Author: bugman
Date: Fri Jan 20 15:43:59 2012
New Revision: 15213
URL: http://svn.gna.org/viewcvs/relax?rev=15213&view=rev
Log:
Merged revisions
14455-14456,14460-14464,14467-14468,14470-14472,14475,14477-14497,14499-14816,14819-14993,14996,14998,15002,15007-15012,15016,15018,15165,15205-15207
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
................
r14455 | bugman | 2011-08-25 16:34:49 +0200 (Thu, 25 Aug 2011) | 3 lines
Added the empty() method to the GUI interpreter thread to determine if the
internal queue is empty.
................
r14456 | bugman | 2011-08-25 16:36:12 +0200 (Thu, 25 Aug 2011) | 3 lines
Added a join() wrapper method for the GUI interpreter thread internal queue.
................
r14460 | bugman | 2011-08-25 17:59:23 +0200 (Thu, 25 Aug 2011) | 3 lines
Created the GUI interpreter thread flush() method for blocking until the
queue is empty.
................
r14461 | bugman | 2011-08-25 18:03:43 +0200 (Thu, 25 Aug 2011) | 3 lines
The GUI interpreter thread is now flushed prior to execution of the
auto-analyses.
................
r14462 | bugman | 2011-08-26 08:50:33 +0200 (Fri, 26 Aug 2011) | 5 lines
The auto-analysis GUI pages are now waiting for the data pipe to be created.
This fixes race conditions.
................
r14463 | bugman | 2011-08-26 09:03:30 +0200 (Fri, 26 Aug 2011) | 5 lines
Fixes for all the calls to the GUI interpreter instance.
This is now a special thread object, and user function calls are now queued.
................
r14464 | bugman | 2011-08-26 09:49:59 +0200 (Fri, 26 Aug 2011) | 3 lines
Fix for the pipe editor window - it is now updated when initially created
to show all loaded pipes.
................
r14467 | bugman | 2011-08-26 10:40:21 +0200 (Fri, 26 Aug 2011) | 3 lines
Fix for the results viewer window in testing mode - it is now not shown.
................
r14468 | bugman | 2011-08-26 10:44:12 +0200 (Fri, 26 Aug 2011) | 5 lines
Created the model-free PyMOL macro functions by copying the Molmol ones.
This will need to be modified as Molmol commands are still being issued.
................
r14470 | bugman | 2011-08-26 11:20:54 +0200 (Fri, 26 Aug 2011) | 7 lines
Fixes for the pymol.write and molmol.write user function GUI pages.
The directory argument to the user function back end is now set to None as
otherwise it defaults to
a directory such as 'pymol' which is then incompatible with the absolute
file path from the file
dialog.
................
r14471 | bugman | 2011-08-26 11:23:11 +0200 (Fri, 26 Aug 2011) | 3 lines
The force flag now defaults to True for the molmol.write and pymol.write
user function GUI pages.
................
r14472 | bugman | 2011-08-26 11:24:40 +0200 (Fri, 26 Aug 2011) | 3 lines
The PyMOL macro is registered as a pymol file in the results file structure
rather than a Grace file.
................
r14475 | bugman | 2011-08-26 11:46:58 +0200 (Fri, 26 Aug 2011) | 3 lines
The PyMOL macro file extension is now correct in the pymol.write user
function GUI page.
................
r14477 | bugman | 2011-08-26 12:09:13 +0200 (Fri, 26 Aug 2011) | 6 lines
Renamed the PyMOL macro related user functions in the prompt/script front
end.
The pymol.macro_exec() function is now called pymol.macro_apply(), and
pymol.write() is now called
pymol.macro_write() to make it clearer.
................
r14478 | bugman | 2011-08-26 12:12:07 +0200 (Fri, 26 Aug 2011) | 5 lines
Created the front end for the pymol.macro_run user function.
This will be used to open and execute macros from text files.
................
r14479 | bugman | 2011-08-26 12:19:56 +0200 (Fri, 26 Aug 2011) | 3 lines
Some fixes and improvements to the PyMOL macro related user functions.
................
r14480 | bugman | 2011-08-26 12:21:21 +0200 (Fri, 26 Aug 2011) | 8 lines
Modified the Molmol macro related user function front end to match those of
PyMOL.
These are:
- molmol.macro_exec() is now molmol.macro_apply().
