<div class="centered" lang="en">
<h1>Molby</h1>
<h2>An Interactive Molecular Modeling Software<br />with Integrated Ruby Interpreter</h2>
-<h3>Version 0.6.2</h3> <!-- version -->
+<h3>Version 0.6.3</h3> <!-- version -->
<h3>Toshi Nagata</h3>
<p><a href="http://molby.sourceforge.jp/index-en.html">http://molby.sourceforge.jp/index-en.html</a></p>
</div>
<div class="centered" lang="ja">
<h1>Molby</h1>
<h2>対話型分子モデリングソフトウェア<br />（Ruby インタプリタ内蔵）</h2>
-<h3>Version 0.6.2</h3> <!-- version -->
+<h3>Version 0.6.3</h3> <!-- version -->
<h3>永田 央</h3>
<p><a href="http://molby.sourceforge.jp/index.html">http://molby.sourceforge.jp/index.html</a></p>
</div>
Molby is a copyrighted product of Toshi Nagata.
</p>
<p>
-Copyright (C) 2009-2012 Toshi Nagata <!-- copyright -->
+Copyright (C) 2008-2012 Toshi Nagata <!-- copyright -->
</p>
<p>
Molby includes the following softwares, which are copyrighted products as described below:
Molby: An Interactive Molecular Modeling Software with Integrated Ruby Interpreter
</p>
<p>
-Copyright (C) 2009-2012 Toshi Nagata <!-- copyright -->
+Copyright (C) 2008-2012 Toshi Nagata <!-- copyright -->
</p>
<p>
This program is free software; you can redistribute it and/or modify
Molby の著作権は永田 央が保持しています。
</p>
<p>
-Copyright (C) 2009-2012 Toshi Nagata <!-- copyright -->
+Copyright (C) 2008-2012 Toshi Nagata <!-- copyright -->
</p>
<p>
Molby は以下のソフトウェアを含んでいます。それぞれの著作権表示は下の通りです。
Molby: 対話型分子モデルソフトウェア（Ruby インタプリタ内蔵）
</p>
<p>
-Copyright (C) 2009-2012 Toshi Nagata <!-- copyright -->
+Copyright (C) 2008-2012 Toshi Nagata <!-- copyright -->
</p>
<p>
このプログラムはフリーソフトウェアです。あなたはこれを、フリーソフトウェア財団によって発行された GNU 一般公衆利用許諾契約書(バージョン2か、希望によってはそれ以降のバージョンのうちどれか)の定める条件の下で再頒布または改変することができます。
- 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.
+
+2012.6.18.
+Version 0.6.3
+
+リリースノート
+- LAMatrix クラスのドキュメントを作成。
+- 量子化学計算ソフトウェアとの連携のドキュメントを作成。
+- CIFファイルから読み込んだ座標値・異方性温度因子・セルパラメータの標準偏差を mbsf ファイルに保存するようにした。
+- Ruby コマンド新設: Molecule#fit_coordinates, Molecule#amend_by_symmetry, Molecule#set(get)_view_center, Molecule#hidden_atoms, Molecule#set_hidden_atoms, Molecule#charge, Kernel#lookup_menu
+- Bond, angle などのテーブルから分子力学パラメータを編集するとき、Universal Force Field (UFF) で力の定数を見積もる機能をつけた。
+- 分子力学パラメータを原子のインデックスで指定できるようにした（実はもともとあった機能だが、分子を編集してもパラメータが維持されるようになった）。
+- その他バグ修正（ChangeLog を参照）
+
+- Document for the LAMatrix class was written.
+- Document for the collaboration with other quantum chemistry softwares was written.
+- Mbsf files now retain sigmas for the crystallographic parameters (imported from CIF).
+- New Ruby commands: Molecule#fit_coordinates, Molecule#amend_by_symmetry, Molecule#set(get)_view_center, Molecule#hidden_atoms, Molecule#set_hidden_atoms, Molecule#charge, Kernel#lookup_menu
+- When the MM parameters are edited from the bond/angle table, the force constant can be guessed by Universal Force Field (UFF).
+- The MM parameters can now be specified by explicit atom indices.
+- Other bug fixes (see the change log).
+
+ChangeLog
+- Features of Molecule#cell and Molecule#box are modified so that the handling of the sigma values of the cell parameters looks more consistent.
+- Mbsf format now retains anisotropic parameters and sigma (for crystallographic data)
+- Crash during creating bonds when ellipsoid display is on is fixed.
+- Ruby: Molecule#fit_coordinates is implemented.
+- LAMatrix#new, #zero, #submatrix now accept arguments in 'column,row' order.
+- MM forces are updated after 'run(0)'
+- Load/save mbsf files were broken when atom type variants were used for atom types with 3 or 4 characters. Fixed.
+- The order of parameters in cmd_edit_local_parameter_in_mainview dialog was inconsistent. Fixed. Also fixed Ruby exception in UFF guess dialog.
+- Molecule#transform, rotate, invert, etc. are now aware of symmetry related atoms. That is, the symmetry operation is updated so that the atoms are also symmetry related after transformation.
+- Ruby: AtomRef#symop can now be set from script.
+- Ruby: Molecule#amend_by_symmetry is implemented.
+- Ruby: Molecule#set(get)_view_translation is now obsolete and replaced by set(get)_view_center.
+- The order of the anisotropic thermal parameters is changed to 'b11, b22, b33, b12, b13, b23'. Inconsistency in some of the codes is fixed. TODO: when symmetry expansion is done, the anisotropic thermal parameters should be correctly converted.
+- Ruby: Molecule#hidden_atoms and Molecule#set_hidden_atoms are implemented.
+- The order of columns for MD parameters in the bond/angle/dihedral tables are changed, so that the columns appear in the same order as in the parameter table.
+- UFF parameter guess is implemented.
+- Molecule#neutralize was not working correctly. Fixed, and Molecule#charge was implemented.
+- The load/unload global parameters dialog is sometimes out of the screen. Fixed.
+- Windows version does not display last build date in the about dialog. Fixed.
+- Parameters now can be specified by using both explicit indices and atom types, like '7-ca-8'.
+- Parameter editing is improved.
+- Restructure MolAction.c.
+- Atom range specification for the vdw cutoff parameter is now made obsolete.
+- Vector3D[] and Transform[] are modified to accept an LAMatrix argument. The document is written for LAMatrix.
+- Load Script Menu caused crash when no window is open. Fixed.
+- Ruby: Kernel#lookup_menu is implemented.
+- Document is written for LAMatrix.
+- LAMatrix#multiply was not working correctly when on-the-fly size conversion was required. Fixed.
+- Execute Script command was broken. Fixed.
+- CIF import may fail when _geom_bond_site_symmetry_1 field is missing. Fixed.
+- Document was written for the collaboration with other quantum chemistry softwares.
+- .log and .out are both accepted as the extension of the Gaussian and GAMESS log files.
+- update_version.rb is improved.
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