OSDN Git Service
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
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
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 11 Oct 2011 16:45:16 +0000 (16:45 +0000)]
Special parameters with atom indices were not working. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@133
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 11 Oct 2011 15:09:27 +0000 (15:09 +0000)]
Inserting/removing frames now work more consistently. The minimum number of frames is 1 instead of 0.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@132
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 5 Oct 2011 15:45:32 +0000 (15:45 +0000)]
Atoms to be excluded from MM/MD calculations are now specified by mm_exclude instead of occupancy.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@131
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 5 Oct 2011 14:44:26 +0000 (14:44 +0000)]
MM/MD calculation crashed when periodic cell is removed after calculation with non-nil cell. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@130
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 30 Sep 2011 16:02:19 +0000 (16:02 +0000)]
Makefile: "make depend" now creates a dependency file in the building directory.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@129
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 30 Sep 2011 09:33:21 +0000 (09:33 +0000)]
On windows, Molecule#path, Molecule#dir does not work correctly when the path includes double-byte characters. Fixed. (MyMBConv.h added)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@128
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 30 Sep 2011 09:32:27 +0000 (09:32 +0000)]
On windows, Molecule#path, Molecule#dir does not work correctly when the path includes double-byte characters. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@127
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 30 Sep 2011 02:45:53 +0000 (02:45 +0000)]
After MD run, coordinates are copied back to the molecule even when MD stopped abnormally. MDArena#init_velocities and MDArena#scale_velocities are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@126
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 30 Sep 2011 02:44:17 +0000 (02:44 +0000)]
During alchemical perturbation, graphite energy/forces were calculated incorrectly; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@125
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 28 Sep 2011 11:47:14 +0000 (11:47 +0000)]
Implementation of alchemical perturbation seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@124
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 27 Sep 2011 23:05:08 +0000 (23:05 +0000)]
Experimental implementation of alchemical perturbation (not tested yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@123
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 26 Sep 2011 15:50:15 +0000 (15:50 +0000)]
Improve crd/mdcrd import.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@122
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 26 Sep 2011 10:14:36 +0000 (10:14 +0000)]
The \'r_eq14\' parameter was not editable in the property table. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@121
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 26 Sep 2011 10:13:45 +0000 (10:13 +0000)]
Crash occurs when a Ruby exception is raised while editing property table. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@120
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 20 Sep 2011 11:49:19 +0000 (11:49 +0000)]
Mac: use pthread instead of SIGALRM for interval timer (experimental)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@119
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sun, 18 Sep 2011 13:41:46 +0000 (13:41 +0000)]
Ruby: Molecule#dup now duplicates the unit cell, symmetry operations, and MD settings.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@118
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 15 Sep 2011 10:29:51 +0000 (10:29 +0000)]
Remove \'build xxxxxxxx\' string from the version description.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@117
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 14 Sep 2011 16:21:31 +0000 (16:21 +0000)]
AtomRef.exclusion causes bus error when the MDArena is not yet built. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@116
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 13 Sep 2011 16:17:53 +0000 (16:17 +0000)]
After loading the molecule, occupancy factors are checked, and if all atoms have zero occupancy then all are set to 1.0.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@115
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 7 Sep 2011 16:00:28 +0000 (16:00 +0000)]
Remove some startup code when building a command line tool
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@114
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 7 Sep 2011 15:59:51 +0000 (15:59 +0000)]
Exclude atoms with occupancy = 0 from MM/MD-graphite calculations
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@113
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 6 Sep 2011 15:06:15 +0000 (15:06 +0000)]
Ruby command get_coord_from_frame(index, group=nil, cflag=nil) is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@112
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 6 Sep 2011 10:24:16 +0000 (10:24 +0000)]
Exclude atoms with occupancy = 0 from MM/MD calculations
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@111
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 6 Sep 2011 09:22:36 +0000 (09:22 +0000)]
Exclude atoms with occupancy = 0 from MM/MD calculations
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@110
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 5 Sep 2011 10:06:12 +0000 (10:06 +0000)]
