OSDN Git Service
toshinagata1964 [Tue, 17 Jan 2012 06:42:55 +0000 (06:42 +0000)]
Vector3D and Transform objects are converted to LAMatrix object with dimensions 3 or 4 depending upon the context.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@174
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toshinagata1964 [Mon, 16 Jan 2012 10:45:21 +0000 (10:45 +0000)]
LAMatrix#new errornously allows matrix with dimension 0. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@173
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toshinagata1964 [Mon, 16 Jan 2012 10:43:56 +0000 (10:43 +0000)]
AtomRef#molecule is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@172
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toshinagata1964 [Mon, 16 Jan 2012 10:13:37 +0000 (10:13 +0000)]
Empty Console Window command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@171
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toshinagata1964 [Fri, 13 Jan 2012 11:07:55 +0000 (11:07 +0000)]
LAMatrix.multiply was not working correctly when the first argument is a scalar. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@170
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toshinagata1964 [Thu, 22 Dec 2011 11:32:49 +0000 (11:32 +0000)]
General matrix calculation (LAMatrix class in Ruby) is implemented. Seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@169
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toshinagata1964 [Wed, 21 Dec 2011 00:40:23 +0000 (00:40 +0000)]
Some of the document figures are updated.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@168
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toshinagata1964 [Wed, 21 Dec 2011 00:02:41 +0000 (00:02 +0000)]
General matrix calculation is being implemented (still on the way)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@167
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toshinagata1964 [Tue, 20 Dec 2011 23:53:21 +0000 (23:53 +0000)]
Figures in the MD section of the document are added.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@166
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toshinagata1964 [Tue, 20 Dec 2011 10:48:33 +0000 (10:48 +0000)]
In the document, navigation between the English/Japanese versions is possible in most pages.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@165
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toshinagata1964 [Tue, 20 Dec 2011 09:00:53 +0000 (09:00 +0000)]
Document for MD calculation is written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@164
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toshinagata1964 [Mon, 19 Dec 2011 10:24:13 +0000 (10:24 +0000)]
The "log file" field is set to blank unless explicitly set by the user.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@163
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toshinagata1964 [Mon, 19 Dec 2011 10:23:10 +0000 (10:23 +0000)]
Document for MD calculation is being written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@162
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toshinagata1964 [Wed, 7 Dec 2011 11:07:33 +0000 (11:07 +0000)]
The structure Mat33 and Transform are now column-first arrangement (no change on Ruby interface and mbsf file format)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@161
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toshinagata1964 [Wed, 30 Nov 2011 11:10:35 +0000 (11:10 +0000)]
Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@160
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toshinagata1964 [Wed, 30 Nov 2011 04:59:56 +0000 (04:59 +0000)]
Memo update for 0.6.1; also updated molby.iss for building Windows executable.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@159
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toshinagata1964 [Sat, 26 Nov 2011 16:18:03 +0000 (16:18 +0000)]
Version 0.6.1
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@158
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toshinagata1964 [Sat, 26 Nov 2011 16:15:44 +0000 (16:15 +0000)]
Document on ring fusion capability is written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@157
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toshinagata1964 [Sat, 26 Nov 2011 16:15:00 +0000 (16:15 +0000)]
Selection after ring fusion by 'double-click and type-in' now includes all atoms in the newly formed ring.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@156
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toshinagata1964 [Sat, 26 Nov 2011 11:11:31 +0000 (11:11 +0000)]
Behavior of paste is improved when two dangling bonds are present in the fragment and the target molecule (i.e. ring fusion does work)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@155
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toshinagata1964 [Sat, 26 Nov 2011 07:25:35 +0000 (07:25 +0000)]
Some typical cyclic structures as well as solvent boxes are now accessible from 'Open Predefined' menu.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@154
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toshinagata1964 [Fri, 25 Nov 2011 09:31:13 +0000 (09:31 +0000)]
Ruby: Molecule object is now unique to each open molecule, i.e. the same Molecule object is returned when requested for the same molecule.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@153
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toshinagata1964 [Wed, 23 Nov 2011 16:08:17 +0000 (16:08 +0000)]
Ring fusion (e.g. expanding benzene to naphthalene) is implemented; still experimental, but seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@152
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toshinagata1964 [Tue, 22 Nov 2011 11:59:39 +0000 (11:59 +0000)]
__FILE__ is now set to the script file during execute_script.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@151
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toshinagata1964 [Mon, 31 Oct 2011 06:22:35 +0000 (06:22 +0000)]
Some cleanup to suppress warnings
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@150
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toshinagata1964 [Mon, 31 Oct 2011 06:10:41 +0000 (06:10 +0000)]
CIF import is improved, so that bonds including the calculated hydrogen atoms are created by guess.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@149
