| Tags | Date | Developer | Last 200 Commit Logs |
|---|
| | 2009-11-22 | ltrabuco | Calculate periodic box information using water molecules only, as opposed
to all molecules. That cures problems with water-membrane simulations in
which lipid tails stick out of the periodic cell.
* mdff/mdff_setup.tcl 1.4 (changed +11 -5)
|
| | 2009-11-20 | saam | Cleanup and comments.
* include/molfile_plugin.h 1.100 (changed +6 -5)
Improved error messages and comments.
* molfile_plugin/src/gamessplugin.c 1.200 (changed +25 -11)
Renamed opt_status flag to status since it describes a general
calculation status, not only the geometryoptimization status.
* molfile_plugin/src/qmplugin.h 1.15 (changed +3 -3)
* molfile_plugin/src/gamessplugin.c 1.199 (changed +17 -17)
|
| | 2009-11-20 | akohlmey | Add support for reading and writing .xyz trajectories with variable
number of atoms by automatically adding padding atoms and flagging
them in the user field for visualization.
add initial support for generating 'fake' gromacs style topology
files with the minimal information required to generate .tpr files
(no export of masses and atom types).
* topotools/topovarxyz.tcl 1.1 (added +223 -0)
* topotools/topotools.tcl 1.17 (changed +55 -1)
* topotools/topohelpers.tcl 1.6 (changed +25 -4)
* topotools/topogromacs.tcl 1.1 (added +144 -0)
* topotools/topoatoms.tcl 1.6 (changed +44 -1)
* topotools/Makefile 1.8 (changed +1 -1)
|
| | 2009-11-19 | saam | Add MOLFILE_RUNTYPE_* macros.
* include/molfile_plugin.h 1.98 (changed +14 -1)
Canonicalize names for QMSTATUS macros.
* include/molfile_plugin.h 1.99 (changed +7 -10)
Move RUNTYPE macros to molfileplugin.h.
* molfile_plugin/src/qmplugin.h 1.13 (changed +1 -9)
* molfile_plugin/src/gamessplugin.c 1.197 (changed +28 -23)
Turn MOLFILE_SCFTYPE_* enum into #defines. They will be used unly in the
plugins and in MolFilePlugin.C.
* include/molfile_plugin.h 1.97 (changed +12 -13)
Update comments
* molfile_plugin/src/qmplugin.h 1.12 (changed +4 -4)
Use new QMSTATUS macro names.
* molfile_plugin/src/qmplugin.h 1.14 (changed +2 -2)
* molfile_plugin/src/gamessplugin.c 1.198 (changed +16 -16)
|
| | 2009-11-17 | saam | Added helper functions for initialization.
* molfile_plugin/src/qmplugin.h 1.11 (changed +78 -11)
Added macros for the SCF type.
* include/molfile_plugin.h 1.96 (changed +13 -1)
Enable reading wavefunction coefficients.
* molfile_plugin/src/moldenplugin.c 1.27 (changed +425 -36)
Make use of angular_momentum_expon() helper function from qmplugins.h.
* molfile_plugin/src/gamessplugin.c 1.195 (changed +4 -20)
Updated comments.
* molfile_plugin/src/gamessplugin.c 1.196 (changed +7 -5)
Use SCF type macros from molfile_plugin.
Use initialization function from qmplugin.h.
Fix memory leak.
* molfile_plugin/src/gamessplugin.c 1.194 (changed +26 -59)
|
| | 2009-11-14 | ltrabuco | NAMD's gridforces syntax changed from 2.7b1 to 2.7b2. Now that 2.7b2 is
released, write MDFF config files with the current syntax.
* mdff/mdff_template.namd 1.2 (changed +5 -11)
|
| | 2009-11-13 | saam | Enable splitting SP-shells into one S- and one P-shell.
* molfile_plugin/src/moldenplugin.c 1.24 (changed +36 -30)
Pretty.
* molfile_plugin/src/moldenplugin.c 1.26 (changed +18 -27)
Remove debugging output.
* molfile_plugin/src/basissetplugin.c 1.13 (changed +3 -7)
Renamed struct qmdata holding data structures useful for QM file parsing
to qmdata_t for disambiguation purpose.
* molfile_plugin/src/qmplugin.h 1.10 (changed +2 -2)
* molfile_plugin/src/moldenplugin.c 1.25 (changed +16 -16)
* molfile_plugin/src/gamessplugin.c 1.193 (changed +77 -77)
* molfile_plugin/src/basissetplugin.c 1.12 (changed +16 -16)
Send sasis set data, including correct atomic numbers, to VMD.
* molfile_plugin/src/moldenplugin.c 1.23 (changed +7 -1)
|
| | 2009-11-12 | kvandivo | Comment formatting
* multiseqdialog/multiseqdialog.tcl 1.7 (changed +13 -13)
|
| | 2009-11-11 | saam | Cleanup.
* molfile_plugin/src/moldenplugin.c 1.21 (changed +19 -19)
Enable reading trajectories. (Works but needs cleanup)
* molfile_plugin/src/moldenplugin.c 1.20 (changed +125 -70)
Fix memory leak.
* molfile_plugin/src/moldenplugin.c 1.22 (changed +2 -1)
|
| | 2009-11-10 | saam | Added function iswhiteline().
* molfile_plugin/src/qmplugin.h 1.8 (changed +11 -1)
Added strtoupper().
* molfile_plugin/src/qmplugin.h 1.9 (changed +19 -1)
Cleanup.
Documentation.
* molfile_plugin/src/moldenplugin.c 1.18 (changed +66 -49)
First version of basis set aware molden file parser.
* molfile_plugin/src/moldenplugin.c 1.15 (changed +636 -205)
Fix comment.
* molfile_plugin/src/basissetplugin.c 1.11 (changed +2 -2)
Fix memory leak.
