Merged revisions 10117,10157,10178-10188,10197,10204-10205,10240,10242-10245,10267,10296-10302,10304-10326,10330,10404,10431-10435,10443,10450,10461-10462,10611-10612,10626-10631,10645,10652,10668-10671,10674,10676,10680,10684,10688-10689,10691,10694,10699,10703-10704,10708-10754,10766-10789,10794-10829,10838,10841-10842,10845-10860,10862,10865 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r10117 | bugman | 2010-01-06 18:57:55 +0100 (Wed, 06 Jan 2010) | 6 lines
Modified the IO redirection methods.
The original IO streams are stored and then restore instead of sys.__stdout__ and sys.__stderr__.
This might help in the multi-processor branch where IO redirection has gone haywire.
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r10157 | bugman | 2010-01-08 10:57:41 +0100 (Fri, 08 Jan 2010) | 6 lines
Big bug fix for the model-free grid search!!!
The lower and upper bounds were being scaled iteratively for each spin causing the values to be
ridiculously bigger and bigger. This caused a total failure of the grid search.
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r10178 | bugman | 2010-01-12 13:20:36 +0100 (Tue, 12 Jan 2010) | 3 lines
Modified the import of euler_zyz_to_R to allow easy switching later on to a different notation.
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r10179 | bugman | 2010-01-12 13:21:01 +0100 (Tue, 12 Jan 2010) | 3 lines
Copyright notice update.
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r10180 | bugman | 2010-01-12 13:32:12 +0100 (Tue, 12 Jan 2010) | 3 lines
Renamed all euler_ijk_to_R() functions to euler_to_R_ijk().
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r10181 | bugman | 2010-01-12 13:35:04 +0100 (Tue, 12 Jan 2010) | 3 lines
Ordered the euler angle conversion functions.
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r10182 | bugman | 2010-01-12 13:40:33 +0100 (Tue, 12 Jan 2010) | 3 lines
Fixes for all the euler angle to rotation matrix unit tests.
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r10183 | bugman | 2010-01-12 13:42:00 +0100 (Tue, 12 Jan 2010) | 3 lines
Fix for reverse_euler_zyz() due to the function renaming.
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r10184 | bugman | 2010-01-12 14:22:09 +0100 (Tue, 12 Jan 2010) | 3 lines
Created a unit test to check all hard-coded conversion functions for all 12 static axis rotations.
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r10185 | bugman | 2010-01-12 14:22:52 +0100 (Tue, 12 Jan 2010) | 3 lines
Fix for the euler_to_axis_angle_xzx() function.
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r10186 | bugman | 2010-01-12 15:10:54 +0100 (Tue, 12 Jan 2010) | 5 lines
Improvements to the test_euler_cycle_1() unit test.
This includes verbose printing of data structures and checking of the rotation matrix at each cycle.
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r10187 | bugman | 2010-01-12 15:36:01 +0100 (Tue, 12 Jan 2010) | 5 lines
Added 12 unit tests for all notations of R -> Euler -> R.
This uses a random rotation matrix and sees if the matrix is returned.
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r10188 | bugman | 2010-01-12 15:39:31 +0100 (Tue, 12 Jan 2010) | 6 lines
Important bug fix for the R_to_euler() function.
The special angle wrapping when beta was negative is only for the ijk Euler notation when i == k!
When i != k, another type of wrapping will be required.
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r10197 | bugman | 2010-01-13 15:15:37 +0100 (Wed, 13 Jan 2010) | 3 lines
Removed the alpha Euler angle from the isotropic code frame order model.
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r10204 | bugman | 2010-01-13 17:33:24 +0100 (Wed, 13 Jan 2010) | 5 lines
Bug fix for the frame order isotropic cone target function.
The optimised rotation matrix for the alignment tensor orientations was being applied in reverse!!!
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r10205 | bugman | 2010-01-13 19:21:19 +0100 (Wed, 13 Jan 2010) | 6 lines
Reverted r10204 as this was a not a bug and the revision introduced a bug!!!