- molmol.write() is now molmol.macro_write().
- molmol.macro.run() has been added to execute macros from text files.
................
r14481 | bugman | 2011-08-26 12:23:00 +0200 (Fri, 26 Aug 2011) | 3 lines
Renamed the PyMOL and Molmol macro user function back ends.
................
r14482 | bugman | 2011-08-26 12:36:18 +0200 (Fri, 26 Aug 2011) | 3 lines
Built the back end of the pymol.macro_run user function.
................
r14483 | bugman | 2011-08-26 12:37:10 +0200 (Fri, 26 Aug 2011) | 3 lines
Built the back end of the molmol.macro_run user function.
................
r14484 | bugman | 2011-08-26 13:49:12 +0200 (Fri, 26 Aug 2011) | 3 lines
Renamed the PyMOL and Molmol macro user functions to match the back end.
................
r14485 | bugman | 2011-08-26 13:56:18 +0200 (Fri, 26 Aug 2011) | 3 lines
Updated the pymol and molmol macro menu entries to match the back end.
................
r14486 | bugman | 2011-08-26 13:58:49 +0200 (Fri, 26 Aug 2011) | 3 lines
Created the pymol.macro_run and molmol.macro_run user function GUI pages.
................
r14487 | bugman | 2011-08-26 14:02:45 +0200 (Fri, 26 Aug 2011) | 3 lines
The pymol.macro_run and molmol.macro_run user function GUI pages can now
have the file name preset.
................
r14488 | bugman | 2011-08-26 14:03:08 +0200 (Fri, 26 Aug 2011) | 3 lines
The results viewer will now open PyMOL files in PyMOL via pymol.macro_run.
................
r14489 | bugman | 2011-08-26 14:16:11 +0200 (Fri, 26 Aug 2011) | 5 lines
Bug fix for the molmol.macro_run and pymol.macro_run user function back
ends.
The force flag does not exist.
................
r14490 | bugman | 2011-08-26 14:17:14 +0200 (Fri, 26 Aug 2011) | 5 lines
The molmol macro files are no registered in the results file list as such.
They were previously registered as Grace files.
................
r14491 | bugman | 2011-08-26 14:18:58 +0200 (Fri, 26 Aug 2011) | 3 lines
The results viewer window can now open Molmol macro files.
................
r14492 | bugman | 2011-08-26 14:20:10 +0200 (Fri, 26 Aug 2011) | 3 lines
Fix for the results viewer window file opening.
................
r14493 | bugman | 2011-08-26 14:22:18 +0200 (Fri, 26 Aug 2011) | 5 lines
Fix for the molmol.macro_run user function GUI page.
The directory argument should have been None.
................
r14494 | bugman | 2011-08-26 15:25:06 +0200 (Fri, 26 Aug 2011) | 3 lines
Missing import of relax_io.open_read_file.
................
r14495 | bugman | 2011-08-26 17:21:26 +0200 (Fri, 26 Aug 2011) | 3 lines
Updated the pymol.macro_write user function docstring.
................
r14496 | bugman | 2011-08-26 17:23:09 +0200 (Fri, 26 Aug 2011) | 3 lines
The file name is optional in the pymol.macro_write user function.
................
r14497 | bugman | 2011-08-26 17:25:02 +0200 (Fri, 26 Aug 2011) | 3 lines
Fix for the pymol.macro_write back end - the default file extension is now
*.pml, not *.mac.
................
r14499 | bugman | 2011-08-29 12:17:02 +0200 (Mon, 29 Aug 2011) | 3 lines
The menu icons for the pymol.macro_run and molmol.macro_run user functions
is now the open icon.
................
r14500 | bugman | 2011-08-29 12:18:42 +0200 (Mon, 29 Aug 2011) | 3 lines
The PyMOL macro header has now been converted from Molmol to PyMOL commands.
................
r14501 | bugman | 2011-08-29 13:28:13 +0200 (Mon, 29 Aug 2011) | 5 lines
Completely converted the PyMOL model-free macro creation from Molmol to
PyMOL commands.
This now reproduces the Molmol 'classic' representation.
................
r14502 | bugman | 2011-08-29 14:07:03 +0200 (Mon, 29 Aug 2011) | 6 lines
Abstracted the model-free 'classic' Molmol and PyMOL creation in to a base
class.