* molfile_plugin/src/moldenplugin.c 1.19 (changed +3 -2)
Fix typo.
* molfile_plugin/src/moldenplugin.c 1.17 (changed +2 -2)
Improved parsing logic.
* molfile_plugin/src/moldenplugin.c 1.16 (changed +143 -170)
Move shell type macros from gamessplugin to qmplugin.
Fix some Commments.
* molfile_plugin/src/qmplugin.h 1.7 (changed +17 -1)
* molfile_plugin/src/gamessplugin.c 1.192 (changed +6 -19)
|
| | 2009-11-10 | kvandivo | Programmatic change. No feature addition.
changed proc call to eliminate use of a redundant proc body.
* seqedit/seqedit_widget.tcl 1.9 (changed +1 -1)
* seqdata/seqdata.tcl 1.7 (changed +0 -13)
|
| | 2009-11-08 | ltrabuco | Added (undocumented) option -volume to calculate the molecular volume
given a threshold in sigmas above the mean.
* volutil/src/volmap.h 1.6 (changed +4 -2)
* volutil/src/unary_ops.C 1.4 (changed +23 -1)
* volutil/src/params.h 1.2 (changed +3 -2)
* volutil/src/params.C 1.3 (changed +4 -1)
* volutil/src/main.C 1.2 (changed +6 -1)
|
| | 2009-11-06 | petefred | Remove an apparently unneeded alteration of chain index ranges that causes problems in some cases
* autopsf/doc/index.html 1.12 (changed +1 -1)
Remove an apparently unneeded change that causes problems in some cases
* autopsf/autopsf.tcl 1.115 (changed +2 -2)
|
| | 2009-11-05 | saam | Added documentation about the function call chain and the parsing
strategy.
* molfile_plugin/src/gamessplugin.c 1.191 (changed +116 -2)
Better odering of QM related typedefs
* include/molfile_plugin.h 1.95 (changed +122 -94)
|
| | 2009-11-04 | kvandivo | Clicking on the title column header (which defaults to 'Sequence Name')
now allows you to choose the text that you wish to describe each sequence.
You can choose to display "Sequence Name", "Sequence Length", "Percent GC",
"Domain Of Life", "Common Name", "Scientific Name - Short",
"Scientific Name - Long", "Sequence Sources", "Lineage",
"Enzyme Commision Number", "Sequence Type", "Temperature Class".
If a given sequence doesn't have a value for the property you have chosen,
you will be shown the <Sequence Name>, surrounded by angle brackets.
* seqedit/seqedit_widget.tcl 1.8 (changed +107 -9)
|
| | 2009-11-03 | saam | Extended documentation of the QM interface.
* include/molfile_plugin.h 1.94 (changed +49 -23)
Fix C++-ism.
* molfile_plugin/src/basissetplugin.c 1.10 (changed +3 -2)
Improve comments
* include/molfile_plugin.h 1.93 (changed +13 -10)
Move
#include <math.h>
to qmplugin.h where it is being used.
* molfile_plugin/src/qmplugin.h 1.6 (changed +2 -1)
* molfile_plugin/src/gamessplugin.c 1.190 (changed +3 -4)
|
| | 2009-11-02 | saam | Fixed a bug reported by Olaf Lenz:
> % pbc readxst kiley.xst -alignx
> atomselection move:: need a 4x4 matrix
Now xst files containing PBC vectors that don't follow the standard
alignment (A||x, B in x-y plane) are read and the molecule is
aligned accordingly when using -alignx option.
Fixed indentation in a few places.
* pbctools/pkgIndex.tcl 1.8 (changed +2 -2)
* pbctools/pbcwrap.tcl 1.14 (changed +2 -2)
* pbctools/pbcunwrap.tcl 1.12 (changed +2 -2)
* pbctools/pbctools.tcl 1.12 (changed +2 -2)
* pbctools/pbcset.tcl 1.13 (changed +296 -301)
* pbctools/pbcjoin.tcl 1.12 (changed +2 -2)
* pbctools/pbcbox.tcl 1.13 (changed +2 -2)
* pbctools/Makefile 1.8 (changed +1 -1)
|
| | 2009-10-23 | saam | Fix the menus so that they work under MACOSX.
* qmtool/qmtool.tcl 1.45 (changed +86 -62)
* namdgui/namdgui.tcl 1.35 (changed +39 -19)
|
| | 2009-10-23 | johns | Updated URL for Intervor plugin
* doc/index.html 1.85 (changed +3 -0)
|
| | 2009-10-22 | saam | Fix menubutton (for MACOSX).
* symmetrytool/symmetry.tcl 1.14 (changed +1 -1)
Fix the menus so that they work on MACOSX.
* ilstools/ilstools.tcl 1.11 (changed +15 -15)
|
| | 2009-10-22 | akohlmey | Add support for new acceleration field.
* molfile_plugin/src/hoomdplugin.c 1.14 (changed +14 -4)
|
| | 2009-10-17 | akohlmey | Allow remapping of data field labels via an environment variable.
* molfile_plugin/src/lammpsplugin.c 1.28 (changed +82 -2)
More intuitive name for remap environment variable.
* molfile_plugin/src/lammpsplugin.c 1.29 (changed +2 -2)
|
| | 2009-10-10 | ltrabuco | Add reference for the Dowser plugin.
* dowser/doc/index.html 1.5 (changed +5 -2)
* dowser/doc/dowser-rna.html 1.2 (changed +6 -1)
|
| | 2009-10-10 | akohlmey | "rebrand" the hoomd plugin to reflect the change of name to HOOMD-blue.
update contact e-mail address and step plugin minor version number.
* molfile_plugin/src/hoomdplugin.c 1.13 (changed +18 -17)
Added code to determine angle and dihedral definitions from the bond
topology and guess elements from masses.
