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プロジェクト概要

画面上でグラフィカルに分子モデルを組み立てるソフトウェア。Mac OS X と Windows で動作する。GAMESS, Gaussian などの計算化学ソフトウェアとの連携、組み込み Ruby インタプリタによる自動編集などの機能を持つ。 公式ホームページ: https://molby.osdn.jp/

システム要件

システム要件が設定されていません

リリース時刻: 2011-07-30 19:28
molby 0.5.6 (3 個のファイル 非表示)

リリースノート

Gaff and parm99 parameters: the equilibrium bond lengths have now three significant digits after the decimal point.
Crash on antechamber/parmchk dialog (and other Ruby-based dialogs as well) is fixed.
Ruby: New methods: AtomRef#exclusion, Molecule#resize_to_fit, Molecule#bond_par/angle_par/dihedral_par/improper_par/vdw_par, $stdin.gets, $stdin.readline. Improved: Molecule#each_atom, Molecule#duplicate, Molecule#open, Kernel#message_box, Dialog#item.
MM/MD: minimization gets improved stability; the "solvate" command now sets the segment name 'SOLV' for the solvent atoms.
New menu commands: "Create New Atom", "Create New Parameter", "Create SANDER Input", "Import AMBER Lib", "Import AMBER Frcmod".
New file formats: cif (import), AMBER mdcrd (import).
Tables: cut/copy/paste in parameter table is improved. Mac: table did not get focus under certain conditions; fixed.

Gaff, parm99 パラメータ: 結合長を小数点以下3桁まで有効にした。
Antechamber/parmchk ダイアログ(および Ruby で書かれたその他のダイアログ)のクラッシュを修正。
Ruby: 新しいメソッド: AtomRef#exclusion, Molecule#resize_to_fit, Molecule#bond_par/angle_par/dihedral_par/improper_par/vdw_par, $stdin.gets, $stdin.readline. 改良したメソッド: Molecule#each_atom, Molecule#duplicate, Molecule#open, Kernel#message_box, Dialog#item.
分子力学: 構造最適化計算の安定性が向上。"Solvate" コマンドで溶媒分子に "SOLV" セグメント名が付与されるようになった。
新しいメニューコマンド:"Create New Atom", "Create New Parameter", "Create SANDER Input", "Import AMBER Lib", "Import AMBER Frcmod".
新しいファイルフォーマット: cif(読み込み), AMBER mdcrd(読み込み)。
属性テーブルでのカット/コピー/ペーストの安定性が向上。
Mac: 属性テーブルがときどきフォーカスされない問題を解決。

変更履歴

Parameter cut was not working correctly when the selection was non-contiguous; fixed. Mac: property table did not get focus under certain conditions; fixed. Document: the English version had the page titles in Japanese; fixed. Navigation prev/next has been added on top of each page.

Step 5 of the tutorial is complete.

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r82 | toshinagata1964 | 2011-07-29 20:51:16 +0900 (金, 29 7 2011) | 1 line

Import AMBER Frcmod menu command is implemented.
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r81 | toshinagata1964 | 2011-07-29 01:28:40 +0900 (金, 29 7 2011) | 1 line

The property table section of the tutorial is being written. Trying to fix the problem (on Mac) that the table does not get focus after MyGLCanvas get one, but still unsuccessful.
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r80 | toshinagata1964 | 2011-07-28 20:42:06 +0900 (木, 28 7 2011) | 1 line

CIF import is implemented (maybe still incomplete)
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r79 | toshinagata1964 | 2011-07-27 00:54:43 +0900 (水, 27 7 2011) | 1 line

Create New Parameter menu command is implemented. MoleculePrepareMDArena() is implmeneted in Molecule.c. Crash in RubyDialogFrame.cpp (sizeOfString) was fixed.
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r78 | toshinagata1964 | 2011-07-22 01:45:41 +0900 (金, 22 7 2011) | 1 line

Create New Atom menu command is being implemented (not tested at all yet)
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r77 | toshinagata1964 | 2011-07-21 20:44:31 +0900 (木, 21 7 2011) | 1 line

Document is being updated (the property table section)
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r76 | toshinagata1964 | 2011-07-21 17:44:49 +0900 (木, 21 7 2011) | 1 line

Importing frcmod is improved. Import AMBER Lib (in MM/MD->Tools menu) is implemented. Ruby: Molecule#resize_to_fit is implemented. Molecule.open now accepts empty arguments for creating a new untitled document. Kernel.message_box was causing exception when :ok is given; fixed.
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r75 | toshinagata1964 | 2011-07-20 19:00:50 +0900 (水, 20 7 2011) | 1 line

