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toshinagata1964 [Tue, 26 Jun 2012 11:57:25 +0000 (11:57 +0000)]
Molecule#is_atom_hidden and AtomRef#hidden, hidden= are implemented, and Molecule#hidden_atoms and hidden_atoms= are made obsolete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@236
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toshinagata1964 [Tue, 26 Jun 2012 11:03:01 +0000 (11:03 +0000)]
Molecule#set/get_view_rotation: the sign of the angle is made opposite (left-hand screw in respect to the axis), so that it is consistent with Transform#rotation. This is opposite to the convention of the OpenGL rotator.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@235
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toshinagata1964 [Mon, 25 Jun 2012 11:06:58 +0000 (11:06 +0000)]
The restriction on the number of bonds (12) is removed (modified so heavily, that it is likely that there is still some bugs left...)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@234
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toshinagata1964 [Fri, 22 Jun 2012 04:09:38 +0000 (04:09 +0000)]
Include periodicity flags in the 'define unit cell' dialog
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@233
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toshinagata1964 [Thu, 21 Jun 2012 07:07:58 +0000 (07:07 +0000)]
Problem on guessing UFF angle parameter was fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@232
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toshinagata1964 [Thu, 21 Jun 2012 02:45:39 +0000 (02:45 +0000)]
Fixed a very stupid bug in drawing unit cell.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@231
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toshinagata1964 [Thu, 21 Jun 2012 01:02:21 +0000 (01:02 +0000)]
Handling of frame-specific cell parameters was very inconsistent. Hopefully fixed, but may be still incomplete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@230
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toshinagata1964 [Wed, 20 Jun 2012 16:11:15 +0000 (16:11 +0000)]
Graphite potential in MM/MD gets recalculated much less frequently now.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@229
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toshinagata1964 [Wed, 20 Jun 2012 15:02:31 +0000 (15:02 +0000)]
Building verlet list seems to be working. Handling of MD output files are (hopefully) improved.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@228
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toshinagata1964 [Wed, 20 Jun 2012 11:36:11 +0000 (11:36 +0000)]
Building verlet list is being reworked to implement complete search of the periodic lattice points. Still in progress.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@227
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toshinagata1964 [Wed, 20 Jun 2012 06:18:47 +0000 (06:18 +0000)]
Symmetry operations from the CIF file were not read correctly for hexagonal system. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@226
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toshinagata1964 [Tue, 19 Jun 2012 13:34:54 +0000 (13:34 +0000)]
Mac (only 10.6?): when the graphite display is on, the lighting of the molecule model looks strange. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@225
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toshinagata1964 [Mon, 18 Jun 2012 13:54:16 +0000 (13:54 +0000)]
Version 0.6.3
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@223
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toshinagata1964 [Mon, 18 Jun 2012 11:04:34 +0000 (11:04 +0000)]
Features of Molecule#cell and Molecule#box are modified so that the handling of the sigma values of the cell parameters looks more consistent.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@222
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toshinagata1964 [Mon, 18 Jun 2012 10:15:43 +0000 (10:15 +0000)]
Mbsf format now retains anisotropic parameters and sigma (for crystallographic data)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@221
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toshinagata1964 [Mon, 18 Jun 2012 07:36:58 +0000 (07:36 +0000)]
Crash during creating bonds when ellipsoid display is on is fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@220
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toshinagata1964 [Sun, 17 Jun 2012 09:33:33 +0000 (09:33 +0000)]
Ruby: Molecule#fit_coordinates seems to be working now.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@219
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toshinagata1964 [Sat, 16 Jun 2012 04:09:51 +0000 (04:09 +0000)]
Ruby: Molecule#fit_coordinates is being implemented (still not working)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@218
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toshinagata1964 [Fri, 15 Jun 2012 00:34:44 +0000 (00:34 +0000)]
LAMatrix#new, #zero, #submatrix now accept arguments in 'column,row' order.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@217
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toshinagata1964 [Thu, 14 Jun 2012 11:26:02 +0000 (11:26 +0000)]
MM forces are updated even after 'run(0)'
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@216
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toshinagata1964 [Thu, 14 Jun 2012 11:10:50 +0000 (11:10 +0000)]
Load/save mbsf files were broken when atom type variants were used for atom types with 3 or 4 characters. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@215
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toshinagata1964 [Wed, 13 Jun 2012 14:23:17 +0000 (14:23 +0000)]
The order of parameters in cmd_edit_local_parameter_in_mainview dialog was inconsistent. Fixed. Also fixed Ruby exception in UFF guess dialog.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@214
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toshinagata1964 [Thu, 7 Jun 2012 15:05:32 +0000 (15:05 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@213
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toshinagata1964 [Wed, 6 Jun 2012 16:16:55 +0000 (16:16 +0000)]
MoleculeGetTransformForSymop() and MoleculeGetSymopForTransform() are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@212