* topotools/topotools.tcl 1.15 (changed +20 -0)
* topotools/topodihedrals.tcl 1.4 (changed +57 -0)
* topotools/topoatoms.tcl 1.4 (changed +85 -0)
* topotools/topoangles.tcl 1.5 (changed +51 -0)
Consistent naming of intermediate angle/dihedral/improper lists
to avoid cut-n-paste bugs.
* topotools/topoimpropers.tcl 1.4 (changed +6 -6)
* topotools/topodihedrals.tcl 1.5 (changed +10 -10)
* topotools/topoangles.tcl 1.6 (changed +9 -9)
Fix bug in assignment of angles, dihedrals and impropers to a subsystem
via a selection argument. consistent naming of atomindex maps.
update e-mail address and homepage.
* topotools/topoutils.tcl 1.8 (changed +2 -0)
* topotools/topolammps.tcl 1.19 (changed +1 -1)
* topotools/topoimpropers.tcl 1.3 (changed +23 -21)
* topotools/topohelpers.tcl 1.4 (changed +3 -0)
* topotools/topodihedrals.tcl 1.3 (changed +28 -22)
* topotools/topocgcmm.tcl 1.3 (changed +1 -1)
* topotools/topobonds.tcl 1.8 (changed +1 -1)
* topotools/topoatoms.tcl 1.3 (changed +1 -1)
* topotools/topoangles.tcl 1.4 (changed +20 -18)
* topotools/doc/index.html 1.9 (changed +1 -1)
Fix cut-n-paste bug in replicatemols proc.
* topotools/topoutils.tcl 1.9 (changed +1 -1)
Need to swap indices together with types when retyping dihedrals and impropers.
* topotools/topoutils.tcl 1.10 (changed +1 -0)
* topotools/topotools.tcl 1.16 (changed +1 -1)
* topotools/topolammps.tcl 1.20 (changed +2 -1)
* topotools/topoimpropers.tcl 1.5 (changed +3 -1)
* topotools/topohelpers.tcl 1.5 (changed +1 -1)
* topotools/topodihedrals.tcl 1.6 (changed +5 -1)
* topotools/topocgcmm.tcl 1.4 (changed +2 -1)
* topotools/topobonds.tcl 1.9 (changed +1 -1)
* topotools/topoatoms.tcl 1.5 (changed +1 -1)
* topotools/topoangles.tcl 1.7 (changed +1 -1)
Remove platform specific scratchdir code that is no longer used.
step version number to 1.1 in anticipation of the next commits
with added features requested by topotools users.
* topotools/topotools.tcl 1.14 (changed +5 -33)
* topotools/pkgIndex.tcl 1.4 (changed +1 -1)
* topotools/README 1.7 (changed +2 -4)
* topotools/Makefile 1.7 (changed +1 -1)
Step version number to 1.1 in anticipation of the next commits
with added features requested by topotools users.
* topotools/doc/index.html 1.8 (changed +1 -1)
Update documentation for added code.
* topotools/doc/index.html 1.10 (changed +8 -0)
|
| | 2009-10-06 | ltrabuco | Modified 'mdff gridpdb' so that only atoms that should be coupled to the
map will be considered by NAMD's gridForces, which should improve performance
for explicit-solvent MDFF. Also don't couple hydrogens by default, which
should also improve both performance and stability.
* mdff/mdff_setup.tcl 1.2 (changed +5 -3)
Remove redundant NAMD wrapping commands in 'mdff setup'.
* mdff/mdff_setup.tcl 1.3 (changed +1 -3)
|
| | 2009-09-25 | akohlmey | Avoid NULL pointer dereference in case a parse error has
happenend in one of the psf file blocks, which is indicated
by closing the file and setting the pointer to NULL.
stepped plugin minor version number.
* molfile_plugin/src/psfplugin.c 1.62 (changed +8 -3)
|
| | 2009-09-22 | saam | Use correct scope for getargs function. (It is in ::util::getargs)
* symmetrytool/symmetry.tcl 1.13 (changed +14 -13)
* symmetrytool/pkgIndex.tcl 1.5 (changed +1 -1)
* symmetrytool/Makefile 1.5 (changed +1 -1)
Various little improvements.
Replace shell_symmetry in basissetplugin.c.
* molfile_plugin/src/qmplugin.h 1.5 (changed +2 -2)
* molfile_plugin/src/gamessplugin.c 1.189 (changed +10 -10)
* molfile_plugin/src/basissetplugin.c 1.9 (changed +36 -38)
|
| | 2009-09-21 | saam | Cleanup.
Improved comments.
* molfile_plugin/src/qmplugin.h 1.2 (changed +93 -113)
* molfile_plugin/src/gamessplugin.h 1.84 (changed +6 -45)
* molfile_plugin/src/gamessplugin.c 1.186 (changed +39 -50)
Finish renaming shell_symmetry.
* molfile_plugin/src/qmplugin.h 1.4 (changed +4 -4)
* molfile_plugin/src/gamessplugin.c 1.188 (changed +40 -40)
* include/molfile_plugin.h 1.92 (changed +2 -2)
Improve comment.
* molfile_plugin/src/gamessplugin.c 1.187 (changed +5 -8)
Improve comments.
* molfile_plugin/src/qmplugin.h 1.3 (changed +32 -5)
Remove unused free().
* molfile_plugin/src/basissetplugin.c 1.8 (changed +1 -3)
|
| | 2009-09-20 | saam | Add and improve comments.
* molfile_plugin/src/gamessplugin.c 1.185 (changed +37 -23)
Add qmplugin.h containing data structures and helper functions for
QM file parsing.
