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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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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