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toshinagata1964 [Wed, 6 Jun 2012 14:50:51 +0000 (14:50 +0000)]
Ruby: AtomRef#symop can now be set from script.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@211
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toshinagata1964 [Wed, 6 Jun 2012 01:53:23 +0000 (01:53 +0000)]
Ruby: Molecule#amend_by_symmetry is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@210
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toshinagata1964 [Mon, 4 Jun 2012 15:21:51 +0000 (15:21 +0000)]
Ruby: Molecule#set(get)_view_translation is now obsolete and replaced by set(get)_view_center.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@209
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toshinagata1964 [Mon, 4 Jun 2012 15:20:50 +0000 (15:20 +0000)]
Undoing change in revision 207 (forgot to commit different changes separately)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@208
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toshinagata1964 [Mon, 4 Jun 2012 14:46:18 +0000 (14:46 +0000)]
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 are not correctly converted.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@207
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toshinagata1964 [Mon, 4 Jun 2012 10:25:50 +0000 (10:25 +0000)]
Ruby: Molecule#hidden_atoms and Molecule#set_hidden_atoms are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@206
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toshinagata1964 [Wed, 9 May 2012 14:22:10 +0000 (14:22 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@205
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toshinagata1964 [Wed, 9 May 2012 10:42:06 +0000 (10:42 +0000)]
UFF parameter guess is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@204
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toshinagata1964 [Wed, 9 May 2012 10:41:36 +0000 (10:41 +0000)]
Molecule.neutralize was not working correctly. Fixed, and Molecule.charge was implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@203
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toshinagata1964 [Tue, 8 May 2012 05:28:40 +0000 (05:28 +0000)]
Fix the position of load/unload global parameters dialog.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@202
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toshinagata1964 [Tue, 8 May 2012 05:27:51 +0000 (05:27 +0000)]
Windows version does not display last build date in the about dialog. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@201
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toshinagata1964 [Tue, 8 May 2012 04:37:53 +0000 (04:37 +0000)]
MyAppCallback_lookupScriptMenu() is added to cmdtool_stubs.c, to allow compilation of the command line tool.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@200
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toshinagata1964 [Tue, 8 May 2012 04:30:35 +0000 (04:30 +0000)]
Parameters now can be specified by using both explicit indices and atom types, like '7-ca-8'.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@199
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toshinagata1964 [Tue, 8 May 2012 02:05:36 +0000 (02:05 +0000)]
Parameter editing is under overhaul.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@198
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toshinagata1964 [Mon, 7 May 2012 16:36:02 +0000 (16:36 +0000)]
Handling of parameters are being improved, but still not complete
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@197
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toshinagata1964 [Mon, 7 May 2012 11:48:21 +0000 (11:48 +0000)]
Handling of parameters is being reworked (still going on)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@196
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toshinagata1964 [Mon, 7 May 2012 09:10:17 +0000 (09:10 +0000)]
Restructure MolAction.c
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@195
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toshinagata1964 [Mon, 7 May 2012 02:55:55 +0000 (02:55 +0000)]
Atom range specification for the vdw cutoff parameter is now made obsolete
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@194
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toshinagata1964 [Thu, 3 May 2012 10:23:34 +0000 (10:23 +0000)]
LAMatrix.html was added to the repository.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@193
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toshinagata1964 [Thu, 3 May 2012 10:22:50 +0000 (10:22 +0000)]
Vector3D[] and Transform[] are modified to accept an LAMatrix argument. The document is written for LAMatrix.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@192
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toshinagata1964 [Thu, 3 May 2012 10:22:06 +0000 (10:22 +0000)]
Load Script Menu caused crash when no window is open. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@191
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toshinagata1964 [Thu, 3 May 2012 04:04:39 +0000 (04:04 +0000)]
Ruby: Kernel.lookup_menu is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@190
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toshinagata1964 [Thu, 3 May 2012 03:19:34 +0000 (03:19 +0000)]
LAMatrix.multiply was not working correctly when on-the-fly size conversion was required. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@189
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toshinagata1964 [Wed, 2 May 2012 10:00:56 +0000 (10:00 +0000)]
Execute Script command was broken. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@188
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toshinagata1964 [Thu, 29 Mar 2012 11:18:56 +0000 (11:18 +0000)]
CIF import may fail when _geom_bond_site_symmetry_1 field is missing. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@187
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toshinagata1964 [Thu, 1 Mar 2012 13:50:30 +0000 (13:50 +0000)]
Figures for the document are added
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@186
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toshinagata1964 [Sun, 26 Feb 2012 07:54:03 +0000 (07:54 +0000)]
