/cv_dashboard_main.tcl 1.3 (changed +564 -135)
* cv_dashboard/cv_dashboard_editor.tcl 1.2 (changed +92 -48)
* cv_dashboard/cv_dashboard_display.tcl 1.1 (added +119 -0)
* cv_dashboard/cv_dashboard.tcl 1.3 (changed +235 -21)
* cv_dashboard/Makefile 1.2 (changed +1 -1)
|
| | 2020-10-21 | johns | Changed use of "long" integer types to "ptrdiff_t" for portability to
64-bit Windows.
* molfile_plugin/src/endianswap.h 1.8 (changed +15 -13)
Changed use of "long" integer types to "ptrdiff_t" for portability to
64-bit Windows. Added conditional compilation checks for _WIN64 to
force the use of Windows-specific _fseeki64() and _ftelli64() when working
with potentially large files.
* molfile_plugin/src/ccp4plugin.C 1.45 (changed +25 -13)
Changed use of "long" integer types to "ptrdiff_t" for portability to
64-bit Windows. Since this plugin uses fastio.h, there were no changes
for _WIN64 conditional compilation for calls to fseek/ftell type APIs, but
we'll need to test and do any updates in fastio.h if the Windows-specific
I/O APIs aren't sufficient as-is.
* molfile_plugin/src/jsplugin.c 1.91 (changed +33 -32)
* molfile_plugin/src/dcdplugin.c 1.87 (changed +9 -8)
Ensure initialization of some local variables.
* molfile_plugin/src/ccp4plugin.C 1.46 (changed +2 -2)
|
| | 2020-10-17 | johns | Updated unsigned integer pointer type conditional compilation rule for
64-bit Windows builds.
* molfile_plugin/src/jsplugin.c 1.90 (changed +9 -5)
|
| | 2020-10-16 | johns | Set correct VS2017 paths for both x86 and x64 targets on 'sphere'
* build.csh 1.143 (changed +2 -2)
Updated WIN64 target compilation and linkage flags.
* Make-arch 1.94 (changed +3 -3)
Updated plugin build rules to properly compile VMD C/C++ plugins
for 64-bit Windows platforms.
* include/vmdplugin.h 1.35 (changed +3 -3)
Updates for standalone cygwin-based plugin compilation w/ VS2017 on 'sphere'
* build.csh 1.142 (changed +28 -1)
Use parallel make for MSVC builds on 'sphere'.
* build.csh 1.144 (changed +2 -2)
|
| | 2020-10-13 | johns | Corrected a comment line that was interfering with the correct behavior
of the TkCon initialization routine.
* vmdtkcon/tkcon-modified.tcl 1.15 (changed +3 -3)
|
| | 2020-10-01 | johns | Added missing ifdef for conditional compilation of standalone test binary
with GPU-Direct Storage support.
* molfile_plugin/src/jsplugin.c 1.89 (changed +6 -3)
|
| | 2020-09-25 | gumbart | Tiny fix if segname is missing when clicking "analyze input" in BuildPar
* fftk/fftk_guiInterface.tcl 1.50 (changed +4 -1)
|
| | 2020-09-16 | johns | Added dependency on molfilelibs for the non-win32 targets to prevent
a race condition with building the libmolfile_plugin.a dependency that
the standalone binaries expect to link against.
* Makefile 1.147 (changed +2 -2)
|
| | 2020-09-05 | johns | Add Tcl/Tk 8.6-compatible TkCon 2.7 for future reference.