Importing mdcrd with periodic box now works correctly.
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r74 | toshinagata1964 | 2011-07-20 18:29:07 +0900 (水, 20 7 2011) | 1 line

AMBER prmtop/inpcrd export is improved for periodic systems.
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r73 | toshinagata1964 | 2011-07-08 02:58:01 +0900 (金, 08 7 2011) | 1 line

Copy/paste now handle parameters properly (hopefully...). The Ruby method 'duplicate' also now copies parameters.
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r72 | toshinagata1964 | 2011-07-07 13:13:35 +0900 (木, 07 7 2011) | 1 line

.gets now appends a newline after the input string. AmberTools: antechamber sometimes created strange intermediate file; fixed.
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r71 | toshinagata1964 | 2011-07-07 08:13:28 +0900 (木, 07 7 2011) | 1 line

Ruby: stdin.{gets, readline} are implemented (other stdin methods will cause exception).
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r70 | toshinagata1964 | 2011-07-06 15:25:01 +0900 (水, 06 7 2011) | 1 line

Importing Amber mdcrd files is implemented.
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r69 | toshinagata1964 | 2011-07-06 02:46:20 +0900 (水, 06 7 2011) | 1 line

Molecule#{bond,angle,dihedral,improper,vdw}_par were wrongly implemented. Fixed. 'Create SANDER input' is implemented (still not tested much).
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r68 | toshinagata1964 | 2011-07-04 00:53:23 +0900 (月, 04 7 2011) | 1 line

Ruby: AtomRef#exclusion method was incorrectly calling Molecule#md_arena. Fixed.
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r67 | toshinagata1964 | 2011-07-03 23:46:35 +0900 (日, 03 7 2011) | 1 line

Ruby: Molecule#bond_par, angle_par, dihedral_par, improper_par, vdw_par are implemented. Molecule#each_atom now accepts an IntGroup argument to limit iteration in some atom group. Initialition of the MDArena is now explicitly two-stage (specified by the is_initialized flag 0 -> 1 -> 2). molecule.rb: the solvate procedure now set the segment name 'SOLV' for the added solvent atoms.
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r66 | toshinagata1964 | 2011-07-03 00:24:26 +0900 (日, 03 7 2011) | 1 line

Gaff and parm99 parameters: the equilibrium bond lengths have now three significant digits after the decimal point. Ruby: AtomRef#exclusion method is implemented. MM/MD: minimization sometimes caused crash. Hopefully fixed.
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r65 | toshinagata1964 | 2011-04-26 23:06:19 +0900 (火, 26 4 2011) | 1 line

Memo update.
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r63 | toshinagata1964 | 2011-04-26 13:40:11 +0900 (火, 26 4 2011) | 1 line

Importing GaussianW fch(k) files were not working because of the different end-of-line characters. Fixed. The extension '.fch' is now recognized as a Gaussian formatted checkpoint files.
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r62 | toshinagata1964 | 2011-03-02 19:25:09 +0900 (水, 02 3 2011) | 1 line

Pasting MD parameters to a molecule with no parameters was not working. Fixed.
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r61 | toshinagata1964 | 2010-06-03 22:47:32 +0900 (木, 03 6 2010) | 1 line

Crash in MM minimization when no unit cell is defined (enbug in r59); fixed.
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r60 | toshinagata1964 | 2010-06-03 00:45:11 +0900 (木, 03 6 2010) | 1 line

Xcode project: GCC4.0 is explicitly designated (necessary for building for Mac OS 10.4 on Snow Leopard)
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r59 | toshinagata1964 | 2010-05-31 20:41:11 +0900 (月, 31 5 2010) | 1 line

The nearest-neighbor lookup of nonbonding force calculation was problematic; fixed.
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r58 | toshinagata1964 | 2010-05-18 23:36:00 +0900 (火, 18 5 2010) | 1 line

The view settings for mbsf files now can be restored correctly (hopefully). A comment in the mbsf format file was fixed (the description 'charge' was erroneously omitted).
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r57 | toshinagata1964 | 2010-05-18 00:09:10 +0900 (火, 18 5 2010) | 1 line

wxSources/docview.cpp is added to the project. Trackball.c is added to the Molby_command target (xcode only, still experimental)
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r56 | toshinagata1964 | 2010-05-16 12:09:36 +0900 (日, 16 5 2010) | 1 line

The native format (mbsf) now preserves the display conditions, such as scale, orientation, and show/hide unit cell, periodic images, etc.
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r55 | toshinagata1964 | 2010-05-15 01:03:12 +0900 (土, 15 5 2010) | 1 line

