| 2012-01-17 |
toshinagata1964 | Dialog#layout: the :align and :vertical_align options...
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commit | commitdiff | tree |
| 2012-01-17 |
toshinagata1964 | The separator line in the Ruby Dialog was not working...
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commit | commitdiff | tree |
| 2012-01-17 |
toshinagata1964 | Vector3D and Transform objects are converted to LAMatrix...
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commit | commitdiff | tree |
| 2012-01-16 |
toshinagata1964 | LAMatrix#new errornously allows matrix with dimension...
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commit | commitdiff | tree |
| 2012-01-16 |
toshinagata1964 | AtomRef#molecule is implemented.
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commit | commitdiff | tree |
| 2012-01-16 |
toshinagata1964 | Empty Console Window command is implemented.
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commit | commitdiff | tree |
| 2012-01-13 |
toshinagata1964 | LAMatrix.multiply was not working correctly when the...
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commit | commitdiff | tree |
| 2011-12-22 |
toshinagata1964 | General matrix calculation (LAMatrix class in Ruby...
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commit | commitdiff | tree |
| 2011-12-21 |
toshinagata1964 | Some of the document figures are updated.
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commit | commitdiff | tree |
| 2011-12-21 |
toshinagata1964 | General matrix calculation is being implemented (still...
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commit | commitdiff | tree |
| 2011-12-20 |
toshinagata1964 | Figures in the MD section of the document are added.
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commit | commitdiff | tree |
| 2011-12-20 |
toshinagata1964 | In the document, navigation between the English/Japanese...
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commit | commitdiff | tree |
| 2011-12-20 |
toshinagata1964 | Document for MD calculation is written.
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commit | commitdiff | tree |
| 2011-12-19 |
toshinagata1964 | The "log file" field is set to blank unless explicitly...
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commit | commitdiff | tree |
| 2011-12-19 |
toshinagata1964 | Document for MD calculation is being written.
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commit | commitdiff | tree |
| 2011-12-07 |
toshinagata1964 | The structure Mat33 and Transform are now column-first...
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commit | commitdiff | tree |
| 2011-11-30 |
toshinagata1964 | Rms of crystallographic parameters (from the CIF file...
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commit | commitdiff | tree |
| 2011-11-30 |
toshinagata1964 | Memo update for 0.6.1; also updated molby.iss for building...
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commit | commitdiff | tree |
| 2011-11-26 |
toshinagata1964 | Version 0.6.1
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commit | commitdiff | tree |
| 2011-11-26 |
toshinagata1964 | Document on ring fusion capability is written.
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commit | commitdiff | tree |
| 2011-11-26 |
toshinagata1964 | Selection after ring fusion by 'double-click and type...
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commit | commitdiff | tree |
| 2011-11-26 |
toshinagata1964 | Behavior of paste is improved when two dangling bonds...
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commit | commitdiff | tree |
| 2011-11-26 |
toshinagata1964 | Some typical cyclic structures as well as solvent boxes...
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commit | commitdiff | tree |
| 2011-11-25 |
toshinagata1964 | Ruby: Molecule object is now unique to each open molecule...
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commit | commitdiff | tree |
| 2011-11-23 |
toshinagata1964 | Ring fusion (e.g. expanding benzene to naphthalene...
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commit | commitdiff | tree |
| 2011-11-22 |
toshinagata1964 | __FILE__ is now set to the script file during execute_script.
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commit | commitdiff | tree |
| 2011-10-31 |
toshinagata1964 | Some cleanup to suppress warnings
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commit | commitdiff | tree |
| 2011-10-31 |
toshinagata1964 | CIF import is improved, so that bonds including the...
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commit | commitdiff | tree |
| 2011-10-31 |
toshinagata1964 | Ruby: Molecule#find_close_atoms is implemented.
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commit | commitdiff | tree |
| 2011-10-21 |
toshinagata1964 | Enable undo for importing pdb and dcd.
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commit | commitdiff | tree |
| 2011-10-19 |
toshinagata1964 | Import/export of dcd format is implemented.
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commit | commitdiff | tree |
| 2011-10-19 |
toshinagata1964 | Creating AMBER input now allows to select between AMBER8...
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commit | commitdiff | tree |
| 2011-10-15 |
toshinagata1964 | Version 0.6
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commit | commitdiff | tree |
| 2011-10-15 |
toshinagata1964 | On Windows, Molby::{Mbsf,Resource,Script}Path return...
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commit | commitdiff | tree |
| 2011-10-13 |
toshinagata1964 | The solvate command does not correctly remove conflicting...
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commit | commitdiff | tree |
| 2011-10-13 |
toshinagata1964 | Ruby: find_conflicts now exclude atom pairs separated...
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commit | commitdiff | tree |
| 2011-10-13 |
toshinagata1964 | export_prmtop can now be used from script
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Merging molecule was resulting in strange order of...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Occasional crash on merging molecules is fixed. (Duplicating...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Some solvent box are included in Scripts/mbsf folder...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | rotate_with_axis now can accept atom indices or names...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Setting external forces during MM/MD is implemented.
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commit | commitdiff | tree |
| 2011-10-11 |
toshinagata1964 | Special parameters with atom indices were not working...
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commit | commitdiff | tree |
| 2011-10-11 |
toshinagata1964 | Inserting/removing frames now work more consistently...
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commit | commitdiff | tree |
| 2011-10-05 |
toshinagata1964 | Atoms to be excluded from MM/MD calculations are now...