* molfile_plugin/src/qmplugin.h 1.1 (added +956 -0)
* molfile_plugin/src/gamessplugin.h 1.83 (changed +3 -277)
* molfile_plugin/src/gamessplugin.c 1.183 (changed +124 -721)
* molfile_plugin/src/basissetplugin.c 1.7 (changed +54 -99)
* molfile_plugin/src/basissetplugin.h 1.2 (changed +4 -20)
Replaced by qmplugin.h
* molfile_plugin/src/basissetplugin.h 1.3 (removed +0 -111)
Use qmplugin.h.
* molfile_plugin/Makefile 1.104 (changed +3 -3)
|
| | 2009-09-20 | johns | Corrected C++ism and cranked version number
* molfile_plugin/src/gamessplugin.c 1.184 (changed +5 -4)
Fixed old reference to basissetplugin.h, now replaced by qmplugin.h
* molfile_plugin/Makefile 1.105 (changed +2 -2)
Updated PSF plugin for latest CHARMM Drude PSF format from Wei Jiang
at the Roux lab.
* molfile_plugin/src/psfplugin.c 1.61 (changed +4 -6)
|
| | 2009-09-18 | akohlmey | Major GUI overhaul. Option to properly select molecule and representation
when using autoscale mode to pick the range, instead of the previous loop
over all rep 0 of all molecules. Option to add a title text added as well.
* colorscalebar/colorscalebar.tcl 1.23 (changed +249 -71)
New image to reflect the changed layout.
* colorscalebar/doc/colorscalebar.png 1.3 (changed binary)
Update color scale bar version number throughout.
* colorscalebar/pkgIndex.tcl 1.4 (changed +1 -1)
* colorscalebar/doc/index.html 1.6 (changed +1 -1)
|
| | 2009-09-17 | johns | Cranked version number of recently modified colorscalebar plugin
* colorscalebar/colorscalebar.tcl 1.21 (changed +2 -2)
* colorscalebar/Makefile 1.4 (changed +1 -1)
|
| | 2009-09-17 | akohlmey | Save and restore current views of all molecules around the addition of
the colorscale bar, since adding the colorbar requires resetting the view.
* colorscalebar/colorscalebar.tcl 1.20 (changed +16 -1)
Take list of text colors in colorscalebar GUI from [colorinfo colors]
instead of hardcoding it.
* colorscalebar/colorscalebar.tcl 1.22 (changed +3 -19)
|
| | 2009-09-15 | johns | Pretty
* molfile_plugin/src/psfplugin.c 1.59 (changed +5 -5)
Updated PSF plugin to recognize new Charmm36 Drude polarizable FF models.
* molfile_plugin/src/psfplugin.c 1.58 (changed +15 -6)
Updated PSF plugin with more stuff related to the CHARMM DRUDE mode
* molfile_plugin/src/psfplugin.c 1.60 (changed +29 -6)
|
| | 2009-09-06 | ltrabuco | Added support for Amber RNA residue names.
* ssrestraints/ssrestraints.tcl 1.13 (changed +8 -7)
|
| | 2009-09-04 | kvandivo | Removed unneeded comments
* seqdata/seqdata_genbank.tcl 1.3 (changed +0 -4)
|
| | 2009-09-04 | akohlmey | Don't download the entry from the PDB if the user cancels the file name selection.
* pdbtool/pdbtool.tcl 1.11 (changed +3 -3)
|
| | 2009-09-01 | ltrabuco | Fix typo in parsing a command-line option.
* volutil/src/params.C 1.2 (changed +2 -2)
|
| | 2009-08-31 | kvandivo | Removed extraneous comments
* multiseqdialog/multiseqdialog.tcl 1.6 (changed +0 -5)
|
| | 2009-08-27 | johns | Fix uninitialized return code variable.
* molfile_plugin/src/netcdfplugin.c 1.25 (changed +2 -2)
Updated the volmap header to use the _isnan() routine when compiling for win32.
* volutil/src/volmap.h 1.5 (changed +6 -1)
|
| | 2009-08-26 | ltrabuco | Use isnan macro instead of our own.
* volutil/src/volmap.h 1.4 (changed +3 -2)
|
| | 2009-08-26 | johns | Added a separate shared library flags compilation variable to support
Windows plugins builds that use statically linked plugins.
* molfile_plugin/Makefile 1.103 (changed +64 -64)
Changed Win32 compile flags to prevent executable source files
(e.g. volutil) from being compiled with a DllMain() when they include
plugin headers.
* Make-arch 1.69 (changed +12 -9)
Fixed volutil Makefile to link the win32 executable correctly.
* volutil/Makefile 1.3 (changed +2 -3)
|
| | 2009-08-26 | akohlmey | Update parameter and topology files as requested by WS.
* topotools/top_CG.prm 1.3 (changed +1 -133)
* topotools/par_CG.prm 1.2 (changed +1 -231)
|
| | 2009-08-25 | ltrabuco | Attempted to correct some linking problems on Win32.
* volutil/src/molfile.C 1.2 (changed +2 -2)
* volutil/src/getplugins.C 1.2 (changed +2 -2)
|
| | 2009-08-20 | barryi | Three things:
1) Handles large sturctures better: a) does not effectively freeze on startup for large molecules (the intial calculating for every residue is now skipped b) properly handles segments, including in .tml files, so can be sure have unique atoms specified
2) New version of .tml format (1.4) -- but still must set to handle earlier versions (e.g. not yet backward compatible!)
3) Fixed bug with "ERROR) syntax error". (apparently generated by parsing an
atomselect) near startup. Had been sending a molecule number to an atomselect.
Fixed and made a function that turned out is needed in more than place:
findCursorSelText
* timeline/timeline.tcl 1.60 (changed +173 -70)
|
| | 2009-08-19 | ltrabuco | Avoid "using std::min" and "using std::max" statements to please MS compiler.
