Molby is a software for building molecular models on the graphic screen. It works on Mac OS X and Windows. It can import and export files for other computational chemistry softwares such as GAMESS and Gaussian. It can also edit molecules by Ruby scripts.
This project is moved to GitHub. Updates are only available on GitHub.
GitHub Project Page: https://github.com/toshinagata/Molby
Molby Homepage: https://toshinagata.github.io/Molby/en/
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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