The command used was:
svn merge -r10204:10203 .
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r10240 | bugman | 2010-01-15 15:35:22 +0100 (Fri, 15 Jan 2010) | 5 lines
Bug fixes for the code validator script.
The 4 character spacing check was faulty.
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r10242 | bugman | 2010-01-18 17:15:33 +0100 (Mon, 18 Jan 2010) | 5 lines
Shifted the target function initialisation into _target_fn_setup().
This will be shared by the calculate() method.
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r10243 | bugman | 2010-01-18 17:20:45 +0100 (Mon, 18 Jan 2010) | 3 lines
The calculate() method now uses _target_fn_setup() and stores the chi2 in the cdp.
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r10244 | bugman | 2010-01-18 17:34:19 +0100 (Mon, 18 Jan 2010) | 3 lines
The number of elements in the atomic position arg is now checked to be 3.
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r10245 | bugman | 2010-01-18 18:07:36 +0100 (Mon, 18 Jan 2010) | 5 lines
Removed the print out from _overfit_deselect_dummy().
This was totally unnecessary!
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r10267 | bugman | 2010-01-20 12:01:00 +0100 (Wed, 20 Jan 2010) | 3 lines
Removed the beta angle folding from the frame order module as it was failing.
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r10296 | bugman | 2010-01-25 11:13:06 +0100 (Mon, 25 Jan 2010) | 14 lines
Spun out the automatic model-free protocol code from the full_analysis.py script.
This is discussed in the post https://mail.gna.org/public/relax-devel/2010-01/msg00075.html.
The aim is to have a single code base for the automatic protocols for all UI designs (prompt,
script, GUI, web interface, etc.). The API interface will be via class initialisations. The
automatic model-free protocol has been placed into the dAuvergne_protocol class.
Future aims of this code is to have the UI fill a single data pipe with all the data required for
the analysis, and then to pass in this pipe into the protocol. Then the auto-analysis will copy
this info into any other data pipes it requires. This will allow for better GUI interaction, data
display, etc.
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r10297 | bugman | 2010-01-25 11:33:22 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed all the now unused imports and a useless comment.
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r10298 | bugman | 2010-01-25 11:34:54 +0100 (Mon, 25 Jan 2010) | 3 lines
Updated the copyright notice.
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r10299 | bugman | 2010-01-25 11:37:25 +0100 (Mon, 25 Jan 2010) | 3 lines
Fixed the import of the dAuvergne_protocol class.
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r10300 | bugman | 2010-01-25 12:13:59 +0100 (Mon, 25 Jan 2010) | 3 lines
Modifications to the phthalic_acid_noes.py system test script to allow for standalone operation.
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r10301 | bugman | 2010-01-25 12:40:54 +0100 (Mon, 25 Jan 2010) | 5 lines
Fixes for the N-state model for when only NOEs are present.
This fixes a bug introduced at r10243.
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r10302 | bugman | 2010-01-25 12:54:34 +0100 (Mon, 25 Jan 2010) | 5 lines
Bug fix for the bug fix of r10301!
The bug fix actually introduced a bug, and this commit fixes that!
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r10304 | bugman | 2010-01-25 14:25:32 +0100 (Mon, 25 Jan 2010) | 11 lines
Redesign of the setup of the names spaces for the user functions.
All the user functions and other objects located in the run() method namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax. There may be better ways to
do this.
This has no visible effect on the prompt or script based interfaces. It will change how this is
seen by other modules though, and will allow the namespace to be more easily accessed.
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r10305 | bugman | 2010-01-25 14:26:57 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed some unused and commented out code.
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r10306 | bugman | 2010-01-25 14:31:09 +0100 (Mon, 25 Jan 2010) | 5 lines
Eliminated the dummy mode.
This is only used by the fetch_docstrings script and will soon not be necessary.
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r10307 | bugman | 2010-01-25 15:55:49 +0100 (Mon, 25 Jan 2010) | 7 lines
The relax base object is no longer passed into the class namespace of the user functions.