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toshinagata1964 [Mon, 31 Oct 2011 05:26:04 +0000 (05:26 +0000)]
Ruby: Molecule#find_close_atoms is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@148
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toshinagata1964 [Fri, 21 Oct 2011 00:45:13 +0000 (00:45 +0000)]
Enable undo for importing pdb and dcd.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@147
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toshinagata1964 [Wed, 19 Oct 2011 07:56:10 +0000 (07:56 +0000)]
Import/export of dcd format is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@146
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toshinagata1964 [Wed, 19 Oct 2011 07:55:18 +0000 (07:55 +0000)]
Creating AMBER input now allows to select between AMBER8 (also for NAMD) and AMBER11 formats.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@145
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toshinagata1964 [Sat, 15 Oct 2011 15:07:41 +0000 (15:07 +0000)]
Version 0.6
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@143
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toshinagata1964 [Sat, 15 Oct 2011 14:00:33 +0000 (14:00 +0000)]
On Windows, Molby::{Mbsf,Resource,Script}Path return slash-separated strings instead of backslash-separated strings.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@142
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toshinagata1964 [Thu, 13 Oct 2011 11:57:37 +0000 (11:57 +0000)]
The solvate command does not correctly remove conflicting solvent molecules. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@141
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toshinagata1964 [Thu, 13 Oct 2011 11:56:48 +0000 (11:56 +0000)]
Ruby: find_conflicts now exclude atom pairs separated by 0-3 bonds.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@140
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toshinagata1964 [Thu, 13 Oct 2011 00:27:00 +0000 (00:27 +0000)]
export_prmtop can now be used from script
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@139
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toshinagata1964 [Wed, 12 Oct 2011 16:13:25 +0000 (16:13 +0000)]
Merging molecule was resulting in strange order of merged parameters. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@138
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toshinagata1964 [Wed, 12 Oct 2011 16:12:42 +0000 (16:12 +0000)]
Occasional crash on merging molecules is fixed. (Duplicating parameters was causing problems.)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@137
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toshinagata1964 [Wed, 12 Oct 2011 10:38:37 +0000 (10:38 +0000)]
Some solvent box are included in Scripts/mbsf folder. MolbyResourcePath is now called Molby::ResourcePath (old name is still usable for backward compatibility). Molby::ScriptPath, Molby::MbsfPath are also implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@136
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toshinagata1964 [Wed, 12 Oct 2011 10:14:07 +0000 (10:14 +0000)]
rotate_with_axis now can accept atom indices or names as the first three arguments.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@135
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toshinagata1964 [Wed, 12 Oct 2011 10:13:08 +0000 (10:13 +0000)]
Setting external forces during MM/MD is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@134
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toshinagata1964 [Tue, 11 Oct 2011 16:45:16 +0000 (16:45 +0000)]
Special parameters with atom indices were not working. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@133
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toshinagata1964 [Tue, 11 Oct 2011 15:09:27 +0000 (15:09 +0000)]
Inserting/removing frames now work more consistently. The minimum number of frames is 1 instead of 0.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@132
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toshinagata1964 [Wed, 5 Oct 2011 15:45:32 +0000 (15:45 +0000)]
Atoms to be excluded from MM/MD calculations are now specified by mm_exclude instead of occupancy.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@131
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toshinagata1964 [Wed, 5 Oct 2011 14:44:26 +0000 (14:44 +0000)]
MM/MD calculation crashed when periodic cell is removed after calculation with non-nil cell. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@130
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toshinagata1964 [Fri, 30 Sep 2011 16:02:19 +0000 (16:02 +0000)]
Makefile: "make depend" now creates a dependency file in the building directory.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@129
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toshinagata1964 [Fri, 30 Sep 2011 09:33:21 +0000 (09:33 +0000)]
On windows, Molecule#path, Molecule#dir does not work correctly when the path includes double-byte characters. Fixed. (MyMBConv.h added)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@128
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toshinagata1964 [Fri, 30 Sep 2011 09:32:27 +0000 (09:32 +0000)]
On windows, Molecule#path, Molecule#dir does not work correctly when the path includes double-byte characters. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@127
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toshinagata1964 [Fri, 30 Sep 2011 02:45:53 +0000 (02:45 +0000)]
After MD run, coordinates are copied back to the molecule even when MD stopped abnormally. MDArena#init_velocities and MDArena#scale_velocities are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@126
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toshinagata1964 [Fri, 30 Sep 2011 02:44:17 +0000 (02:44 +0000)]
During alchemical perturbation, graphite energy/forces were calculated incorrectly; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@125
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toshinagata1964 [Wed, 28 Sep 2011 11:47:14 +0000 (11:47 +0000)]
Implementation of alchemical perturbation seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@124
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toshinagata1964 [Tue, 27 Sep 2011 23:05:08 +0000 (23:05 +0000)]
