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

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

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

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

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

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

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

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toshinagata1964 [Wed, 6 Jul 2011 06:25:01 +0000 (06:25 +0000)]

Importing Amber mdcrd files is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@70 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 5 Jul 2011 17:46:20 +0000 (17:46 +0000)]

Molecule#{bond,angle,dihedral,improper,vdw}_par were wrongly implemented. Fixed. 'Create SANDER input' is implemented (still not tested much).

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@69 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 3 Jul 2011 15:53:23 +0000 (15:53 +0000)]

Ruby: AtomRef#exclusion method was incorrectly calling Molecule#md_arena. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@68 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 3 Jul 2011 14:46:35 +0000 (14:46 +0000)]

Ruby: Molecule#bond_par, angle_par, dihedral_par, improper_par, vdw_par are implemented. Molecule#each_atom now accepts an IntGroup argument to limit iteration in some atom group. Initialition of the MDArena is now explicitly two-stage (specified by the is_initialized flag 0 -> 1 -> 2). molecule.rb: the solvate procedure now set the segment name 'SOLV' for the added solvent atoms.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@67 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 2 Jul 2011 15:24:26 +0000 (15:24 +0000)]

Gaff and parm99 parameters: the equilibrium bond lengths have now three significant digits after the decimal point. Ruby: AtomRef#exclusion method is implemented. MM/MD: minimization sometimes caused crash. Hopefully fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@66 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 26 Apr 2011 14:06:19 +0000 (14:06 +0000)]

Memo update.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@65 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 26 Apr 2011 04:40:11 +0000 (04:40 +0000)]

Importing GaussianW fch(k) files were not working because of the different end-of-line characters. Fixed. The extension '.fch' is now recognized as a Gaussian formatted checkpoint files.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@63 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 2 Mar 2011 10:25:09 +0000 (10:25 +0000)]

Pasting MD parameters to a molecule with no parameters was not working. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@62 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 3 Jun 2010 13:47:32 +0000 (13:47 +0000)]

Crash in MM minimization when no unit cell is defined (enbug in r59); fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@61 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 2 Jun 2010 15:45:11 +0000 (15:45 +0000)]

Xcode project: GCC4.0 is explicitly designated (necessary for building for Mac OS 10.4 on Snow Leopard)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@60 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 31 May 2010 11:41:11 +0000 (11:41 +0000)]

The nearest-neighbor lookup of nonbonding force calculation was problematic; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@59 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 18 May 2010 14:36:00 +0000 (14:36 +0000)]

The view settings for mbsf files now can be restored correctly (hopefully). A comment in the mbsf format file was fixed (the description 'charge' was erroneously omitted).

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@58 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 17 May 2010 15:09:10 +0000 (15:09 +0000)]

wxSources/docview.cpp is added to the project. Trackball.c is added to the Molby_command target (xcode only, still experimental)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@57 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 16 May 2010 03:09:36 +0000 (03:09 +0000)]

The native format (mbsf) now preserves the display conditions, such as scale, orientation, and show/hide unit cell, periodic images, etc.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@56 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 14 May 2010 16:03:12 +0000 (16:03 +0000)]

Inconsistency between the Xcode project settings and Makefile_amber11 was resolved. Exception from 'Show periodic image' dialog box was fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@55 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 12 May 2010 16:29:02 +0000 (16:29 +0000)]

Calculation of vdw/elect forces was wrong when the periodic cell is small; fixed. No new frame is generated when md_frame.run/minimize is called from Ruby script.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@54 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 11 May 2010 22:50:35 +0000 (22:50 +0000)]

Flags for 'show graphite' and 'show periodic images' are implemented. In MM/MD engine, the handling of Verlet list seems to be incomplete, but this is still being worked on.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@53 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 8 May 2010 07:29:22 +0000 (07:29 +0000)]

Handling of MD dialog is improved. MM/MD calculation bug (introduced in rev 50) is fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@52 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 8 May 2010 04:09:23 +0000 (04:09 +0000)]

The Ruby command wrap_unit_cell was not working correctly.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@51 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 7 May 2010 16:20:03 +0000 (16:20 +0000)]