Inconsistency between the Xcode project settings and Makefile_amber11 was resolved. Exception from 'Show periodic image' dialog box was fixed.
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r54 | toshinagata1964 | 2010-05-13 01:29:02 +0900 (木, 13 5 2010) | 1 line

Calculation of vdw/elect forces was wrong when the periodic cell is small; fixed. No new frame is generated when md_frame.run/minimize is called from Ruby script.
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r53 | toshinagata1964 | 2010-05-12 07:50:35 +0900 (水, 12 5 2010) | 1 line

Flags for 'show graphite' and 'show periodic images' are implemented. In MM/MD engine, the handling of Verlet list seems to be incomplete, but this is still being worked on.
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r52 | toshinagata1964 | 2010-05-08 16:29:22 +0900 (土, 08 5 2010) | 1 line

Handling of MD dialog is improved. MM/MD calculation bug (introduced in rev 50) is fixed.
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r51 | toshinagata1964 | 2010-05-08 13:09:23 +0900 (土, 08 5 2010) | 1 line

The Ruby command wrap_unit_cell was not working correctly.
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r50 | toshinagata1964 | 2010-05-08 01:20:03 +0900 (土, 08 5 2010) | 1 line

The MM/MD re-initialization after modification of coordinates was incomplete.
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r48 | toshinagata1964 | 2010-05-07 00:29:52 +0900 (金, 07 5 2010) | 1 line

Version 0.5.4
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r47 | toshinagata1964 | 2010-05-07 00:15:39 +0900 (金, 07 5 2010) | 1 line

Introduce MolbyResourcePath global constant, which points to the directory containing 'Scripts' and 'amber11' resources. Ruby command Kernel.call_subprocess is implemented. ParameterRef.par_type= wrongly parsed the atom type string; fixed.
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r46 | toshinagata1964 | 2010-05-07 00:14:32 +0900 (金, 07 5 2010) | 1 line

Windows: the radio buttons with no explicit radio group showed stranged behavior; fixed.
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r45 | toshinagata1964 | 2010-05-07 00:13:59 +0900 (金, 07 5 2010) | 1 line

Some parameter editing caused segmentation fault; fixed.
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r44 | toshinagata1964 | 2010-05-07 00:13:26 +0900 (金, 07 5 2010) | 1 line

Undo of creating atoms caused segmentation fault; fixed.
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r43 | toshinagata1964 | 2010-05-07 00:12:58 +0900 (金, 07 5 2010) | 1 line

Improved handling of DOSish file paths. The functions strdup() and wcsdup() are implemented here so that the malloc libaries for debugging can be used.
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r42 | toshinagata1964 | 2010-05-07 00:12:18 +0900 (金, 07 5 2010) | 1 line

Importing GAMESS dat file was broken; fixed.
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r41 | toshinagata1964 | 2010-05-07 00:11:39 +0900 (金, 07 5 2010) | 1 line

Added instruction for building and copying resp.
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r40 | toshinagata1964 | 2010-05-07 00:11:06 +0900 (金, 07 5 2010) | 1 line

Removal of double-call of wxDocument::Close() (revision 31) was undone, because it caused occasional crashes.
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r39 | toshinagata1964 | 2010-05-07 00:10:27 +0900 (金, 07 5 2010) | 1 line

Undo is kept enabled during 'molload' and related calls. The 'do not keep logs' option for antechamber was not working; fixed.
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r38 | toshinagata1964 | 2010-05-07 00:09:22 +0900 (金, 07 5 2010) | 1 line

Add hydrogen was broken; fixed.
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r37 | toshinagata1964 | 2010-05-07 00:09:03 +0900 (金, 07 5 2010) | 1 line

Ambertools dialog is improved.
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r36 | toshinagata1964 | 2010-05-07 00:08:45 +0900 (金, 07 5 2010) | 1 line

Automatic generation of internal coordinates (NZVAR=#{3n-5}) is supported in the 'Create GAMESS input' dialog.
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r35 | toshinagata1964 | 2010-05-07 00:07:54 +0900 (金, 07 5 2010) | 1 line

The amber11 binaries are now built in the project directory, instead of the 'build' subdirectory. Windows: event.cpp (from wxMSW) is included in the project with a slight modification.
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r34 | toshinagata1964 | 2010-05-07 00:06:52 +0900 (金, 07 5 2010) | 1 line

Windows: interrupting the subprocess (antechamber etc.) caused grandchildren processes to survive as zombies; fixed.