* volutil/src/binary_ops.C 1.2 (changed +19 -19)
Fix make target for Win32.
* volutil/Makefile 1.2 (changed +1 -1)
More changes to please MS compiler:
- Remove "using namespace std" statement
- Avoid calls to std::min and std::max"
- Define M_PI if not available
* volutil/src/volmap.h 1.2 (changed +5 -4)
* volutil/src/unary_ops.C 1.2 (changed +14 -10)
* volutil/src/binary_ops.C 1.3 (changed +1 -4)
Remove unnecessary use of C++ library header files.
* volutil/src/volmap.h 1.3 (changed +1 -4)
* volutil/src/unary_ops.C 1.3 (changed +3 -2)
* volutil/src/convolutions.C 1.2 (changed +4 -2)
* volutil/src/binary_ops.C 1.4 (changed +2 -2)
Remove unused template functions.
* volutil/src/vec.h 1.2 (changed +1 -24)
|
| | 2009-08-17 | johns | Updated cionize CUDA kernels for new behavior of cudaSetDevice() with
runtime versions 2.2 and later.
* cionize/mgpot_cuda_shortrng.cu 1.14 (changed +14 -1)
* cionize/mgpot_cuda_setup.cu 1.12 (changed +15 -1)
* cionize/cudaenergythr.cu 1.13 (changed +17 -3)
|
| | 2009-08-14 | ltrabuco | Fix parsing of -hbonds options.
* ssrestraints/ssrestraints.tcl 1.12 (changed +7 -1)
|
| | 2009-08-14 | johns | Added symmetrytool to the plugin index page
* doc/index.html 1.84 (changed +1 -0)
Grammar
* symmetrytool/doc/index.html 1.3 (changed +3 -2)
|
| | 2009-08-13 | petefred | Add some missing fragments
* molefacture/lib/fragments/phospho.frag 1.1 (added +23 -0)
* molefacture/lib/fragments/nitro.frag 1.1 (added +14 -0)
* molefacture/lib/fragments/nitrile.frag 1.1 (added +11 -0)
* molefacture/lib/fragments/indole.frag 1.1 (added +54 -0)
* molefacture/lib/fragments/epoxide.frag 1.1 (added +25 -0)
* molefacture/lib/fragments/cyclooctane.frag 1.1 (added +76 -0)
* molefacture/lib/fragments/cycloheptane.frag 1.1 (added +67 -0)
* molefacture/lib/fragments/carboxylate.frag 1.1 (added +14 -0)
* molefacture/lib/basemol/sulfate.mfrag 1.1 (added +20 -0)
* molefacture/lib/basemol/pyrrole.mfrag 1.1 (added +37 -0)
* molefacture/lib/basemol/pyridine.mfrag 1.1 (added +40 -0)
* molefacture/lib/basemol/pyrazole.mfrag 1.1 (added +34 -0)
* molefacture/lib/basemol/piperazine.mfrag 1.1 (added +55 -0)
* molefacture/lib/basemol/oxyrane.mfrag 1.1 (added +28 -0)
* molefacture/lib/basemol/norbornane.mfrag 1.1 (added +66 -0)
* molefacture/lib/basemol/indole.mfrag 1.1 (added +57 -0)
* molefacture/lib/basemol/hcn.mfrag 1.1 (added +14 -0)
* molefacture/lib/basemol/formic_acid.mfrag 1.1 (added +17 -0)
* molefacture/lib/basemol/cyclooctane.mfrag 1.1 (added +79 -0)
* molefacture/lib/basemol/cycloheptane.mfrag 1.1 (added +70 -0)
* molefacture/lib/basemol/anthracene.mfrag 1.1 (added +83 -0)
|
| | 2009-08-12 | ltrabuco | Added support for nucleic acid residue naming convention used by Coot, i.e.,
Ar, Ad, Cr, Cd, etc.
* autopsf/autopsf.tcl 1.114 (changed +15 -6)
|
| | 2009-08-11 | saam | A bunch of minor improvements.
* ilstools/pkgIndex.tcl 1.4 (changed +1 -1)
* ilstools/ilstools.tcl 1.9 (changed +60 -11)
* ilstools/Makefile 1.5 (changed +2 -2)
Add graphics for docs.
* symmetrytool/doc/symm_phenanthrene_small.png 1.1 (added +142 -0)
* symmetrytool/doc/symm_gui_labeled_small.png 1.1 (added +327 -0)
* symmetrytool/doc/symm_coronene_small.png 1.1 (added +269 -0)
* symmetrytool/doc/index.html 1.2 (changed +34 -18)
Correcct the range for cases where we don't start with the first frame
of the trajectory.
* ilstools/ilstools.tcl 1.10 (changed +1 -1)
Improved docs.
* ilstools/doc/index.html 1.4 (changed +5 -3)
Made GUI shot a bit bigger.
* symmetrytool/doc/symm_gui_labeled_small.png 1.2 (changed +492 -320)
|
| | 2009-08-07 | ltrabuco | Prevent resetting of top molecule.
* mdff/mdff_check.tcl 1.2 (changed +3 -1)
|
| | 2009-08-07 | barryi | Minor cosmetic fix: 'every residue' button appears now correctly on Windows, Mac OS X (still fine on Linux)
* timeline/timeline.tcl 1.59 (changed +2 -2)
|
| | 2009-08-06 | ltrabuco | Added MDFF plugin.
* mdff/pkgIndex.tcl 1.1 (added +22 -0)
* mdff/mdff_tmp.tcl 1.1 (added +221 -0)
* mdff/mdff_template.namd 1.1 (added +131 -0)
* mdff/mdff_sim.tcl 1.1 (added +131 -0)
* mdff/mdff_setup.tcl 1.1 (added +630 -0)
* mdff/mdff_map.tcl 1.1 (added +360 -0)
* mdff/mdff_correlation.tcl 1.1 (added +154 -0)
* mdff/mdff_check.tcl 1.1 (added +362 -0)
* mdff/mdff.tcl 1.1 (added +103 -0)
* mdff/Makefile 1.1 (added +24 -0)
Added mdff and volutil plugins.
