From 87583a5f3d30c333f3513a55a1ae78b55538a21f Mon Sep 17 00:00:00 2001
From: toshinagata1964 Molby
An Interactive Molecular Modeling Software
-
with Integrated Ruby InterpreterVersion 0.6.2
+Version 0.6.3
Toshi Nagata
Molby
対話åååã¢ããªã³ã°ã½ããã¦ã§ã¢
-
ï¼Ruby ã¤ã³ã¿ããªã¿å
èµï¼Version 0.6.2
+Version 0.6.3
æ°¸ç°ã央
-Copyright (C) 2009-2012 Toshi Nagata +Copyright (C) 2008-2012 Toshi Nagata
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
-Copyright (C) 2009-2012 Toshi Nagata +Copyright (C) 2008-2012 Toshi Nagata
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 ã®èä½æ¨©ã¯æ°¸ç°ã央ãä¿æãã¦ãã¾ãã
-Copyright (C) 2009-2012 Toshi Nagata +Copyright (C) 2008-2012 Toshi Nagata
Molby ã¯ä»¥ä¸ã®ã½ããã¦ã§ã¢ãå«ãã§ãã¾ããããããã®èä½æ¨©è¡¨ç¤ºã¯ä¸ã®éãã§ãã @@ -281,7 +281,7 @@ Molby 㯠GNU General Public License (GNU ä¸è¬å ¬è¡ Molby: 対話åååã¢ãã«ã½ããã¦ã§ã¢ï¼Ruby ã¤ã³ã¿ããªã¿å èµï¼
-Copyright (C) 2009-2012 Toshi Nagata +Copyright (C) 2008-2012 Toshi Nagata
ãã®ããã°ã©ã ã¯ããªã¼ã½ããã¦ã§ã¢ã§ããããªãã¯ããããããªã¼ã½ããã¦ã§ã¢è²¡å£ã«ãã£ã¦çºè¡ããã GNU ä¸è¬å
¬è¡å©ç¨è¨±è«¾å¥ç´æ¸(ãã¼ã¸ã§ã³2ããå¸æã«ãã£ã¦ã¯ãã以éã®ãã¼ã¸ã§ã³ã®ãã¡ã©ãã)ã®å®ããæ¡ä»¶ã®ä¸ã§åé å¸ã¾ãã¯æ¹å¤ãããã¨ãã§ãã¾ãã
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
+
+ãªãªã¼ã¹ãã¼ã
+- LAMatrix ã¯ã©ã¹ã®ããã¥ã¡ã³ããä½æã
+- éååå¦è¨ç®ã½ããã¦ã§ã¢ã¨ã®é£æºã®ããã¥ã¡ã³ããä½æã
+- CIFãã¡ã¤ã«ããèªã¿è¾¼ãã 座æ¨å¤ã»ç°æ¹æ§æ¸©åº¦å åã»ã»ã«ãã©ã¡ã¼ã¿ã®æ¨æºåå·®ã mbsf ãã¡ã¤ã«ã«ä¿åããããã«ããã
+- Ruby ã³ãã³ãæ°è¨: 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 ãªã©ã®ãã¼ãã«ããåååå¦ãã©ã¡ã¼ã¿ãç·¨éããã¨ããUniversal Force Field (UFF) ã§åã®å®æ°ãè¦ç©ããæ©è½ãã¤ããã
+- åååå¦ãã©ã¡ã¼ã¿ãååã®ã¤ã³ããã¯ã¹ã§æå®ã§ããããã«ããï¼å®ã¯ãã¨ãã¨ãã£ãæ©è½ã ããååãç·¨éãã¦ããã©ã¡ã¼ã¿ãç¶æãããããã«ãªã£ãï¼ã
+- ãã®ä»ãã°ä¿®æ£ï¼ChangeLog ãåç
§ï¼
+
+- 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 @@