As most of the code between the specific_fns.model_free.molmol and
specific_fns.model_free.pymol
modules is identical, this significantly simplifies the code base.
................
r14503 | bugman | 2011-08-29 14:13:22 +0200 (Mon, 29 Aug 2011) | 3 lines
Removed unused imports.
................
r14504 | bugman | 2011-08-29 14:15:17 +0200 (Mon, 29 Aug 2011) | 3 lines
Added module docstrings for all the model-free macro modules.
................
r14505 | bugman | 2011-08-29 14:17:05 +0200 (Mon, 29 Aug 2011) | 5 lines
All the model-free macro methods are no longer private.
The class will not be used as a base class for the model-free specific
class.
................
r14506 | bugman | 2011-08-29 14:17:57 +0200 (Mon, 29 Aug 2011) | 3 lines
Added the macro_base module to the __all__ package list.
................
r14507 | bugman | 2011-08-29 14:21:19 +0200 (Mon, 29 Aug 2011) | 3 lines
The Molmol and PyMOL classes are now initialised by the model-free class
and the methods aliased.
................
r14508 | bugman | 2011-08-29 14:23:23 +0200 (Mon, 29 Aug 2011) | 3 lines
Fixes for the user function docstrings for the changes to the macro
modules.
................
r14509 | bugman | 2011-08-29 15:04:26 +0200 (Mon, 29 Aug 2011) | 8 lines
Fix for the execution of pymol macros via the pymol.macro_apply user
function.
The PyMOL commands are now written to a temporary file and this file is
executed via the @x run
syntax. The PyMOL commands sent into the interface are asynchronously
processed so that executing
a macro in that way always fails. However the commands in a *.pml macro
file are processed
synchronously, eliminating the annoying bug.
................
r14510 | bugman | 2011-08-29 15:10:50 +0200 (Mon, 29 Aug 2011) | 6 lines
Bug fix for the pymol.macro_apply user function - the command history is
now cleared.
Without this, previous macro files will be executed, but if they were
temporary and no longer exist,
then pymol fails.
................
r14511 | bugman | 2011-08-29 15:12:53 +0200 (Mon, 29 Aug 2011) | 3 lines
Decreased the amount of time waiting for PyMOL in pymol.macro_apply to 3
seconds.
................
r14512 | bugman | 2011-08-29 15:15:17 +0200 (Mon, 29 Aug 2011) | 3 lines
The backbone oxygen is no longer shown in the PyMOL model-free macros.
................
r14513 | bugman | 2011-08-29 15:48:17 +0200 (Mon, 29 Aug 2011) | 3 lines
Improvement to the PyMOL model-free macros - bonds rather than atoms in
selections are now coloured.
................
r14514 | bugman | 2011-08-29 16:09:07 +0200 (Mon, 29 Aug 2011) | 3 lines
Fix for the dauvergne_protocol auto-analysis for the pymol and molmol write
to macro_write rename.
................
r14515 | bugman | 2011-08-29 16:16:42 +0200 (Mon, 29 Aug 2011) | 3 lines
Fix for the user manual LaTeX longtables for the pymol and molmol write to
macro_write rename.
................
r14516 | bugman | 2011-08-29 16:17:53 +0200 (Mon, 29 Aug 2011) | 3 lines
Fix for the molmol plot sample script for the pymol and molmol write to
macro_write rename.
................
r14517 | bugman | 2011-08-29 16:19:17 +0200 (Mon, 29 Aug 2011) | 3 lines
Fixes to the unit tests for the PyMOL and Molmol macro user function
renamings.
................
r14518 | bugman | 2011-08-30 11:58:00 +0200 (Tue, 30 Aug 2011) | 3 lines
Added the _get_uf() method to the GUI interpreter object for abstracting
the code.
................
r14519 | bugman | 2011-08-30 13:13:41 +0200 (Tue, 30 Aug 2011) | 5 lines
Redesigned the GUI interpreter object so that the thread is a separate
object.
This is to allow both synchronous and asynchronous calls to the interpreter
in the future.
................
r14520 | bugman | 2011-08-30 13:30:32 +0200 (Tue, 30 Aug 2011) | 3 lines
Created the GUI interpreter object apply() for synchronous calls to the
user functions.