* Makefile 1.111 (changed +3 -1)
Added volutil package, required by MDFF at present. A known problem that
we need to address is that volutil relies on a non-portable test for NaN
(breaks down on Solaris with the compiler optimizations we use).
Compilation hasn't been tested on Windows yet.
* volutil/volutil.tcl 1.1 (added +93 -0)
* volutil/src/voxels.C 1.1 (added +224 -0)
* volutil/src/volmap.h 1.1 (added +196 -0)
* volutil/src/volmap.C 1.1 (added +266 -0)
* volutil/src/vec.h 1.1 (added +146 -0)
* volutil/src/vec.C 1.1 (added +49 -0)
* volutil/src/unary_ops.C 1.1 (added +607 -0)
* volutil/src/params.h 1.1 (added +126 -0)
* volutil/src/params.C 1.1 (added +453 -0)
* volutil/src/ops.h 1.1 (added +46 -0)
* volutil/src/ops.C 1.1 (added +94 -0)
* volutil/src/molfile.C 1.1 (added +287 -0)
* volutil/src/main.C 1.1 (added +146 -0)
* volutil/src/io.C 1.1 (added +265 -0)
* volutil/src/hash.h 1.1 (added +61 -0)
* volutil/src/hash.C 1.1 (added +287 -0)
* volutil/src/getplugins.h 1.1 (added +51 -0)
* volutil/src/getplugins.C 1.1 (added +178 -0)
* volutil/src/convolutions.C 1.1 (added +223 -0)
* volutil/src/binary_ops.C 1.1 (added +804 -0)
* volutil/pkgIndex.tcl 1.1 (added +16 -0)
* volutil/Makefile 1.1 (added +112 -0)
|
| | 2009-08-06 | johns | Added a MacOS X build config for cionize.
* cionize/Makefile.specialbuilds 1.24 (changed +17 -1)
Replaced "uint" by "unsigned int" to please MacOS X.
* cionize/mgpot_cuda_latcut04.cu 1.4 (changed +8 -8)
|
| | 2009-08-02 | johns | Built mseq manual
* multiseq/doc/mseq_manual.pdf 1.1 (added binary)
Change url for pre-built mseq_manual.pdf
* multiseq/doc/src/mseq_manual.pdf 1.2 (changed +388 -366)
* multiseq/doc/index.html 1.5 (changed +1 -1)
|
vmd-1-8-7
| 2009-08-01 | johns | Fix behavior of solvate for pathnames containing spaces.
* solvate/solvate.tcl 1.52 (changed +2 -2)
Fix the problem with nonexisting occupancies for MCSCF optimized orbitals.
* molfile_plugin/src/gamessplugin.c 1.182 (changed +29 -2)
Made autoionize gui properly handle spaces in filenames when building
ionize command.
* autoionize/autoionizegui.tcl 1.5 (changed +2 -3)
|
| | 2009-07-31 | saam | Cleanup and modularize the way multiple sets of wavefunctions are
parsed.
Complete the MCSCF parsing scheme so that all wavefunctions are read.
Silence some of the debuggin chatter and make remaining output more
readable.
* molfile_plugin/src/gamessplugin.c 1.180 (changed +148 -178)
|
| | 2009-07-31 | johns | Fixed c++ism in gamessplugin
* molfile_plugin/src/gamessplugin.c 1.181 (changed +2 -2)
|
| | 2009-07-30 | saam | Deny service gracefully if user tris to load a PC GAMESS file.
* molfile_plugin/src/gamessplugin.c 1.179 (changed +44 -40)
Fix parsing of SURFACE scan calculations.
Now all logfiles from 2000 that Axel provided can be loaded.
* molfile_plugin/src/gamessplugin.c 1.178 (changed +93 -50)
|
| | 2009-07-30 | kvandivo | Slight revisions to the status bar changes (for modified bases) that I made
last week. When talking to Elijah I thought up a way to make it show the
3 letter codes for all question marks (including things like HOH for water)
so now that is being displayed.
* seqedit/seqedit_widget_statusbar.tcl 1.6 (changed +3 -2)
|
| | 2009-07-29 | saam | Change a few search strings to be able to read GAMESS logfiles from
2000.
* molfile_plugin/src/gamessplugin.c 1.177 (changed +19 -18)
|
| | 2009-07-29 | johns | Fixed C++isms in gamessplugin
* molfile_plugin/src/gamessplugin.c 1.176 (changed +5 -5)
Switch solaris builds to cupertino due to another machine failure
* build.csh 1.90 (changed +2 -2)
|
| | 2009-07-29 | gumbart | Updated parameter file to latest charmm version including CMAP terms
* readcharmmpar/par_all27_prot_lipid_na.inp 1.3 (changed +1446 -207)
|
| | 2009-07-28 | saam | Allow automatic recentering of the molecule and re-wrapping of the
solvent.
Upgraded version number.
* ilstools/pkgIndex.tcl 1.3 (changed +1 -1)
* ilstools/ilstools.tcl 1.8 (changed +164 -77)
* ilstools/Makefile 1.4 (changed +2 -2)
Eliminated per-molecule charges (ESP) even though some of them are
per-molecule in GAMESS. Instead we have a number of charge sets with
an type associated type per timestep.
* include/molfile_plugin.h 1.91 (changed +9 -7)
Fixed a bunch of problems with reading charges.
Eliminated per-molecule charges (ESP) even though some of them are
per-molecule in GAMESS. Instead we have a number of charge sets with
an type associated type per timestep. These can either be empty or populated.