The MM/MD re-initialization after modification of coordinates was incomplete.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@50 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:29:52 +0000 (15:29 +0000)]

Version 0.5.4

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

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toshinagata1964 [Thu, 6 May 2010 15:15:39 +0000 (15:15 +0000)]

Introduce MolbyResourcePath global constant, which points to the directory containing 'Scripts' and 'amber11' resources. Ruby command Kernel.call_subprocess is implemented. ParameterRef.par_type= wrongly parsed the atom type string; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@47 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:14:32 +0000 (15:14 +0000)]

Windows: the radio buttons with no explicit radio group showed stranged behavior; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@46 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:13:59 +0000 (15:13 +0000)]

Some parameter editing caused segmentation fault; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@45 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:13:26 +0000 (15:13 +0000)]

Undo of creating atoms caused segmentation fault; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@44 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:12:58 +0000 (15:12 +0000)]

Improved handling of DOSish file paths. The functions strdup() and wcsdup() are implemented here so that the malloc libaries for debugging can be used.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@43 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:12:18 +0000 (15:12 +0000)]

Importing GAMESS dat file was broken; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@42 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:11:39 +0000 (15:11 +0000)]

Added instruction for building and copying resp.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@41 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:11:06 +0000 (15:11 +0000)]

Removal of double-call of wxDocument::Close() (revision 31) was undone, because it caused occasional crashes.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@40 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:10:27 +0000 (15:10 +0000)]

Undo is kept enabled during 'molload' and related calls. The 'do not keep logs' option for antechamber was not working; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@39 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:09:22 +0000 (15:09 +0000)]

Add hydrogen was broken; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@38 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:09:03 +0000 (15:09 +0000)]

Ambertools dialog is improved.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@37 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:08:45 +0000 (15:08 +0000)]

generation of internal coordinates (NZVAR=#{3n-5}) is supported in the 'Create GAMESS input' dialog.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@36 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:07:54 +0000 (15:07 +0000)]

The amber11 binaries are now built in the project directory, instead of the 'build' subdirectory. Windows: event.cpp (from wxMSW) is included in the project with a slight modification.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@35 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 6 May 2010 15:06:52 +0000 (15:06 +0000)]

Windows: interrupting the subprocess (antechamber etc.) caused grandchildren processes to survive as zombies; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@34 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 25 Apr 2010 08:07:57 +0000 (08:07 +0000)]

Mac: the text field in the list control remained on the screen even after the window is inactivated; fixed. Win: the text field in the list control often led to crash; (hopefully) fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@32 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 24 Apr 2010 15:31:32 +0000 (15:31 +0000)]

Work around the wxWidgets bug where wxDocument::Close() is called twice. Fix the problem in the Mac version in which the hidden top-level window gets sometimes visible in the Window menu.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@31 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 23 Apr 2010 15:46:48 +0000 (15:46 +0000)]

Improved handling of copy/cut/paste in the parameter table (but still very unsatisfactory)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@30 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 22 Apr 2010 14:50:27 +0000 (14:50 +0000)]

Experimental command-line tool for Mac platform.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@29 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 22 Apr 2010 13:15:11 +0000 (13:15 +0000)]

The MM/MD engine was not aware of modification of coordinates via Ruby scripts. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@28 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 31 Mar 2010 12:46:38 +0000 (12:46 +0000)]

Frames can now have variable unit cell parameters.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@27 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 20 Mar 2010 13:41:57 +0000 (13:41 +0000)]

Version 0.5.2

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@25 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 20 Mar 2010 10:38:41 +0000 (10:38 +0000)]

Some features of Dialog class are modified; Dialog#item now returns DialogItem object instead of Integer; Dialog#layout accepts DialogItem objects; Dialog#run always returns a hash including values for tagged items, plus a value for :status indicating OK or Cancel status.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@24 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 20 Mar 2010 10:34:49 +0000 (10:34 +0000)]

Reference for the Ruby extension is written

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@23 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 13 Mar 2010 10:08:18 +0000 (10:08 +0000)]