................
r14521 | bugman | 2011-08-30 13:32:51 +0200 (Tue, 30 Aug 2011) | 6 lines
The GUI auto-analyses now initialise with a synchronous call to
pipe.create().
This uses the GUI interpreter object apply() method to prevent race
conditions. This is important
as the pipe creation needs to be completed prior to the setting up of the
GUI elements.
................
r14522 | bugman | 2011-08-30 15:34:11 +0200 (Tue, 30 Aug 2011) | 8 lines
The notification of observers in status.observers.gui_uf has been modified.
The GUI user function pages no longer perform this as the calls to the
interpreter are via the
interpreter thread, hence the completion of the page does not signal the
completion of the user
function. Instead the interpreter thread (and the synchronous apply() call
as well) perform the
notification once complete.
................
r14523 | bugman | 2011-08-30 15:45:26 +0200 (Tue, 30 Aug 2011) | 5 lines
The relax controller is no longer shown every time a print out occurs.
This window was appearing far too often causing too much window clutter.
................
r14524 | bugman | 2011-08-30 16:03:22 +0200 (Tue, 30 Aug 2011) | 5 lines
Added the ability to flush the GUI interpreter thread in the wizard prior
to changing to the next page.
This will help in solving races when a series of user functions are strung
one after the other.
................
r14525 | bugman | 2011-08-30 16:05:56 +0200 (Tue, 30 Aug 2011) | 3 lines
The flush flag is set for the first page of the Rx peak height loading
wizard.
................
r14526 | bugman | 2011-08-30 16:06:53 +0200 (Tue, 30 Aug 2011) | 3 lines
Fix for the wizard page _ok() method for the uf_flush flag.
................
r14527 | bugman | 2011-08-30 16:07:28 +0200 (Tue, 30 Aug 2011) | 3 lines
Fix for the Rx peak height wizard, the user function flush flag was
incorrectly named.
................
r14528 | bugman | 2011-08-30 16:10:19 +0200 (Tue, 30 Aug 2011) | 3 lines
The GUI interpreter object has been converted into a singleton.
................
r14529 | bugman | 2011-08-30 16:12:47 +0200 (Tue, 30 Aug 2011) | 5 lines
A copy of the GUI interpreter singleton is now initialised in the wizard.
This is used for the flushing of user functions prior to proceeding.
................
r14530 | bugman | 2011-08-30 16:16:36 +0200 (Tue, 30 Aug 2011) | 5 lines
All pages of the Rx peak list wizard now cannot proceed on an error.
This will trigger the user function flushing.
................
r14531 | bugman | 2011-08-30 16:47:36 +0200 (Tue, 30 Aug 2011) | 5 lines
The analysis spin control GUI element now sets the default value.
This used to set the value, but for some reason no longer did this.
................
r14532 | bugman | 2011-08-31 10:58:58 +0200 (Wed, 31 Aug 2011) | 5 lines
Renamed the execution lock debug flag to fake_lock.
This is a bit different from the normal debugging and allows a different
type of debugging.
................
r14533 | bugman | 2011-08-31 11:00:16 +0200 (Wed, 31 Aug 2011) | 5 lines
The pipe_lock locking object is now the special Relax_lock.
This will allow for fine grained debugging.
................
r14534 | bugman | 2011-08-31 11:02:04 +0200 (Wed, 31 Aug 2011) | 3 lines
The Relax_lock object now has a 'name' argument which will be used in
debugging.
................
r14535 | bugman | 2011-08-31 11:04:03 +0200 (Wed, 31 Aug 2011) | 5 lines
Renamed the Relax_lock debug arg to fake_lock.
Again this is used to fake the locking mechanism, whereas debugging could
be more fine grained.
................
r14536 | bugman | 2011-08-31 12:12:04 +0200 (Wed, 31 Aug 2011) | 3 lines
The Relax_lock object now has much better debugging facilities, and
responds to the debug flag.
................
r14537 | bugman | 2011-08-31 12:19:35 +0200 (Wed, 31 Aug 2011) | 5 lines
All acquire() and release() calls for the spin_lock and pipe_lock objects
now are named.
The name argument is now supplied to these methods.
................
r14538 | bugman | 2011-08-31 12:35:42 +0200 (Wed, 31 Aug 2011) | 3 lines
The observer objects are now printing out execution information when in
debugging mode.
