画面上でグラフィカルに分子モデルを組み立てるソフトウェア。Mac OS X と Windows で動作する。GAMESS, Gaussian などの計算化学ソフトウェアとの連携、組み込み Ruby インタプリタによる自動編集などの機能を持つ。
本プロジェクトは GitHub へ移行しました。今後の更新は GitHub で行い、こちらでは行いません。
GitHub プロジェクトページ： https://github.com/toshinagata/Molby
公式ホームページ： https://toshinagata.github.io/Molby
The reference for built-in Ruby is written. The features of the Ruby commands are cleaned up.
組み込み Ruby のリファレンスを作成。また、Ruby コマンドの仕様を整理。
- 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.
- Reference for the Ruby extension is written.
- DialogItem class is implemented; Dialog#item and Dialog#each_item now use DialogItem objects instead of index integers.
- The class RubyDialog is renamed to Dialog. All Molby classes are now under module Molby.
- MDArena#keys is implemented. MessageOutput class is removed, and $stdout and $stderr are now Object instances that implement appropriate write methods.
- The MDArena attributes 'transient_temperature' and 'average_temperature' are implemented. MDArena#prepare is automatically invoked from Molecule#parameter.
- 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.
- 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.
- 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.
- The Ruby command reorder_atoms is renamed to renumber_atoms.
- The AtomRef methods cr/cx/cy/cz were made obsolete; instead, the methods fract_r/fract_x/fract_y/fract_z were implemented.
- The return value of Ruby command loadout was incorrect (it returned false even when successful). Fixed.
- 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.
- Cleaning up the rdoc comments.
- Ruby commands now handle angles in degree, rather than in radian.
- Ruby commands now handle the angles (rotation etc.) in degree, rather than in radian.
- 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.
- Reference for the Ruby extension is written.
- DialogItem class is implemented; Dialog#item and Dialog#each_item now use DialogItem objects instead of index integers.
- The class RubyDialog is renamed to Dialog. All Molby classes are now under module Molby.
- MDArena#keys is implemented. MessageOutput class is removed, and $stdout and $stderr are now Object instances that implement appropriate write methods.
- The MDArena attributes 'transient_temperature' and 'average_temperature' are implemented. MDArena#prepare is automatically invoked from Molecule#parameter.
- 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.
- 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.
- 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.
- The Ruby command reorder_atoms is renamed to renumber_atoms.
- The AtomRef methods cr/cx/cy/cz were made obsolete; instead, the methods fract_r/fract_x/fract_y/fract_z were implemented.
- The return value of Ruby command loadout was incorrect (it returned false even when successful). Fixed.
- 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.
- Cleaning up the rdoc comments.
- Ruby commands now handle angles in degree, rather than in radian.
- Ruby commands now handle the angles (rotation etc.) in degree, rather than in radian.
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