DialogItem class is implemented; Dialog#item and Dialog#each_item now use DialogItem objects instead of index integers.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@22 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 9 Mar 2010 14:34:56 +0000 (14:34 +0000)]

The class RubyDialog is renamed to Dialog. All Molby classes are now under module Molby.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@21 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 2 Mar 2010 15:03:12 +0000 (15:03 +0000)]

MDArena#keys is implemented. MessageOutput class is removed, and and are now Object instances that implement appropriate write methods.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@20 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 1 Mar 2010 15:01:29 +0000 (15:01 +0000)]

The MDArena attributes 'transient_temperature' and 'average_temperature' are implemented. MDArena#prepare is automatically invoked from Molecule#parameter.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@19 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 28 Feb 2010 02:43:30 +0000 (02:43 +0000)]

The DISPATOM parameters are renamed to ELEMENT, to avoid confusion. The Ruby commands Parameter#atoms etc. are now Parameter#elements, and Scripts/dispatom.par is renamed to Scripts/element.par.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@18 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 24 Feb 2010 16:16:12 +0000 (16:16 +0000)]

Parameter#bond, angle, etc. are no longer implemented as class methods. To use for global parameters, use Parameter.builtin.bond etc. Parameter#lookup is implemented. Parameter::Builtin is now defined as a constant representing the global parameters, and Parameter.builtin returns this value.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@17 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 23 Feb 2010 15:56:09 +0000 (15:56 +0000)]

The methods of Parameter and ParEnumerable change features; Parameter#bond|angle|dihedral|... and ParEnumerable#[] for molecule-local parameters now do not 'automatically' look up the global parameters, and they no longer accept atom-type arguments except for Parameter#atom.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@16 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 23 Feb 2010 14:58:19 +0000 (14:58 +0000)]

The Ruby command reorder_atoms is renamed to renumber_atoms.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@15 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 23 Feb 2010 14:57:22 +0000 (14:57 +0000)]

The AtomRef methods cr/cx/cy/cz were made obsolete; instead, the methods fract_r/fract_x/fract_y/fract_z were implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@14 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 23 Feb 2010 14:55:35 +0000 (14:55 +0000)]

The return value of Ruby command loadout was incorrect (it returned false even when successful). Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@13 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 20 Feb 2010 06:40:58 +0000 (06:40 +0000)]

Ruby commands find_angles and find_dihedrals are made obsolete. remove_bonds is implemented. create_bond (create_bonds) now returns the number of newly added bonds instead of self.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@12 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 18 Feb 2010 14:43:36 +0000 (14:43 +0000)]

Cleaning up the rdoc comments.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@11 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 18 Feb 2010 14:39:06 +0000 (14:39 +0000)]

Cleaning up the rdoc comments.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@10 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 18 Feb 2010 14:37:11 +0000 (14:37 +0000)]

Ruby commands now handle angles in degree, rather than in radian.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@9 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 18 Feb 2010 14:36:03 +0000 (14:36 +0000)]

Ruby commands now handle the angles (rotation etc.) in degree, rather than in radian.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@8 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 6 Feb 2010 02:44:17 +0000 (02:44 +0000)]

Documents: Molecular Mechanics section is written.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@7 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 3 Feb 2010 16:02:23 +0000 (16:02 +0000)]

The multithread handling for MM/MD is improved.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@6 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 2 Feb 2010 15:16:33 +0000 (15:16 +0000)]

Undo was not working after running antechamber. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@5 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 31 Jan 2010 12:12:08 +0000 (12:12 +0000)]

AmberTools-1.3 (part) is bundled.

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

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toshinagata1964 [Sat, 23 Jan 2010 04:59:36 +0000 (04:59 +0000)]

the xcode project files <username>.{mode1v3,pbxuser} are removed from the repository.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@3 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 23 Jan 2010 04:54:13 +0000 (04:54 +0000)]

Ruby command: ParEnumerable.lookup now accepts atom-type arguments with whitespace delimiters. ParameterRef.par_type now reports correct type string.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@2 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 21 Jan 2010 16:56:59 +0000 (16:56 +0000)]

initial import

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@1 a2be9bc6-48de-4e38-9406-05402d4bc13c

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