The (experimental) command line version does not compile; empty MainView_resizeToFit() is added to cmdtool_stubs.c.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@109
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 1 Sep 2011 11:51:05 +0000 (11:51 +0000)]
The MO info table is renamed to MO energy, and the alpha and beta orbitals of same indices are shown in the same row.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@108
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 31 Aug 2011 08:32:48 +0000 (08:32 +0000)]
MO import from GAMESS log file was broken
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@107
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 31 Aug 2011 08:06:50 +0000 (08:06 +0000)]
Fchk import: zero is accepted as the number of alpha/beta electrons
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@106
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 23 Aug 2011 09:59:21 +0000 (09:59 +0000)]
Memo update for version 0.5.6.2
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@104
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 23 Aug 2011 09:49:47 +0000 (09:49 +0000)]
Fchk import was broken (enbug in 0.5.6.1); fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@103
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 19 Aug 2011 11:43:22 +0000 (11:43 +0000)]
Final compile date/time is shown in the 'About' window
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@102
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 19 Aug 2011 11:42:45 +0000 (11:42 +0000)]
Importing mdcrd was still broken. Fixed (hopefully)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@101
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 5 Aug 2011 11:40:07 +0000 (11:40 +0000)]
Fix mdcrd import to allow coordinates using full 8 digits (like -123.456 or 1234.567)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@100
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 5 Aug 2011 11:38:52 +0000 (11:38 +0000)]
Occasional crash during minimization is fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@99
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 5 Aug 2011 11:38:11 +0000 (11:38 +0000)]
memo update
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@98
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:13:34 +0000 (10:13 +0000)]
memo update
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@96
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:12:54 +0000 (10:12 +0000)]
Loading GAMESS dat file now can be interrupted by ESC.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@95
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:12:02 +0000 (10:12 +0000)]
Occasionally, termination of the subprocess (like antechamber) was not detected properly, and the subprocess was left as a zombie. Improved, but may not be completely fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@94
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:10:16 +0000 (10:10 +0000)]
Disable close box of RubyDialogFrame.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@93
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:09:48 +0000 (10:09 +0000)]
On importing frcmod, atom type with a single character (like "c") was not recognized properly. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@92
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:02:52 +0000 (10:02 +0000)]
Mac: config.h/Makefiles for AmberTools is modified so that gfortran library is statically linked
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@91
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 3 Aug 2011 10:01:03 +0000 (10:01 +0000)]
ruby-1.8.7-p160.tar.gz is added (required for building)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@90
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 2 Aug 2011 11:24:36 +0000 (11:24 +0000)]
MO import from GAMESS log/dat files seems to be working. Crash on running antechamber/parmchk on PPC Mac is (hopefully) fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@89
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 1 Aug 2011 12:04:34 +0000 (12:04 +0000)]
MO import from GAMESS output is being implemented (not complete yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@88
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 30 Jul 2011 10:28:12 +0000 (10:28 +0000)]
Memo update.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@86
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 30 Jul 2011 10:01:29 +0000 (10:01 +0000)]
Add missing document figures.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@85
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 30 Jul 2011 09:14:53 +0000 (09:14 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@84
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 30 Jul 2011 06:40:37 +0000 (06:40 +0000)]
Step 5 of the tutorial is complete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@83
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 29 Jul 2011 11:51:16 +0000 (11:51 +0000)]
Import AMBER Frcmod menu command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@82
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 28 Jul 2011 16:28:40 +0000 (16:28 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@81
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 28 Jul 2011 11:42:06 +0000 (11:42 +0000)]
CIF import is implemented (maybe still incomplete)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@80
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 26 Jul 2011 15:54:43 +0000 (15:54 +0000)]
Create New Parameter menu command is implemented. MoleculePrepareMDArena() is implmeneted in Molecule.c. Crash in RubyDialogFrame.cpp (sizeOfString) was fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@79
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 21 Jul 2011 16:45:41 +0000 (16:45 +0000)]