................
r14539 | bugman | 2011-08-31 12:36:53 +0200 (Wed, 31 Aug 2011) | 3 lines
Fixes for the calls to sys.stderr.write() in the objects of the status
module.
................
r14540 | bugman | 2011-08-31 12:39:07 +0200 (Wed, 31 Aug 2011) | 3 lines
Improvements and fixes for the debugging print outs from the status module.
................
r14541 | bugman | 2011-08-31 12:40:10 +0200 (Wed, 31 Aug 2011) | 3 lines
Missing imports of the sys module.
................
r14542 | bugman | 2011-08-31 12:42:38 +0200 (Wed, 31 Aug 2011) | 3 lines
More improvements to the status module debugging print outs, and the text
now goes to sys.stdout.
................
r14543 | bugman | 2011-08-31 12:50:12 +0200 (Wed, 31 Aug 2011) | 3 lines
The relax controller is now colouring the status module lock and observer
print outs.
................
r14544 | bugman | 2011-08-31 12:52:11 +0200 (Wed, 31 Aug 2011) | 3 lines
Cleaned up the relax locking debugging print outs.
................
r14545 | bugman | 2011-08-31 14:17:00 +0200 (Wed, 31 Aug 2011) | 3 lines
The RelaxInvalidSeqError now prints out a more detailed message for the
validate_sequence() fn.
................
r14546 | bugman | 2011-08-31 14:38:28 +0200 (Wed, 31 Aug 2011) | 3 lines
Clean up and fixes for the generic_fns.sequence.validate_sequence() fn.
................
r14547 | bugman | 2011-08-31 14:40:14 +0200 (Wed, 31 Aug 2011) | 3 lines
The spin_id_to_data_list error messages are now more informative.
................
r14548 | bugman | 2011-08-31 14:50:56 +0200 (Wed, 31 Aug 2011) | 6 lines
Fix for the reading of the sequence from generic formatted files with None
in some of the columns.
The generic_fns.mol_res_spin.generate_spin_id_data_array() fn now checks
for when the data list
contains 'None'.
................
r14549 | bugman | 2011-08-31 14:55:32 +0200 (Wed, 31 Aug 2011) | 3 lines
Changed the debugging print outs for the status module.
................
r14550 | bugman | 2011-08-31 16:23:38 +0200 (Wed, 31 Aug 2011) | 6 lines
Fix for the reading of the sequence from generic formatted files with None
in some of the columns.
This second problem is for the non-integer columns as the text 'None' was
being interpreted as the
name.
................
r14551 | bugman | 2011-08-31 16:43:31 +0200 (Wed, 31 Aug 2011) | 3 lines
Fix for the validate_sequence() function - the eval() calls raise all sorts
of errors.
................
r14552 | bugman | 2011-08-31 16:56:22 +0200 (Wed, 31 Aug 2011) | 3 lines
Fix for the model-free auto-analysis GUI tab - the max iteration default
should be an integer.
................
r14553 | bugman | 2011-08-31 16:58:43 +0200 (Wed, 31 Aug 2011) | 3 lines
The default max_iter value is no longer a string. This fixes the
model-free auto-analysis GUI tab.
................
r14554 | bugman | 2011-09-01 11:09:18 +0200 (Thu, 01 Sep 2011) | 3 lines
Added some debugging print outs for the GUI interpreter object.
................
r14555 | bugman | 2011-09-01 11:13:17 +0200 (Thu, 01 Sep 2011) | 3 lines
The fake_lock variable in the status module classes is now private.
................
r14556 | bugman | 2011-09-01 11:14:17 +0200 (Thu, 01 Sep 2011) | 3 lines
The status container instance is now private in the Relax_lock objects.
................
r14557 | bugman | 2011-09-01 11:16:28 +0200 (Thu, 01 Sep 2011) | 3 lines
The relax execution lock now has debugging print outs.
................
r14558 | bugman | 2011-09-01 11:30:34 +0200 (Thu, 01 Sep 2011) | 3 lines
Clean up of the debugging printouts from the status module.
................
r14559 | bugman | 2011-09-01 11:37:04 +0200 (Thu, 01 Sep 2011) | 7 lines
[... 3706 lines stripped ...]
r15213 - in /branches/inversion-recovery: ./ auto_analyses/ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ grap...