* vmdtkcon/tkcon-2.7/tclconfig/tcl.m4 1.1 (added +4181 -0)
* vmdtkcon/tkcon-2.7/tclconfig/install-sh 1.1 (added +533 -0)
* vmdtkcon/tkcon-2.7/tclconfig/README.txt 1.1 (added +31 -0)
* vmdtkcon/tkcon-2.7/tclconfig/ChangeLog 1.1 (added +1008 -0)
* vmdtkcon/tkcon-2.7/icons/tkcon-small48.png 1.1 (added binary)
* vmdtkcon/tkcon-2.7/icons/tkcon-small.svg 1.1 (added binary)
* vmdtkcon/tkcon-2.7/extra/stripped.tcl 1.1 (added +1088 -0)
* vmdtkcon/tkcon-2.7/extra/console1_1.tcl 1.1 (added +2214 -0)
* vmdtkcon/tkcon-2.7/docs/todo.html 1.1 (added +104 -0)
* vmdtkcon/tkcon-2.7/docs/tkconrc.5.man 1.1 (added +254 -0)
* vmdtkcon/tkcon-2.7/docs/tkcon.n.man 1.1 (added +145 -0)
* vmdtkcon/tkcon-2.7/docs/tkcon.html 1.1 (added +194 -0)
* vmdtkcon/tkcon-2.7/docs/tkcon.1.man 1.1 (added +374 -0)
* vmdtkcon/tkcon-2.7/docs/style.css 1.1 (added +55 -0)
* vmdtkcon/tkcon-2.7/docs/start.html 1.1 (added +363 -0)
* vmdtkcon/tkcon-2.7/docs/purpose.html 1.1 (added +92 -0)
* vmdtkcon/tkcon-2.7/docs/procs.html 1.1 (added +172 -0)
* vmdtkcon/tkcon-2.7/docs/plugin.html 1.1 (added +118 -0)
* vmdtkcon/tkcon-2.7/docs/perl.txt 1.1 (added +114 -0)
* vmdtkcon/tkcon-2.7/docs/observe.n.man 1.1 (added +60 -0)
* vmdtkcon/tkcon-2.7/docs/observe.html 1.1 (added +109 -0)
* vmdtkcon/tkcon-2.7/docs/nontcl.html 1.1 (added +80 -0)
* vmdtkcon/tkcon-2.7/docs/limits.html 1.1 (added +81 -0)
* vmdtkcon/tkcon-2.7/docs/license.terms 1.1 (added +38 -0)
* vmdtkcon/tkcon-2.7/docs/index.html 1.1 (added +86 -0)
* vmdtkcon/tkcon-2.7/docs/idebug.n.man 1.1 (added +88 -0)
* vmdtkcon/tkcon-2.7/docs/idebug.html 1.1 (added +130 -0)
* vmdtkcon/tkcon-2.7/docs/dump.n.man 1.1 (added +65 -0)
* vmdtkcon/tkcon-2.7/docs/dump.html 1.1 (added +105 -0)
* vmdtkcon/tkcon-2.7/docs/demopic.png 1.1 (added binary)
* vmdtkcon/tkcon-2.7/docs/changes.txt 1.1 (added +820 -0)
* vmdtkcon/tkcon-2.7/docs/bindings.html 1.1 (added +159 -0)
* vmdtkcon/tkcon-2.7/README.txt 1.2 (changed +5 -0)
Added extra initialization check since the new TkCon 2.7 ::AtSource
method doesn't trigger initialization when run as a VMD plugin.
* vmdtkcon/tkcon-modified.tcl 1.13 (changed +9 -2)
Began import of Tcl/Tk 8.6-compatible version of TkCon 2.7 to ensure
correct behavior on MacOS X Catalina, and other current VMD builds.
* vmdtkcon/tkcon-modified.tcl 1.11 (changed +1998 -776)
Begin adding the Tcl/Tk 8.6-compatible TkCon 2.7 to the tree for long-term
reference.
* vmdtkcon/tkcon-2.7/tkcon.tcl 1.1 (added +6548 -0)
* vmdtkcon/tkcon-2.7/tkcon-console.desktop 1.1 (added +15 -0)
* vmdtkcon/tkcon-2.7/pkgIndex.tcl 1.1 (added +16 -0)
* vmdtkcon/tkcon-2.7/install-desktop-menu.sh 1.1 (added +31 -0)
* vmdtkcon/tkcon-2.7/index.html 1.1 (added +75 -0)
* vmdtkcon/tkcon-2.7/configure.ac 1.1 (added +196 -0)
* vmdtkcon/tkcon-2.7/configure 1.1 (added +6268 -0)
* vmdtkcon/tkcon-2.7/aclocal.m4 1.1 (added +14 -0)
* vmdtkcon/tkcon-2.7/README.txt 1.1 (added +47 -0)
* vmdtkcon/tkcon-2.7/Makefile.in 1.1 (added +463 -0)
* vmdtkcon/tkcon-2.7/ChangeLog 1.1 (added +612 -0)
Disable multi-tabb associated interpreter creation/deletion buttons
since these are totally disjoint from the VMD Tcl interpreter and would
just cause trouble otherwise. Hid other buttons that are either confusing
or not particularly functional in the context of the VMD plugin use case.
