git.osdn.net Git - molby/Molby.git/log

toshinagata1964 [Tue, 31 Jan 2012 10:04:29 +0000 (10:04 +0000)]

Ruby: Molecule#make_front, set_name, get_view_rotation, get_view_scale, get_view_translation, set_view_rotation, set_view_scale, set_view_translation, set_graphic_color, hide_graphic, show_graphic are implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@179 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 30 Jan 2012 16:39:24 +0000 (16:39 +0000)]

Drawing custom graphics on the model view is being implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@178 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 30 Jan 2012 10:59:30 +0000 (10:59 +0000)]

Ruby Dialog: modeless dialog is now implemented; interval timer is implemented. Ruby: $KCODE is set on startup, and coding:{shift-jis, utf-8} is recognized as the source code encoding (for executing script from file). Molecule#all returns IntGroup[0] when the molecule is empty (it should return IntGroup[]), which causes crash on Molecule#delete.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@177 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 17 Jan 2012 09:17:08 +0000 (09:17 +0000)]

Dialog#layout: the :align and :vertical_align options can now be specified as item attributes

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@176 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 17 Jan 2012 08:06:49 +0000 (08:06 +0000)]

The separator line in the Ruby Dialog was not working correctly.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@175 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c

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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 a2be9bc6-48de-4e38-9406-05402d4bc13c