This was only being used for access to the intro flag (a few other cases exist, but these should be
fixed). Now a new container object with this flag is being passed in. This significantly
simplifies the code paths and removes the need for the test suite to create 'fake' relax instances.
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r10308 | bugman | 2010-01-25 16:08:41 +0100 (Mon, 25 Jan 2010) | 7 lines
Modified how the Exec_info data container is handled.
The class was shifted from prompt.interpreter to prompt.base_class. In addition if not container
is passed into the user function classes, then one is created with the intro flag set to a default
of True.
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r10309 | bugman | 2010-01-25 16:34:44 +0100 (Mon, 25 Jan 2010) | 8 lines
The prompt info has been shifted into the execution info container.
The sys.ps1, sys.ps2, and sys.ps3 prompts are still set, but these strings are hardcoded into the
execution info container. This allows the user functions to be imported and operate outside of the
prompt/scripting based interface, as the no longer require sys.ps3 to be set or the relax main
instance passed into them.
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r10310 | bugman | 2010-01-25 16:39:34 +0100 (Mon, 25 Jan 2010) | 5 lines
Eliminated the fake_relax instance dependence.
This is no longer necessary as the user functions can be initialised without relax.
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r10311 | bugman | 2010-01-25 16:53:14 +0100 (Mon, 25 Jan 2010) | 3 lines
Created the populate_self() method to place all user functions into the interpreter namespace.
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r10312 | bugman | 2010-01-25 16:58:57 +0100 (Mon, 25 Jan 2010) | 5 lines
The relax main instance is no longer passed into the test suite.
This can be done as the prompt/script interface has been detached from relax.
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r10313 | bugman | 2010-01-25 17:00:12 +0100 (Mon, 25 Jan 2010) | 5 lines
The relax main instance is no longer passed into the prompt/script interface.
This can be done as the prompt/script interface has been detached from relax.
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r10314 | bugman | 2010-01-25 17:06:28 +0100 (Mon, 25 Jan 2010) | 3 lines
The relax main instance is no longer handled by the system test initialisation code.
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r10315 | bugman | 2010-01-25 18:04:17 +0100 (Mon, 25 Jan 2010) | 5 lines
Created the SystemTestCase base class for all the system tests to use.
This base class initialises the relax interpreter within the TestCase class instances.
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r10316 | bugman | 2010-01-25 18:13:12 +0100 (Mon, 25 Jan 2010) | 3 lines
The interpreter _on() method does not need to be called as user fn intros are turned on by default.
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r10317 | bugman | 2010-01-25 18:52:04 +0100 (Mon, 25 Jan 2010) | 5 lines
Fixed all the calls to the user functions located in the interpreter class.
self.relax is no longer referenced and the user functions are now directly called.
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r10318 | bugman | 2010-01-25 18:52:38 +0100 (Mon, 25 Jan 2010) | 3 lines
Fixed the script user function.
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r10319 | bugman | 2010-01-25 18:54:20 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed redundant and now non-functional code from interact_script().
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r10320 | bugman | 2010-01-25 19:04:45 +0100 (Mon, 25 Jan 2010) | 3 lines
Comment fix.
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r10321 | bugman | 2010-01-25 19:11:25 +0100 (Mon, 25 Jan 2010) | 6 lines
Update the user function print out functions.
_off() and _on() are no longer private, and accept the verbose keyword arg to allow the print out to
be suppressed.
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r10322 | bugman | 2010-01-25 19:11:59 +0100 (Mon, 25 Jan 2010) | 3 lines
Alphabetical ordering of methods.
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r10323 | bugman | 2010-01-25 19:21:05 +0100 (Mon, 25 Jan 2010) | 3 lines
The dAuvergne_protocol class now calls the user functions from the self.interpreter instance directly.
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r10324 | bugman | 2010-01-25 19:26:36 +0100 (Mon, 25 Jan 2010) | 5 lines
Fix for the automatic model-free protocol in dAuvergne_protocol.
