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/
Incomplete MM/MD re-initialization after modification of coordinates was fixed.
The Ruby command wrap_unit_cell now works correctly.
Periodic images can be displayed when a unit cell is defined.
Wrong calculation of vdw/elect forces under periodic boundary conditions was fixed.
The native format (mbsf) now preserves the display conditions, such as scale, orientation etc.
Pasting MD parameters to a molecule with no parameters now works correctly.
Importing GaussianW fch(k) files was not working; fixed. The extension ".fch" is now recognized as a Gaussian formatted checkpoint files.
原子座標を修正したあとの MM/MD の不具合を修正。
wrap_unit_cell コマンドの不具合を修正。
単位格子が定義されているときに、周期的なイメージを表示する機能を実装。
周期境界条件での vdW／静電力計算の不具合を修正。
mbsf ファイルにスケール、配向などの表示に関する設定を保存。
MD パラメータがない分子に他の分子からのパラメータをペーストできない不具合を修正。
GaussianW の fch(k) ファイルが読めない不具合を修正。また、拡張子 ".fch" を Gaussian Checkpoint File として認識するよう設定。
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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
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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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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)
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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).
------------------------------------------------------------------------
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)
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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
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