From: toshinagata1964 <toshinagata1964@a2be9bc6-48de-4e38-9406-05402d4bc13c>
Date: Mon, 18 Jun 2012 13:54:16 +0000 (+0000)
Subject: Version 0.6.3
X-Git-Tag: v1.0.2~412
X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=87583a5f3d30c333f3513a55a1ae78b55538a21f;p=molby%2FMolby.git

Version 0.6.3

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@223 a2be9bc6-48de-4e38-9406-05402d4bc13c
---

diff --git a/Documents/src/doc_source.html b/Documents/src/doc_source.html
index 485f0d2..1bb7e39 100644
--- a/Documents/src/doc_source.html
+++ b/Documents/src/doc_source.html
@@ -14,14 +14,14 @@
 <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>
@@ -203,7 +203,7 @@ Molbyフォルダの中にアンインストーラがあります。「スター
 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:
@@ -232,7 +232,7 @@ Molby is distributed under the GNU General Public License (version 2).
 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
@@ -255,7 +255,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 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。
@@ -281,7 +281,7 @@ Molby は <a href="../etc/gpl.txt">GNU General Public License (GNU 一般公衆
 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。
diff --git a/README b/README
index 7e4ce51..8ab8e6d 100644
--- a/README
+++ b/README
@@ -5,7 +5,7 @@
     An Interactive Molecular Modeling Software
         with Integrated Ruby Interpreter
   
-          Version 0.6.2
+          Version 0.6.3
 
                   Toshi Nagata
 
@@ -29,7 +29,7 @@ Molby runs on Mac OS X (10.4 and later) and Microsoft Windows (XP and later). Ex
 
 Molby is a copyrighted product of Toshi Nagata.
 
-       Copyright (C) 2009-2010 Toshi Nagata
+       Copyright (C) 2008-2012 Toshi Nagata
 
 Molby includes (more technically: is statically linked to) the following softwares, which are copyrighted products as described below:
 
diff --git a/Version b/Version
index e4c20a7..216e0dd 100644
--- a/Version
+++ b/Version
@@ -1,2 +1,2 @@
-version = "0.6.2"
-date = "20120202"
+version = "0.6.3"
+date = "20120618"
diff --git a/memo.txt b/memo.txt
index 38801af..c568b91 100755
--- a/memo.txt
+++ b/memo.txt
@@ -376,3 +376,58 @@ ChangeLog
 - 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.
diff --git a/msw-build/molby.iss b/msw-build/molby.iss
index c9eab33..347e06a 100755
--- a/msw-build/molby.iss
+++ b/msw-build/molby.iss
@@ -1,6 +1,6 @@
 [Setup]
 AppName = Molby
-AppVerName = Molby (v0.6.2)
+AppVerName = Molby (v0.6.3)
 DefaultDirName = {pf}\Molby
 DefaultGroupName = Molby
 UninstallDisplayIcon = {app}\Molby.exe
diff --git a/wxSources/MyVersion.c b/wxSources/MyVersion.c
index b34b8ef..1a80e63 100644
--- a/wxSources/MyVersion.c
+++ b/wxSources/MyVersion.c
@@ -15,5 +15,5 @@
  GNU General Public License for more details.
  */
 
-const char *gVersionString = "v0.6.2";
+const char *gVersionString = "v0.6.3";
 const char *gCopyrightString = "Copyright (c) 2008-2011 Toshi Nagata";
diff --git a/xcode-build/Info.plist b/xcode-build/Info.plist
index 47bf778..863a9a9 100755
--- a/xcode-build/Info.plist
+++ b/xcode-build/Info.plist
@@ -36,6 +36,6 @@
 	<key>CFBundleSignature</key>
 	<string>????</string>
 	<key>CFBundleVersion</key>
-	<string>v0.6.2</string>
+	<string>v0.6.3</string>
 </dict>
 </plist>