Create New Atom menu command is being implemented (not tested at all yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@78
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 21 Jul 2011 11:44:31 +0000 (11:44 +0000)]
Document is being updated (the property table section)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@77
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 21 Jul 2011 08:44:49 +0000 (08:44 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@76
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 20 Jul 2011 10:00:50 +0000 (10:00 +0000)]
Importing mdcrd with periodic box now works correctly.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@75
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 20 Jul 2011 09:29:07 +0000 (09:29 +0000)]
AMBER prmtop/inpcrd export is improved for periodic systems.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@74
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 7 Jul 2011 17:58:01 +0000 (17:58 +0000)]
Copy/paste now handle parameters properly (hopefully...). The Ruby method 'duplicate' also now copies parameters.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@73
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 7 Jul 2011 04:13:35 +0000 (04:13 +0000)]
.gets now appends a newline after the input string. AmberTools: antechamber sometimes created strange intermediate file; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@72
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 6 Jul 2011 23:13:28 +0000 (23:13 +0000)]
Ruby: stdin.{gets, readline} are implemented (other stdin methods will cause exception).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@71
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 6 Jul 2011 06:25:01 +0000 (06:25 +0000)]
Importing Amber mdcrd files is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@70
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 5 Jul 2011 17:46:20 +0000 (17:46 +0000)]
Molecule#{bond,angle,dihedral,improper,vdw}_par were wrongly implemented. Fixed. 'Create SANDER input' is implemented (still not tested much).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@69
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sun, 3 Jul 2011 15:53:23 +0000 (15:53 +0000)]
Ruby: AtomRef#exclusion method was incorrectly calling Molecule#md_arena. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@68
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sun, 3 Jul 2011 14:46:35 +0000 (14:46 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@67
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 2 Jul 2011 15:24:26 +0000 (15:24 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@66
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 26 Apr 2011 14:06:19 +0000 (14:06 +0000)]
Memo update.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@65
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 26 Apr 2011 04:40:11 +0000 (04:40 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@63
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 2 Mar 2011 10:25:09 +0000 (10:25 +0000)]
Pasting MD parameters to a molecule with no parameters was not working. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@62
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Thu, 3 Jun 2010 13:47:32 +0000 (13:47 +0000)]
Crash in MM minimization when no unit cell is defined (enbug in r59); fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@61
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 2 Jun 2010 15:45:11 +0000 (15:45 +0000)]
Xcode project: GCC4.0 is explicitly designated (necessary for building for Mac OS 10.4 on Snow Leopard)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@60
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 31 May 2010 11:41:11 +0000 (11:41 +0000)]
The nearest-neighbor lookup of nonbonding force calculation was problematic; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@59
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 18 May 2010 14:36:00 +0000 (14:36 +0000)]
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).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@58
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Mon, 17 May 2010 15:09:10 +0000 (15:09 +0000)]
wxSources/docview.cpp is added to the project. Trackball.c is added to the Molby_command target (xcode only, still experimental)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@57
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sun, 16 May 2010 03:09:36 +0000 (03:09 +0000)]
The native format (mbsf) now preserves the display conditions, such as scale, orientation, and show/hide unit cell, periodic images, etc.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@56
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Fri, 14 May 2010 16:03:12 +0000 (16:03 +0000)]
Inconsistency between the Xcode project settings and Makefile_amber11 was resolved. Exception from 'Show periodic image' dialog box was fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@55
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Wed, 12 May 2010 16:29:02 +0000 (16:29 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@54
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Tue, 11 May 2010 22:50:35 +0000 (22:50 +0000)]
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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@53
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 8 May 2010 07:29:22 +0000 (07:29 +0000)]
Handling of MD dialog is improved. MM/MD calculation bug (introduced in rev 50) is fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@52
a2be9bc6-48de-4e38-9406-
05402d4bc13c
toshinagata1964 [Sat, 8 May 2010 04:09:23 +0000 (04:09 +0000)]
The Ruby command wrap_unit_cell was not working correctly.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@51
a2be9bc6-48de-4e38-9406-
05402d4bc13c
OSDN Git Service