Experimental implementation of alchemical perturbation (not tested yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@123
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toshinagata1964 [Mon, 26 Sep 2011 15:50:15 +0000 (15:50 +0000)]
Improve crd/mdcrd import.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@122
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toshinagata1964 [Mon, 26 Sep 2011 10:14:36 +0000 (10:14 +0000)]
The \'r_eq14\' parameter was not editable in the property table. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@121
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toshinagata1964 [Mon, 26 Sep 2011 10:13:45 +0000 (10:13 +0000)]
Crash occurs when a Ruby exception is raised while editing property table. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@120
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toshinagata1964 [Tue, 20 Sep 2011 11:49:19 +0000 (11:49 +0000)]
Mac: use pthread instead of SIGALRM for interval timer (experimental)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@119
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toshinagata1964 [Sun, 18 Sep 2011 13:41:46 +0000 (13:41 +0000)]
Ruby: Molecule#dup now duplicates the unit cell, symmetry operations, and MD settings.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@118
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toshinagata1964 [Thu, 15 Sep 2011 10:29:51 +0000 (10:29 +0000)]
Remove \'build xxxxxxxx\' string from the version description.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@117
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toshinagata1964 [Wed, 14 Sep 2011 16:21:31 +0000 (16:21 +0000)]
AtomRef.exclusion causes bus error when the MDArena is not yet built. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@116
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toshinagata1964 [Tue, 13 Sep 2011 16:17:53 +0000 (16:17 +0000)]
After loading the molecule, occupancy factors are checked, and if all atoms have zero occupancy then all are set to 1.0.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@115
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toshinagata1964 [Wed, 7 Sep 2011 16:00:28 +0000 (16:00 +0000)]
Remove some startup code when building a command line tool
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@114
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toshinagata1964 [Wed, 7 Sep 2011 15:59:51 +0000 (15:59 +0000)]
Exclude atoms with occupancy = 0 from MM/MD-graphite calculations
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@113
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toshinagata1964 [Tue, 6 Sep 2011 15:06:15 +0000 (15:06 +0000)]
Ruby command get_coord_from_frame(index, group=nil, cflag=nil) is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@112
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toshinagata1964 [Tue, 6 Sep 2011 10:24:16 +0000 (10:24 +0000)]
Exclude atoms with occupancy = 0 from MM/MD calculations
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@111
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toshinagata1964 [Tue, 6 Sep 2011 09:22:36 +0000 (09:22 +0000)]
Exclude atoms with occupancy = 0 from MM/MD calculations
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@110
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toshinagata1964 [Mon, 5 Sep 2011 10:06:12 +0000 (10:06 +0000)]
The (experimental) command line version does not compile; empty MainView_resizeToFit() is added to cmdtool_stubs.c.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@109
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toshinagata1964 [Thu, 1 Sep 2011 11:51:05 +0000 (11:51 +0000)]
The MO info table is renamed to MO energy, and the alpha and beta orbitals of same indices are shown in the same row.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@108
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toshinagata1964 [Wed, 31 Aug 2011 08:32:48 +0000 (08:32 +0000)]
MO import from GAMESS log file was broken
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@107
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toshinagata1964 [Wed, 31 Aug 2011 08:06:50 +0000 (08:06 +0000)]
Fchk import: zero is accepted as the number of alpha/beta electrons
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@106
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toshinagata1964 [Tue, 23 Aug 2011 09:59:21 +0000 (09:59 +0000)]
Memo update for version 0.5.6.2
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@104
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toshinagata1964 [Tue, 23 Aug 2011 09:49:47 +0000 (09:49 +0000)]
Fchk import was broken (enbug in 0.5.6.1); fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@103
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toshinagata1964 [Fri, 19 Aug 2011 11:43:22 +0000 (11:43 +0000)]
Final compile date/time is shown in the 'About' window
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@102
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toshinagata1964 [Fri, 19 Aug 2011 11:42:45 +0000 (11:42 +0000)]
Importing mdcrd was still broken. Fixed (hopefully)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@101
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toshinagata1964 [Fri, 5 Aug 2011 11:40:07 +0000 (11:40 +0000)]
Fix mdcrd import to allow coordinates using full 8 digits (like -123.456 or 1234.567)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@100
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toshinagata1964 [Fri, 5 Aug 2011 11:38:52 +0000 (11:38 +0000)]
Occasional crash during minimization is fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@99
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toshinagata1964 [Fri, 5 Aug 2011 11:38:11 +0000 (11:38 +0000)]
memo update
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@98
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toshinagata1964 [Wed, 3 Aug 2011 10:13:34 +0000 (10:13 +0000)]
memo update
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@96
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toshinagata1964 [Wed, 3 Aug 2011 10:12:54 +0000 (10:12 +0000)]
Loading GAMESS dat file now can be interrupted by ESC.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@95