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commit | commitdiff | tree |
| 2011-10-05 |
toshinagata1964 | MM/MD calculation crashed when periodic cell is removed...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | Makefile: "make depend" now creates a dependency file...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | On windows, Molecule#path, Molecule#dir does not work...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | On windows, Molecule#path, Molecule#dir does not work...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | After MD run, coordinates are copied back to the molecule...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | During alchemical perturbation, graphite energy/forces...
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commit | commitdiff | tree |
| 2011-09-28 |
toshinagata1964 | Implementation of alchemical perturbation seems to...
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commit | commitdiff | tree |
| 2011-09-27 |
toshinagata1964 | Experimental implementation of alchemical perturbation...
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commit | commitdiff | tree |
| 2011-09-26 |
toshinagata1964 | Improve crd/mdcrd import.
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commit | commitdiff | tree |
| 2011-09-26 |
toshinagata1964 | The \'r_eq14\' parameter was not editable in the property...
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commit | commitdiff | tree |
| 2011-09-26 |
toshinagata1964 | Crash occurs when a Ruby exception is raised while...
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commit | commitdiff | tree |
| 2011-09-20 |
toshinagata1964 | Mac: use pthread instead of SIGALRM for interval timer...
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commit | commitdiff | tree |
| 2011-09-18 |
toshinagata1964 | Ruby: Molecule#dup now duplicates the unit cell, symmetry...
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commit | commitdiff | tree |
| 2011-09-15 |
toshinagata1964 | Remove \'build xxxxxxxx\' string from the version description.
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commit | commitdiff | tree |
| 2011-09-14 |
toshinagata1964 | AtomRef.exclusion causes bus error when the MDArena...
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commit | commitdiff | tree |
| 2011-09-13 |
toshinagata1964 | After loading the molecule, occupancy factors are checked...
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commit | commitdiff | tree |
| 2011-09-07 |
toshinagata1964 | Remove some startup code when building a command line...
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commit | commitdiff | tree |
| 2011-09-07 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD-graphite...
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commit | commitdiff | tree |
| 2011-09-06 |
toshinagata1964 | Ruby command get_coord_from_frame(index, group=nil...
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commit | commitdiff | tree |
| 2011-09-06 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD calculations
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commit | commitdiff | tree |
| 2011-09-06 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD calculations
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commit | commitdiff | tree |
| 2011-09-05 |
toshinagata1964 | The (experimental) command line version does not compile...
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commit | commitdiff | tree |
| 2011-09-01 |
toshinagata1964 | The MO info table is renamed to MO energy, and the...
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commit | commitdiff | tree |
| 2011-08-31 |
toshinagata1964 | MO import from GAMESS log file was broken
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commit | commitdiff | tree |
| 2011-08-31 |
toshinagata1964 | Fchk import: zero is accepted as the number of alpha...
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commit | commitdiff | tree |
| 2011-08-23 |
toshinagata1964 | Memo update for version 0.5.6.2
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commit | commitdiff | tree |
| 2011-08-23 |
toshinagata1964 | Fchk import was broken (enbug in 0.5.6.1); fixed.
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commit | commitdiff | tree |
| 2011-08-19 |
toshinagata1964 | Final compile date/time is shown in the 'About' window
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commit | commitdiff | tree |
| 2011-08-19 |
toshinagata1964 | Importing mdcrd was still broken. Fixed (hopefully)
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commit | commitdiff | tree |
| 2011-08-05 |
toshinagata1964 | Fix mdcrd import to allow coordinates using full 8...
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commit | commitdiff | tree |
| 2011-08-05 |
toshinagata1964 | Occasional crash during minimization is fixed.
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commit | commitdiff | tree |
| 2011-08-05 |
toshinagata1964 | memo update
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | memo update
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Loading GAMESS dat file now can be interrupted by ESC.
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Occasionally, termination of the subprocess (like antechambe...
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Disable close box of RubyDialogFrame.
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | On importing frcmod, atom type with a single character...
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Mac: config.h/Makefiles for AmberTools is modified...
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | ruby-1.8.7-p160.tar.gz is added (required for building)
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commit | commitdiff | tree |
| 2011-08-02 |
toshinagata1964 | MO import from GAMESS log/dat files seems to be working...
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commit | commitdiff | tree |
| 2011-08-01 |
toshinagata1964 | MO import from GAMESS output is being implemented ...
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Memo update.
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Add missing document figures.
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Parameter cut was not working correctly when the selection...
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Step 5 of the tutorial is complete.
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commit | commitdiff | tree |
| 2011-07-29 |
toshinagata1964 | Import AMBER Frcmod menu command is implemented.
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commit | commitdiff | tree |
| 2011-07-28 |
toshinagata1964 | The property table section of the tutorial is being...
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commit | commitdiff | tree |
| 2011-07-28 |
toshinagata1964 | CIF import is implemented (maybe still incomplete)
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commit | commitdiff | tree |
| 2011-07-26 |
toshinagata1964 | Create New Parameter menu command is implemented. MoleculePr...
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commit | commitdiff | tree |
| 2011-07-21 |
toshinagata1964 | Create New Atom menu command is being implemented ...
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commit | commitdiff | tree |
| 2011-07-21 |
toshinagata1964 | Document is being updated (the property table section)
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commit | commitdiff | tree |
| 2011-07-21 |
toshinagata1964 | Importing frcmod is improved. Import AMBER Lib (in...
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commit | commitdiff | tree |
| 2011-07-20 |
toshinagata1964 | Importing mdcrd with periodic box now works correctly.
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commit | commitdiff | tree |
| 2011-07-20 |
toshinagata1964 | AMBER prmtop/inpcrd export is improved for periodic...
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commit | commitdiff | tree |
| 2011-07-07 |
toshinagata1964 | Copy/paste now handle parameters properly (hopefully...
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commit | commitdiff | tree |
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