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/
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。
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.
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