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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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