* vmdtkcon/tkcon-modified.tcl 1.14 (changed +12 -11)
Re-apply previous VMD plugin modifications to the base
Tcl/Tk 8.6-compatible version of TkCon 2.7.
* vmdtkcon/tkcon-modified.tcl 1.12 (changed +148 -56)
Updated binding free energy estimator version tags
* bfeestimator/pkgIndex.tcl 1.2 (changed +1 -1)
Updated comments with more details about modifications required for
operation within the VMD plugin system.
* vmdtkcon/README 1.3 (changed +18 -6)
Updated the 'vmdtkcon' plugin version to 2.0, and updated build scripts
and plumbing to correctly launch the new code built on TkCon 2.7.
* vmdtkcon/vmdtkcon.tcl 1.12 (changed +2 -2)
* vmdtkcon/pkgIndex.tcl 1.4 (changed +1 -1)
* vmdtkcon/README 1.2 (changed +17 -11)
* vmdtkcon/Makefile 1.10 (changed +3 -3)
|
| | 2020-09-01 | johns | Incorporated major FFTK updates from Andrew Pang and J.C. Gumbart, extending
it with support for lone pair (LP) particles, as used in recent versions
of CGenFF. The new FFTK also adds support for improper fitting, a
highly user-requested feature. Since the prior commits had not yet taken on
major version number update, the major version was updated to 2, and as of
these changes, the minor version is now 1, so all of the Makefile and
Tcl package version tags and documentation notes are now updated to 2.1 as
they should be.
* fftk/pkgIndex.tcl 1.5 (changed +1 -1)
* fftk/fftk_guiProcs.tcl 1.49 (changed +373 -19)
* fftk/fftk_guiInterface.tcl 1.49 (changed +1192 -52)
* fftk/fftk_distort.tcl 1.6 (changed +7 -1)
* fftk/fftk_SharedFcns.tcl 1.18 (changed +505 -10)
* fftk/fftk_QMORCA.tcl 1.4 (changed +68 -28)
* fftk/fftk_QMGaussian.tcl 1.2 (changed +62 -36)
* fftk/fftk_GeomOpt.tcl 1.11 (changed +28 -4)
* fftk/fftk_GenZMatrix.tcl 1.17 (changed +10 -6)
* fftk/fftk_GenDihScan.tcl 1.15 (changed +6 -7)
* fftk/fftk_DihOpt.tcl 1.24 (changed +614 -18)
* fftk/fftk_ChargeOpt.tcl 1.28 (changed +19 -9)
* fftk/fftk_BuildPar.tcl 1.20 (changed +73 -14)
* fftk/fftk_BondAngleOpt.tcl 1.22 (changed +2 -2)
* fftk/fftk.tcl 1.16 (changed +2 -2)
* fftk/doc/index.html 1.20 (changed +3 -3)
* fftk/Makefile 1.9 (changed +1 -1)
|
| | 2020-08-31 | johns | Updated NAMDPlot plugin for NAMD 3.0 (and typos in early versions)
* namdplot/pkgIndex.tcl 1.4 (changed +1 -1)
* namdplot/namdplot.tcl 1.17 (changed +7 -3)
* namdplot/Makefile 1.4 (changed +1 -1)
|
| | 2020-08-17 | mariano | Fixed bug with bond parametrization using ORCA
* fftk/fftk_QMORCA.tcl 1.3 (changed +3 -2)
|
| | 2020-08-13 | mariano | Added new procs based on qwikmd molecular orbital plot
plotOrbitals, addQMOrbDeltaLine and deletePlotLines
At the moment, only QMtool uses this.