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toshinagata1964 [Wed, 3 Aug 2011 10:12:02 +0000 (10:12 +0000)]
Occasionally, termination of the subprocess (like antechamber) was not detected properly, and the subprocess was left as a zombie. Improved, but may not be completely fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@94
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toshinagata1964 [Wed, 3 Aug 2011 10:10:16 +0000 (10:10 +0000)]
Disable close box of RubyDialogFrame.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@93
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toshinagata1964 [Wed, 3 Aug 2011 10:09:48 +0000 (10:09 +0000)]
On importing frcmod, atom type with a single character (like "c") was not recognized properly. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@92
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toshinagata1964 [Wed, 3 Aug 2011 10:02:52 +0000 (10:02 +0000)]
Mac: config.h/Makefiles for AmberTools is modified so that gfortran library is statically linked
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@91
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toshinagata1964 [Wed, 3 Aug 2011 10:01:03 +0000 (10:01 +0000)]
ruby-1.8.7-p160.tar.gz is added (required for building)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@90
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toshinagata1964 [Tue, 2 Aug 2011 11:24:36 +0000 (11:24 +0000)]
MO import from GAMESS log/dat files seems to be working. Crash on running antechamber/parmchk on PPC Mac is (hopefully) fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@89
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toshinagata1964 [Mon, 1 Aug 2011 12:04:34 +0000 (12:04 +0000)]
MO import from GAMESS output is being implemented (not complete yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@88
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toshinagata1964 [Sat, 30 Jul 2011 10:28:12 +0000 (10:28 +0000)]
Memo update.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@86
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toshinagata1964 [Sat, 30 Jul 2011 10:01:29 +0000 (10:01 +0000)]
Add missing document figures.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@85
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toshinagata1964 [Sat, 30 Jul 2011 09:14:53 +0000 (09:14 +0000)]
Parameter cut was not working correctly when the selection was non-contiguous; fixed. Mac: property table did not get focus under certain conditions; fixed. Document: the English version had the page titles in Japanese; fixed. Navigation prev/next has been added on top of each page.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@84
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toshinagata1964 [Sat, 30 Jul 2011 06:40:37 +0000 (06:40 +0000)]
Step 5 of the tutorial is complete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@83
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toshinagata1964 [Fri, 29 Jul 2011 11:51:16 +0000 (11:51 +0000)]
Import AMBER Frcmod menu command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@82
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toshinagata1964 [Thu, 28 Jul 2011 16:28:40 +0000 (16:28 +0000)]
The property table section of the tutorial is being written. Trying to fix the problem (on Mac) that the table does not get focus after MyGLCanvas get one, but still unsuccessful.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@81
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toshinagata1964 [Thu, 28 Jul 2011 11:42:06 +0000 (11:42 +0000)]
CIF import is implemented (maybe still incomplete)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@80
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toshinagata1964 [Tue, 26 Jul 2011 15:54:43 +0000 (15:54 +0000)]
Create New Parameter menu command is implemented. MoleculePrepareMDArena() is implmeneted in Molecule.c. Crash in RubyDialogFrame.cpp (sizeOfString) was fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@79
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toshinagata1964 [Thu, 21 Jul 2011 16:45:41 +0000 (16:45 +0000)]
Create New Atom menu command is being implemented (not tested at all yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@78
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toshinagata1964 [Thu, 21 Jul 2011 11:44:31 +0000 (11:44 +0000)]
Document is being updated (the property table section)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@77
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toshinagata1964 [Thu, 21 Jul 2011 08:44:49 +0000 (08:44 +0000)]
Importing frcmod is improved. Import AMBER Lib (in MM/MD->Tools menu) is implemented. Ruby: Molecule#resize_to_fit is implemented. Molecule.open now accepts empty arguments for creating a new untitled document. Kernel.message_box was causing exception when :ok is given; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@76
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toshinagata1964 [Wed, 20 Jul 2011 10:00:50 +0000 (10:00 +0000)]
Importing mdcrd with periodic box now works correctly.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@75
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toshinagata1964 [Wed, 20 Jul 2011 09:29:07 +0000 (09:29 +0000)]
AMBER prmtop/inpcrd export is improved for periodic systems.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@74
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toshinagata1964 [Thu, 7 Jul 2011 17:58:01 +0000 (17:58 +0000)]
Copy/paste now handle parameters properly (hopefully...). The Ruby method 'duplicate' also now copies parameters.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@73
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toshinagata1964 [Thu, 7 Jul 2011 04:13:35 +0000 (04:13 +0000)]
.gets now appends a newline after the input string. AmberTools: antechamber sometimes created strange intermediate file; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@72
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toshinagata1964 [Wed, 6 Jul 2011 23:13:28 +0000 (23:13 +0000)]
Ruby: stdin.{gets, readline} are implemented (other stdin methods will cause exception).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@71
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