Fork| Rev. | 日時 | 作者 |
|---|---|---|
| e9ee338 | 2011-07-21 17:44:49 | toshinagata1964 |
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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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| c2e23d7 | 2011-07-20 19:00:50 | toshinagata1964 |
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Importing mdcrd with periodic box now works correctly. |
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| 76bff65 | 2011-07-20 18:29:07 | toshinagata1964 |
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AMBER prmtop/inpcrd export is improved for periodic systems. |
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| e42f593 | 2011-07-08 02:58:01 | toshinagata1964 |
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Copy/paste now handle parameters properly (hopefully...). The Ruby method 'duplicate' also now copies parameters. |
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| 1de3244 | 2011-07-07 13:13:35 | toshinagata1964 |
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.gets now appends a newline after the input string. AmberTools: antechamber sometimes created strange intermediate file; fixed. |
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| 33480e3 | 2011-07-07 08:13:28 | toshinagata1964 |
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Ruby: stdin.{gets, readline} are implemented (other stdin methods will cause exception). |
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| 6aaec16 | 2011-07-06 15:25:01 | toshinagata1964 |
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Importing Amber mdcrd files is implemented. |
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| c745bfe | 2011-07-06 02:46:20 | toshinagata1964 |
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Molecule#{bond,angle,dihedral,improper,vdw}_par were wrongly implemented. Fixed. 'Create SANDER input' is implemented (still not tested much). |
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| 8335899 | 2011-07-04 00:53:23 | toshinagata1964 |
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Ruby: AtomRef#exclusion method was incorrectly calling Molecule#md_arena. Fixed. |
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| 1e866ad | 2011-07-03 23:46:35 | toshinagata1964 |
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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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| 7a73717 | 2011-07-03 00:24:26 | toshinagata1964 |
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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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| cd7c355 | 2011-04-26 23:06:19 | toshinagata1964 |
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Memo update. |
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| 7870dde | 2011-04-26 13:40:11 | toshinagata1964 |
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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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| c84669b | 2011-03-02 19:25:09 | toshinagata1964 |
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Pasting MD parameters to a molecule with no parameters was not working. Fixed. |
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| 89a5018 | 2010-06-03 22:47:32 | toshinagata1964 |
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Crash in MM minimization when no unit cell is defined (enbug in r59); fixed. |
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| 216b1b2 | 2010-06-03 00:45:11 | toshinagata1964 |
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Xcode project: GCC4.0 is explicitly designated (necessary for building for Mac OS 10.4 on Snow Leopard) |
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| 64c80e3 | 2010-05-31 20:41:11 | toshinagata1964 |
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The nearest-neighbor lookup of nonbonding force calculation was problematic; fixed. |
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| 4570f45 | 2010-05-18 23:36:00 | toshinagata1964 |
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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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| 98194f0 | 2010-05-18 00:09:10 | toshinagata1964 |
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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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| 1fd46e0 | 2010-05-16 12:09:36 | toshinagata1964 |
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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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| 3ea4011 | 2010-05-15 01:03:12 | toshinagata1964 |
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Inconsistency between the Xcode project settings and Makefile_amber11 was resolved. Exception from 'Show periodic image' dialog box was fixed. |
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| ebe73ff | 2010-05-13 01:29:02 | toshinagata1964 |
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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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| addd49d | 2010-05-12 07:50:35 | toshinagata1964 |
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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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| 608596b | 2010-05-08 16:29:22 | toshinagata1964 |
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Handling of MD dialog is improved. MM/MD calculation bug (introduced in rev 50) is fixed. |
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| 0b015a7 | 2010-05-08 13:09:23 | toshinagata1964 |
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The Ruby command wrap_unit_cell was not working correctly. |
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| bda1de4 | 2010-05-08 01:20:03 | toshinagata1964 |
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The MM/MD re-initialization after modification of coordinates was incomplete. |
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| 763a298 | 2010-05-07 00:29:52 | toshinagata1964 |
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Version 0.5.4 |
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| 5c819d4 | 2010-05-07 00:15:39 | toshinagata1964 |
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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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| d86ffb4 | 2010-05-07 00:14:32 | toshinagata1964 |
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Windows: the radio buttons with no explicit radio group showed stranged behavior; fixed. |
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| cbbf234 | 2010-05-07 00:13:59 | toshinagata1964 |
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Some parameter editing caused segmentation fault; fixed. |
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