* multiplot/multiplot.tcl 1.41 (changed +257 -1)
Changes to include QMtool compatibility
Added "File > Export to QMtool" functionality
based on "File > Apply changes to parent" case.
Modified "Apply changes to parent" to include
call from QMtool to edit structure.
In both cases, Molefacture closes and raises QMtool.
* molefacture/molefacture_internals.tcl 1.57 (changed +37 -2)
* molefacture/molefacture_gui.tcl 1.75 (changed +14 -7)
* molefacture/molefacture.tcl 1.112 (changed +12 -1)
New qmtool 2.0 plugin
Separated the gui code into qmtool_gui.tcl file.
Added specific QM code that deal with input generation
to the files qmtool_gamess.tcl, qmtool_gaussian.tcl and
qmtool_orca.tcl
Molecular orbital analysis was taken from QwikMD and
rewritten into multiplot (i.e. MultiPlot::plotOrbitals)
* qmtool/qmtool_setup.tcl 1.29 (changed +142 -716)
* qmtool/qmtool_readwrite.tcl 1.61 (changed +18 -6)
* qmtool/qmtool_orca.tcl 1.1 (added +194 -0)
* qmtool/qmtool_gui.tcl 1.1 (added +306 -0)
* qmtool/qmtool_gaussian.tcl 1.1 (added +326 -0)
* qmtool/qmtool_gamess.tcl 1.1 (added +178 -0)
* qmtool/qmtool_analysis.tcl 1.12 (changed +557 -49)
* qmtool/qmtool.tcl 1.50 (changed +254 -339)
* qmtool/Makefile 1.5 (changed +4 -2)
|
| | 2020-08-11 | johns | Added missing 'cgenffcaller' to the build/distrib system.
* Makefile 1.146 (changed +2 -1)
|
| | 2020-07-09 | johns | Updated binding free energy estimator plugin w/ new version from Chris Chipot
and collaborators.
* bfeestimator/bfee.tcl 1.2 (changed +482 -98)
* bfeestimator/Makefile 1.2 (changed +1 -1)
|
| | 2020-07-06 | johns | Merged Axel's latest topotools updates.
* topotools/topogromacs.tcl 1.16 (changed +2 -2)
* topotools/topocrossterms.tcl 1.5 (changed +2 -2)
* topotools/Makefile 1.17 (changed +6 -5)
Updated MRC/CCP4 plugin to emit extended header tags stored by some
commercial microscopy tools in the console messages to help with
identifying unusual proprietary file formats. Inhibit printing of
MRC symmetry records when the IMOD stamp has been identified.
* molfile_plugin/src/ccp4plugin.C 1.44 (changed +49 -22)
|
| | 2020-07-03 | johns | Allow jsplugin to be included into other source files with file scope
linkage for early testing of out-of-core APIs in multiple parts of VMD.
* molfile_plugin/src/jsplugin.c 1.88 (changed +4 -1)
|
| | 2020-07-02 | mariano | Added qcschema plugin for LINUXAMD64
* molfile_plugin/Makefile 1.133 (changed +24 -1)
Added qcschema plugin for LINUXAMD64.
Preliminary version uses json parser from
https://github.com/udp/json-parser
included as qcschema_json.c and .h files.
The plugin reads 'molecule' object
including geometry, symbols, charge and
multiplicity.
* molfile_plugin/src/qcschemaplugin.c 1.1 (added +750 -0)
* molfile_plugin/src/qcschema_json.h 1.1 (added +288 -0)
* molfile_plugin/src/qcschema_json.c 1.1 (added +1044 -0)
|
| | 2020-07-01 | johns | Updated Josh Vermaas' current email and corrected spelling typos.
* topotools/topoutils.tcl 1.20 (changed +2 -2)
* topotools/topotools.tcl 1.34 (changed +3 -3)
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| | 2020-06-29 | johns | Corrected missing check for verbose console output state.