Document was written for the collaboration with other quantum chemistry softwares.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@185
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toshinagata1964 [Sun, 26 Feb 2012 07:50:23 +0000 (07:50 +0000)]
.log and .out are both accepted as the extension of the Gaussian and GAMESS log files.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@184
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toshinagata1964 [Sat, 11 Feb 2012 15:03:36 +0000 (15:03 +0000)]
update_version.rb is improved.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@183
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toshinagata1964 [Sat, 11 Feb 2012 14:34:15 +0000 (14:34 +0000)]
version 0.6.2
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@181
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toshinagata1964 [Wed, 1 Feb 2012 15:57:45 +0000 (15:57 +0000)]
Document is updated to include new graphic objects in the model view.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@180
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toshinagata1964 [Tue, 31 Jan 2012 10:04:29 +0000 (10:04 +0000)]
Ruby: Molecule#make_front, set_name, get_view_rotation, get_view_scale, get_view_translation, set_view_rotation, set_view_scale, set_view_translation, set_graphic_color, hide_graphic, show_graphic are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@179
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toshinagata1964 [Mon, 30 Jan 2012 16:39:24 +0000 (16:39 +0000)]
Drawing custom graphics on the model view is being implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@178
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toshinagata1964 [Mon, 30 Jan 2012 10:59:30 +0000 (10:59 +0000)]
Ruby Dialog: modeless dialog is now implemented; interval timer is implemented. Ruby: $KCODE is set on startup, and coding:{shift-jis, utf-8} is recognized as the source code encoding (for executing script from file). Molecule#all returns IntGroup[0] when the molecule is empty (it should return IntGroup[]), which causes crash on Molecule#delete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@177
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toshinagata1964 [Tue, 17 Jan 2012 09:17:08 +0000 (09:17 +0000)]
Dialog#layout: the :align and :vertical_align options can now be specified as item attributes
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@176
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toshinagata1964 [Tue, 17 Jan 2012 08:06:49 +0000 (08:06 +0000)]
The separator line in the Ruby Dialog was not working correctly.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@175
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toshinagata1964 [Tue, 17 Jan 2012 06:42:55 +0000 (06:42 +0000)]
Vector3D and Transform objects are converted to LAMatrix object with dimensions 3 or 4 depending upon the context.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@174
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toshinagata1964 [Mon, 16 Jan 2012 10:45:21 +0000 (10:45 +0000)]
LAMatrix#new errornously allows matrix with dimension 0. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@173
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toshinagata1964 [Mon, 16 Jan 2012 10:43:56 +0000 (10:43 +0000)]
AtomRef#molecule is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@172
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toshinagata1964 [Mon, 16 Jan 2012 10:13:37 +0000 (10:13 +0000)]
Empty Console Window command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@171
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toshinagata1964 [Fri, 13 Jan 2012 11:07:55 +0000 (11:07 +0000)]
LAMatrix.multiply was not working correctly when the first argument is a scalar. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@170
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toshinagata1964 [Thu, 22 Dec 2011 11:32:49 +0000 (11:32 +0000)]
General matrix calculation (LAMatrix class in Ruby) is implemented. Seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@169
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toshinagata1964 [Wed, 21 Dec 2011 00:40:23 +0000 (00:40 +0000)]
Some of the document figures are updated.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@168
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toshinagata1964 [Wed, 21 Dec 2011 00:02:41 +0000 (00:02 +0000)]
General matrix calculation is being implemented (still on the way)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@167
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toshinagata1964 [Tue, 20 Dec 2011 23:53:21 +0000 (23:53 +0000)]
Figures in the MD section of the document are added.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@166
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toshinagata1964 [Tue, 20 Dec 2011 10:48:33 +0000 (10:48 +0000)]
In the document, navigation between the English/Japanese versions is possible in most pages.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@165
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toshinagata1964 [Tue, 20 Dec 2011 09:00:53 +0000 (09:00 +0000)]
Document for MD calculation is written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@164
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toshinagata1964 [Mon, 19 Dec 2011 10:24:13 +0000 (10:24 +0000)]
The "log file" field is set to blank unless explicitly set by the user.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@163
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toshinagata1964 [Mon, 19 Dec 2011 10:23:10 +0000 (10:23 +0000)]
Document for MD calculation is being written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@162
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toshinagata1964 [Wed, 7 Dec 2011 11:07:33 +0000 (11:07 +0000)]
The structure Mat33 and Transform are now column-first arrangement (no change on Ruby interface and mbsf file format)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@161
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toshinagata1964 [Wed, 30 Nov 2011 11:10:35 +0000 (11:10 +0000)]
Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@160
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toshinagata1964 [Wed, 30 Nov 2011 04:59:56 +0000 (04:59 +0000)]