The sequence.read() and relax_data.read() user functions args are now sent in as keywords.
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r10325 | bugman | 2010-01-25 20:31:25 +0100 (Mon, 25 Jan 2010) | 3 lines
Created the RelaxFileEmptyWarning class.
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r10326 | bugman | 2010-01-25 20:36:30 +0100 (Mon, 25 Jan 2010) | 3 lines
Modified read_spin_data() to throw a warning rather than error when an empty file is encountered.
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r10330 | bugman | 2010-01-25 21:01:23 +0100 (Mon, 25 Jan 2010) | 3 lines
As a precaution, the spins will always be named in the automatic model-free protocol.
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r10404 | bugman | 2010-01-26 18:38:14 +0100 (Tue, 26 Jan 2010) | 3 lines
The generic_fns.state.save_state() pickle arg now defaults to False.
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r10431 | bugman | 2010-01-27 12:54:10 +0100 (Wed, 27 Jan 2010) | 7 lines
Epydoc is now documenting everything!
The whitelist system of selected what to document was not working! Too many packages are changing,
especially in the branches. Therefore absolutely everything is now being documented, including the
test suite. This will allow all new packages to be automatically documented.
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r10432 | bugman | 2010-01-27 13:01:21 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes for the dauvergne_protocol module docstring.
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r10433 | bugman | 2010-01-27 13:32:04 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes throughout the 'data' package.
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r10434 | bugman | 2010-01-27 13:33:11 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes for the 'opendx' package.
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r10435 | bugman | 2010-01-27 13:42:02 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes throughout the test suite.
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r10443 | bugman | 2010-01-27 17:22:00 +0100 (Wed, 27 Jan 2010) | 3 lines
The generic_fns.state.save_state() function can now have the verbosity level changed.
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r10450 | bugman | 2010-01-27 18:24:53 +0100 (Wed, 27 Jan 2010) | 5 lines
Variable name fix for the from_xml() method.
relax_node should have been called pipe_node!
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r10461 | bugman | 2010-01-28 09:37:58 +0100 (Thu, 28 Jan 2010) | 3 lines
The generic_fns.state.load_state() function can now have the verbosity level changed.
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r10462 | bugman | 2010-01-28 09:38:30 +0100 (Thu, 28 Jan 2010) | 3 lines
Epydoc fix for generic_fns.state.save_state(). Verbosity is a keyword arg!
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r10611 | bugman | 2010-02-01 23:36:57 +0100 (Mon, 01 Feb 2010) | 5 lines
Bug fix for the running of the test suite.
The interpreter _on() and _off() methods are now called on() and off()!
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r10612 | bugman | 2010-02-02 00:19:55 +0100 (Tue, 02 Feb 2010) | 3 lines
Switched from using a cone angle to using an order parameter in the isotropic cone frame order model.
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r10626 | bugman | 2010-02-03 11:22:00 +0100 (Wed, 03 Feb 2010) | 5 lines
Added the stub function maths_fns.order_parameters.iso_cone_S_to_cos_theta().
This will be used to convert the order parameter S into the cosine of the cone angle.
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r10627 | bugman | 2010-02-03 18:00:17 +0100 (Wed, 03 Feb 2010) | 16 lines
Redesigned get_intro_string() to return a container of different strings.
The method is now called get_intro_text() and returns a container with the following str objects:
- title: The program title 'relax'
- version: For example 'repository checkout' or '1.3.8'.
- desc: The short program description.
- copyright: A list of copyright statements.
- licence: Text pertaining to the licencing.
- errors: A list of import errors.
This is being abstracted so that the different UIs can use this differently. The prompt/script can
word wrap to 100 char (80 char in Windows), and print this to stdout. The GUI can use this in the
about prompt and not print to stdout. Other interfaces can use this in any other way. And the
information content can be expanded for different purposes.
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r10628 | bugman | 2010-02-03 18:09:01 +0100 (Wed, 03 Feb 2010) | 6 lines
Shifted the introductory text object into its own module.
This makes the use of this object more flexible as anything and any part of the program can import
it.
