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/
- Graphic objects can be drawn together with the molecule (requires Ruby coding).
- Modeless operation of Ruby Dialog is implemented.
- The first comment line of the Ruby script (that is to be imported by "Execute Ruby Script" command) can now contain "coding:shift-jis" or "coding:utf-8" instruction. At present, only these two codings are recognized.
- LAMatrix (linear algebra matrix) class is implemented in Ruby, which allow matrix arithmetic of arbitrary dimension. No document is provided yet.
- Empty Console Window command is implemented.
- Document for MD calculation is written.
- Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.
- グラフィックオブジェクトを分子に重ねて書けるようにした。ただし Ruby でのコーディングが必要。
- Ruby ダイアログでモードレスな動作ができるようにした。
- Ruby スクリプトの先頭行コメントに coding:shift-jis または coding:utf-8 が書けるようにした。今のところこの２つしか認識しない。
- Ruby の LAMatrix (linear algebra matrix) クラスを実装し、任意の行列演算ができるようにした。ドキュメントはまだ書いていない。
- Empty Console Window コマンドを実装。
- 分子動力学のドキュメントを作成。
- MM/MD で "log file" フィールドは明示的に指定しない限り空にするようにした。
- CIF ファイルの読み込みで、座標値の標準偏差を認識するようにした。ただしmbsfへの保存はされない。
- Document is updated to include new graphic objects in the model view.
- Ruby: Molecule#make_front, set_name, get_view_rotation, get_view_scale, get_view_translation, set_view_rotation, set_view_scale, set_view_translation, set_graphic_color, hide_graphic, show_graphic are implemented.
- Drawing custom graphics on the model view is implemented.
- Ruby Dialog: modeless dialog is now implemented, and interval timer is implemented.
- Ruby: $KCODE is set on startup, and coding:{shift-jis, utf-8} is recognized as the source code encoding (for executing script from file).
- Molecule#all returns IntGroup[0] when the molecule is empty (it should return IntGroup[]), which causes crash on Molecule#delete.
- Dialog#layout: the :align and :vertical_align options can now be specified as item attributes
- The separator line in the Ruby Dialog was not working correctly.
- Vector3D and Transform objects are converted to LAMatrix object with dimensions 3 or 4 depending upon the context.
- LAMatrix#new errornously allows matrix with dimension 0. Fixed.
- AtomRef#molecule is implemented.
- Empty Console Window command is implemented.
- LAMatrix.multiply was not working correctly when the first argument is a scalar. Fixed.
- General matrix calculation (LAMatrix class in Ruby) is implemented. Seems to be working, but not documented yet.
- In the document, navigation between the English/Japanese versions is possible in most pages.
- Document for MD calculation is written.
- The "log file" field is set to blank unless explicitly set by the user.
- The structure Mat33 and Transform are now column-first arrangement (no change on Ruby interface and mbsf file format)
- Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.
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