Memo update for 0.6.1; also updated molby.iss for building Windows executable.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@159
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toshinagata1964 [Sat, 26 Nov 2011 16:18:03 +0000 (16:18 +0000)]
Version 0.6.1
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@158
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toshinagata1964 [Sat, 26 Nov 2011 16:15:44 +0000 (16:15 +0000)]
Document on ring fusion capability is written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@157
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toshinagata1964 [Sat, 26 Nov 2011 16:15:00 +0000 (16:15 +0000)]
Selection after ring fusion by 'double-click and type-in' now includes all atoms in the newly formed ring.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@156
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toshinagata1964 [Sat, 26 Nov 2011 11:11:31 +0000 (11:11 +0000)]
Behavior of paste is improved when two dangling bonds are present in the fragment and the target molecule (i.e. ring fusion does work)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@155
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toshinagata1964 [Sat, 26 Nov 2011 07:25:35 +0000 (07:25 +0000)]
Some typical cyclic structures as well as solvent boxes are now accessible from 'Open Predefined' menu.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@154
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toshinagata1964 [Fri, 25 Nov 2011 09:31:13 +0000 (09:31 +0000)]
Ruby: Molecule object is now unique to each open molecule, i.e. the same Molecule object is returned when requested for the same molecule.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@153
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toshinagata1964 [Wed, 23 Nov 2011 16:08:17 +0000 (16:08 +0000)]
Ring fusion (e.g. expanding benzene to naphthalene) is implemented; still experimental, but seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@152
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toshinagata1964 [Tue, 22 Nov 2011 11:59:39 +0000 (11:59 +0000)]
__FILE__ is now set to the script file during execute_script.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@151
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toshinagata1964 [Mon, 31 Oct 2011 06:22:35 +0000 (06:22 +0000)]
Some cleanup to suppress warnings
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@150
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toshinagata1964 [Mon, 31 Oct 2011 06:10:41 +0000 (06:10 +0000)]
CIF import is improved, so that bonds including the calculated hydrogen atoms are created by guess.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@149
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toshinagata1964 [Mon, 31 Oct 2011 05:26:04 +0000 (05:26 +0000)]
Ruby: Molecule#find_close_atoms is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@148
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toshinagata1964 [Fri, 21 Oct 2011 00:45:13 +0000 (00:45 +0000)]
Enable undo for importing pdb and dcd.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@147
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toshinagata1964 [Wed, 19 Oct 2011 07:56:10 +0000 (07:56 +0000)]
Import/export of dcd format is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@146
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toshinagata1964 [Wed, 19 Oct 2011 07:55:18 +0000 (07:55 +0000)]
Creating AMBER input now allows to select between AMBER8 (also for NAMD) and AMBER11 formats.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@145
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toshinagata1964 [Sat, 15 Oct 2011 15:07:41 +0000 (15:07 +0000)]
Version 0.6
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@143
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toshinagata1964 [Sat, 15 Oct 2011 14:00:33 +0000 (14:00 +0000)]
On Windows, Molby::{Mbsf,Resource,Script}Path return slash-separated strings instead of backslash-separated strings.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@142
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toshinagata1964 [Thu, 13 Oct 2011 11:57:37 +0000 (11:57 +0000)]
The solvate command does not correctly remove conflicting solvent molecules. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@141
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toshinagata1964 [Thu, 13 Oct 2011 11:56:48 +0000 (11:56 +0000)]
Ruby: find_conflicts now exclude atom pairs separated by 0-3 bonds.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@140
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toshinagata1964 [Thu, 13 Oct 2011 00:27:00 +0000 (00:27 +0000)]
export_prmtop can now be used from script
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@139
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toshinagata1964 [Wed, 12 Oct 2011 16:13:25 +0000 (16:13 +0000)]
Merging molecule was resulting in strange order of merged parameters. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@138
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toshinagata1964 [Wed, 12 Oct 2011 16:12:42 +0000 (16:12 +0000)]
Occasional crash on merging molecules is fixed. (Duplicating parameters was causing problems.)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@137
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toshinagata1964 [Wed, 12 Oct 2011 10:38:37 +0000 (10:38 +0000)]
Some solvent box are included in Scripts/mbsf folder. MolbyResourcePath is now called Molby::ResourcePath (old name is still usable for backward compatibility). Molby::ScriptPath, Molby::MbsfPath are also implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@136
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toshinagata1964 [Wed, 12 Oct 2011 10:14:07 +0000 (10:14 +0000)]
rotate_with_axis now can accept atom indices or names as the first three arguments.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@135
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toshinagata1964 [Wed, 12 Oct 2011 10:13:08 +0000 (10:13 +0000)]
Setting external forces during MM/MD is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@134
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