* molfile_plugin/src/gamessplugin.h 1.82 (changed +7 -11)
* molfile_plugin/src/gamessplugin.c 1.175 (changed +111 -42)
* molfile_plugin/src/basissetplugin.c 1.6 (changed +1 -3)
|
| | 2009-07-27 | saam | Fix typo.
* ilstools/ilstools.tcl 1.7 (changed +1 -1)
|
| | 2009-07-27 | akohlmey | Preserve information about atom masses in more cases, particularly
for extended CGCMM style of lammps data files.
* topotools/topolammps.tcl 1.18 (changed +27 -7)
|
| | 2009-07-25 | johns | Comment out link to timeline_examples which doesn't yet exist.
* timeline/doc/index.html 1.12 (changed +3 -0)
Fix timeline plugin doc page
* timeline/doc/index.html 1.10 (changed +1 -1)
More html fixes
* timeline/doc/index.html 1.11 (changed +2 -0)
|
| | 2009-07-25 | akohlmey | Avoid null-pointer dereference.
* molfile_plugin/src/hoomdplugin.c 1.12 (changed +7 -5)
|
| | 2009-07-24 | barryi | Documentation additions, changes
* timeline/doc/timeline.gif 1.2 (changed binary)
* timeline/doc/timeline-thumb.gif 1.2 (changed binary)
* timeline/doc/index.html 1.8 (changed +69 -17)
Documentation changes
* timeline/doc/index.html 1.9 (changed +35 -35)
Gui fixes (appearance)
* timeline/timeline.tcl 1.58 (changed +16 -14)
|
| | 2009-07-24 | akohlmey | Make units scale factor handling more consistent.
allocate storage for velocities so they are not only parsed
but also handed on to VMD.
* molfile_plugin/src/hoomdplugin.c 1.11 (changed +18 -7)
Need to initialize massscale to 1.0 and not 0.0 for
mass tags without the units attribute.
* molfile_plugin/src/hoomdplugin.c 1.10 (changed +2 -1)
|
| | 2009-07-23 | johns | Changed string table allocations to use calloc so that unused
string table memory is always cleared to zeros. This makes it possible
to do binary compares on files that contain identical payload data but were
written on different hosts, or at different times.
* molfile_plugin/src/jsplugin.c 1.37 (changed +7 -7)
Fix bug in the length of the swap4() calls for some of the string
table length parameters when reading an opposite-endian file.
* molfile_plugin/src/jsplugin.c 1.35 (changed +7 -7)
Fixed another endian swapping buglet
* molfile_plugin/src/jsplugin.c 1.36 (changed +6 -6)
|
| | 2009-07-22 | johns | Replaced failed sundemo build box with asuncion, which is freshtly reinstalled
* build.csh 1.89 (changed +2 -2)
|
| | 2009-07-21 | gumbart | Update docs to ver. 1.4
* multiplot/doc/index.html 1.12 (changed +24 -2)
|
| | 2009-07-21 | akohlmey | Adding full support for atom style dpd and partial support for style hybrid.
* topotools/topolammps.tcl 1.17 (changed +15 -2)
Need to use atom index maps when merging selections to molecules.
* topotools/topoutils.tcl 1.7 (changed +20 -6)
Sorting the atom index map is very useful to optimize for the common case
that we don't need a hashtable, however, that destroys the map for the
less common case that we actually need it. with the imminent release we
have to stick to to always using the hashtable.
* molfile_plugin/src/lammpsplugin.c 1.27 (changed +11 -4)
|
| | 2009-07-20 | saam | Added JC's changes. multiplot now accepts parameters -xmin -xmax -ymin -ymax to specify the
plot range manually.
* multiplot/pkgIndex.tcl 1.5 (changed +1 -1)
* multiplot/multiplot.tcl 1.31 (changed +211 -40)
* multiplot/Makefile 1.5 (changed +2 -2)
Fix a few minor problems with molecule update.
* symmetrytool/symmetry.tcl 1.12 (changed +22 -9)
Improved behaviour of the molecule selector/updater. List molecule
ID and name instead of just the ID.
* symmetrytool/symmetry.tcl 1.11 (changed +22 -13)
* symmetrytool/pkgIndex.tcl 1.4 (changed +1 -1)
* symmetrytool/Makefile 1.4 (changed +2 -2)
Set the working molecule to the first molecule with numframes>0 when
the current molecule gets deleted by the user.
* symmetrytool/symmetry.tcl 1.10 (changed +11 -3)
|
| | 2009-07-20 | kvandivo | Removed a couple of commented out lines
* libbiokit/src/libbiokit/alphabetBuilder.cpp 1.2 (changed +0 -4)
|
| | 2009-07-19 | akohlmey | Bond types need to be canonicalized on retyping.
* topotools/topobonds.tcl 1.7 (changed +1 -0)
|
| | 2009-07-18 | akohlmey | We have to canonicalize dihedral- and impropertypes based on the
types of atoms 1 and 4, if the types of 2 and 3 are identical.
* topotools/topoimpropers.tcl 1.2 (changed +2 -1)
* topotools/topodihedrals.tcl 1.2 (changed +2 -1)
|
| | 2009-07-17 | kvandivo | Add the pdf manual and change the main multiseq html page to reference it
* multiseq/doc/src/mseq_manual.pdf 1.1 (added +7326 -0)
* multiseq/doc/src/.cvsignore 1.2 (changed +0 -1)
* multiseq/doc/index.html 1.4 (changed +6 -52)
Added in a check to see if bead definitions have been loaded before trying
to apply them. Should help in debugging incorrect tool usage from the
command line.
* cgtools/cgtools.tcl 1.15 (changed +4 -0)
|
| | 2009-07-16 | barryi | Fixed selection info formatting for free selections, fixed vertical scale problems
for both free and per-res selections.