* molfile_plugin/src/jsplugin.c 1.87 (changed +5 -3)
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| | 2020-06-23 | mariano | Fixed 'pack' vs 'grid' problem. Requires MacOS testing
* qwikmd/qwikmd.tcl 1.84 (changed +5 -3)
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| | 2020-06-12 | mariano | Modified GUI to remove 'pack' and replace it with 'grid'
Tested in linux, need to test in new macos with tcl8.6
* autopsf/autopsf.tcl 1.151 (changed +91 -90)
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| | 2020-06-11 | gumbart | Fixed pattern matching for Gaussian 09.
* fftk/fftk_SharedFcns.tcl 1.17 (changed +2 -2)
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| | 2020-05-29 | johns | Removed old README in favor of Axel's markdown version
* topotools/README 1.18 (removed +0 -41)
Updated Makefile for markdown version README.md
* topotools/Makefile 1.16 (changed +1 -1)
Updated topotools plugin with Axel's latest v1.8 package.
* topotools/topovarxyz.tcl 1.6 (changed +2 -2)
* topotools/topoutils.tcl 1.19 (changed +1 -1)
* topotools/topotools.tcl 1.33 (changed +4 -4)
* topotools/topolammps.tcl 1.45 (changed +17 -29)
* topotools/topoimpropers.tcl 1.12 (changed +4 -4)
* topotools/topohelpers.tcl 1.11 (changed +1 -1)
* topotools/topogromacs.tcl 1.15 (changed +38 -4)
* topotools/topodihedrals.tcl 1.12 (changed +12 -10)
* topotools/topobonds.tcl 1.16 (changed +2 -2)
* topotools/topoatoms.tcl 1.17 (changed +2 -2)
* topotools/topoangles.tcl 1.13 (changed +2 -2)
* topotools/pkgIndex.tcl 1.11 (changed +1 -1)
* topotools/doc/index.html 1.23 (changed +2 -2)
* topotools/README.md 1.1 (added +66 -0)
* topotools/Makefile 1.15 (changed +1 -1)
* topotools/LICENSE 1.4 (changed +2 -2)
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| | 2020-05-19 | johns | Minor stylistic cleanup revisions in preparation for Tcl 8.6 grid vs. pack
widget layout corrections.
* heatmapper/pkgIndex.tcl 1.3 (changed +1 -1)
* heatmapper/heatmapper.tcl 1.6 (changed +23 -97)
* heatmapper/Makefile 1.3 (changed +1 -1)
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| | 2020-05-09 | johns | Cranked version of clonerep plugin to 1.4 due to GUI fixes for Tk 8.6
to eliminate grid/pack conflicts.
* clonerep/pkgIndex.tcl 1.5 (changed +1 -1)
* clonerep/clonerep.tcl 1.15 (changed +2 -2)
* clonerep/Makefile 1.5 (changed +1 -1)
Revised chirality plugin GUI to eliminate grid/pack conflicts in Tk 8.6.
Cranked plugin version to 1.4. Further testing and GUI optimizations
should be done, but this version now runs on Tk 8.6 without errors thus far.
* torsionplot/torsionplot.tcl 1.6 (changed +21 -27)
* torsionplot/pkgIndex.tcl 1.4 (changed +1 -1)
* torsionplot/Makefile 1.4 (changed +1 -1)
* chirality/pkgIndex.tcl 1.5 (changed +2 -2)
* chirality/doc/index.html 1.5 (changed +1 -1)
* chirality/chirality_gui.tcl 1.8 (changed +13 -14)
* chirality/chirality.tcl 1.30 (changed +3 -1)
* chirality/Makefile 1.4 (changed +1 -1)
Revised cispeptide plugin GUI to eliminate grid/pack conflicts in Tk 8.6.
Cranked plugin version to 1.4. Further testing and GUI optimizations
should be done, but this version now runs on Tk 8.6 without errors thus far.
* cispeptide/pkgIndex.tcl 1.5 (changed +2 -2)
* cispeptide/doc/index.html 1.5 (changed +1 -1)
* cispeptide/cispeptide_gui.tcl 1.8 (changed +21 -21)
* cispeptide/cispeptide.tcl 1.22 (changed +2 -2)
* cispeptide/Makefile 1.4 (changed +1 -1)
Synced version number in docs.
* clonerep/doc/index.html 1.7 (changed +1 -1)
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