* timeline/timeline.tcl 1.57 (changed +14 -16)
|
| | 2009-07-15 | saam | Show non-unique axes of inertia in half size and in grey instead of
white.
Add checkbuttons to show/hide symmetry elements.
* symmetrytool/symmetry.tcl 1.9 (changed +120 -79)
|
| | 2009-07-15 | kvandivo | For modified bases, the status bar now displays the modified 3 letter
residue code. The sequence window still shows a '?' (much more difficult
to change), but a user can now click on a modified base residue and see what
the 3 letter code is, as zls had asked about.
* seqedit/seqedit_widget_statusbar.tcl 1.5 (changed +11 -1)
|
| | 2009-07-14 | saam | Added symmetrytool_tk {} callback function.
Improved color scheme for drawing rotation axes and inversion center.
* symmetrytool/symmetry.tcl 1.7 (changed +14 -5)
Improve color scheme further .
Make output less verbose.
* symmetrytool/symmetry.tcl 1.8 (changed +5 -6)
|
| | 2009-07-14 | kvandivo | Added a note about the main multiseq window redrawing more slowly than
normal if the zoom window is open.
* multiseq/doc/src/viewMenu.tex 1.4 (changed +4 -0)
Added in a check for the temp directory to make sure that: a) it is given,
and b) it is writeable. If not, let the user know, and tell them how to
specify a good one.
* multiseq/multiseq.tcl 1.16 (changed +15 -1)
Fixed a bug where some code didn't like a temp dir not being specified
* multiseq/multiseq.tcl 1.17 (changed +0 -2)
Revise zoom window so that it updates when the main window updates.
* seqedit/seqedit_widget.tcl 1.7 (changed +83 -59)
|
| | 2009-07-13 | saam | Add molecule selector and handle cases where no molecules are present or
where molecules have been deleted.
* symmetrytool/symmetry.tcl 1.5 (changed +137 -27)
Remove debugging output.
* symmetrytool/symmetry.tcl 1.6 (changed +0 -1)
|
| | 2009-07-13 | kvandivo | Added in a check to prevent Residue: -1 from showing up on the statusbar
* seqedit/seqedit_widget_statusbar.tcl 1.4 (changed +1 -1)
Comment shortening
* multiseq/multiseq.tcl 1.15 (changed +1 -1)
Formatting
* seqdata/seqdata.tcl 1.6 (changed +3 -0)
Removed extraneous tcl comments
* phylotree/phylotree_widget.tcl 1.3 (changed +0 -42)
Revised column selection to not duplicate starting column. Also revised proc
that returns curated selected cell information to sort the residues.
* seqedit/seqedit_widget_select.tcl 1.4 (changed +15 -16)
Revised phylotree proc to use curated selected cell information. Fixes
a bug or two that can occur, depending on how cells are being selected.
* multiseq/multiseq.tcl 1.14 (changed +4 -4)
Typos, font changes for readability, and other corrections
* multiseq/doc/src/workingEnviron.tex 1.3 (changed +11 -10)
* multiseq/doc/src/viewMenu.tex 1.3 (changed +30 -30)
* multiseq/doc/src/searchMenu.tex 1.3 (changed +19 -15)
* multiseq/doc/src/savingData.tex 1.2 (changed +24 -24)
* multiseq/doc/src/plotData.tex 1.4 (changed +8 -8)
* multiseq/doc/src/phyloTree.tex 1.4 (changed +8 -8)
* multiseq/doc/src/mseq_manual.tex 1.5 (changed +2 -3)
* multiseq/doc/src/mainWindow.tex 1.4 (changed +8 -7)
* multiseq/doc/src/intro.tex 1.3 (changed +12 -10)
* multiseq/doc/src/editMenu.tex 1.2 (changed +10 -10)
* multiseq/doc/src/data.tex 1.2 (changed +42 -36)
* multiseq/doc/src/alignment.tex 1.2 (changed +1 -1)
When extracting regions, properly handle the cases where no elements in
a region exist because they are all gaps. That particular case wasn't
being checked, which was resulting in a crash.
* seqdata/seqdata_vmd.tcl 1.8 (changed +38 -23)
|
| | 2009-07-13 | johns | Updated molefacture documentation with author list as per Chris Chipot's
request.
* molefacture/doc/index.html 1.13 (changed +11 -1)
Workaround lack of sqrtf() on Windows platforms
* molfile_plugin/src/gamessplugin.c 1.174 (changed +5 -1)
|
| | 2009-07-12 | saam | Add symmetrytool.
* Makefile 1.110 (changed +1 -0)
Correct the file path in pkgIndex.tcl.
Fix a type.
* symmetrytool/pkgIndex.tcl 1.2 (changed +1 -1)
* symmetrytool/Makefile 1.2 (changed +1 -1)
Gracefully ignore everything in case no molecule is loaded.
Fix indentation in several places.
* symmetrytool/symmetry.tcl 1.4 (changed +48 -40)
Increase minor version.
* symmetrytool/symmetry.tcl 1.3 (changed +1 -1)
* symmetrytool/pkgIndex.tcl 1.3 (changed +1 -1)
* symmetrytool/Makefile 1.3 (changed +1 -1)
Minor bugfix, allowing to list Cinf axes correctly.
* symmetrytool/symmetry.tcl 1.2 (changed +6 -5)
|
| | 2009-07-11 | saam | Expand symmetry unique atoms by creating images of
the atoms so that we have the full coordinate set.
For now we need this for MEX trajectories but, I suspect there are many
more cases where GAMESS doesn't print the full set of atoms.
* molfile_plugin/src/gamessplugin.h 1.81 (changed +6 -2)
* molfile_plugin/src/gamessplugin.c 1.173 (changed +309 -19)
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