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r10629 | bugman | 2010-02-03 18:15:59 +0100 (Wed, 03 Feb 2010) | 5 lines
Shifted the spacing() method from relax to the intro module and renamed it to centre().
The docstring has also been expanded to include epydoc tags.
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r10630 | bugman | 2010-02-03 18:26:28 +0100 (Wed, 03 Feb 2010) | 6 lines
The introductory text for the prompt/script based interface is now recreated.
The _build_intro_text() method has been added to replicate the formatting of the deleted
get_intro_text() method of the main relax class. This formatting is only to be used in these 2 UIs.
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r10631 | bugman | 2010-02-03 18:28:49 +0100 (Wed, 03 Feb 2010) | 7 lines
Changed the program description again.
The program is now described as "Molecular dynamics by NMR data analysis". This takes into account
that this is for proteins, RNA, DNA, organic molecules, sugars, etc., and for relaxation data, RDCs,
PCSs, NOEs, and all NMR data.
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r10645 | bugman | 2010-02-04 17:33:24 +0100 (Thu, 04 Feb 2010) | 3 lines
Added the website and a long description to the Intro_text container.
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r10652 | bugman | 2010-02-04 18:31:37 +0100 (Thu, 04 Feb 2010) | 7 lines
Better UI separation in the Intro_text descriptions.
The 'help' assistance message has been shifted directly into prompt.interpreter as it is only part
of the prompt/script interface. The GPL message has been changed to specify that it is at the
prompt that you type GPL.
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r10668 | bugman | 2010-02-05 17:54:15 +0100 (Fri, 05 Feb 2010) | 5 lines
Renamed the intro.Intro_text class to info.Info_box.
This is used for introduction strings, but can be used at any point in relax as well.
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r10669 | bugman | 2010-02-05 18:14:30 +0100 (Fri, 05 Feb 2010) | 3 lines
Updated the d'Auvergne and Gooley, 2008 references to have the full medline info.
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r10670 | bugman | 2010-02-05 19:56:18 +0100 (Fri, 05 Feb 2010) | 3 lines
Fixes for the d'Auvergne and Gooley, 2008 references.
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r10671 | bugman | 2010-02-05 19:58:02 +0100 (Fri, 05 Feb 2010) | 5 lines
References pertaining to relax have been added to the info box container.
Each reference is a container placed within the 'bib' dictionary of the info box class.
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r10674 | bugman | 2010-02-06 01:15:52 +0100 (Sat, 06 Feb 2010) | 3 lines
Created the reference base class 'Ref' and added cite_short() to build a short citation.
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r10676 | bugman | 2010-02-06 01:34:06 +0100 (Sat, 06 Feb 2010) | 3 lines
Fixes for some journal titles. Periods have been added.
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r10680 | bugman | 2010-02-06 02:16:35 +0100 (Sat, 06 Feb 2010) | 6 lines
Created the module for the automatic relaxation curve fitting protocol.
This should better help define the API interface between the UIs and the core, allowing all UIs to
benefit from advances in this code base.
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r10684 | bugman | 2010-02-06 02:52:44 +0100 (Sat, 06 Feb 2010) | 5 lines
A couple of fixes for the Relax_fit auto analysis class.
The interpreter was not being imported and a class variable was missing the 'self.' part!
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r10688 | bugman | 2010-02-09 11:36:44 +0100 (Tue, 09 Feb 2010) | 5 lines
Added support for using Me pseudo-atom RDCs.
This follows the method of Verdier, et al., JMR, 2003, 163, 353-359.
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r10689 | bugman | 2010-02-11 14:26:13 +0100 (Thu, 11 Feb 2010) | 3 lines
Added the cite_html() method to the citation base class to produce a HTML formatted citation.
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r10691 | bugman | 2010-02-11 15:03:14 +0100 (Thu, 11 Feb 2010) | 5 lines
Fix for the cite_html() method.
The hyperlinks were incorrectly formed.
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r10694 | bugman | 2010-02-12 10:50:17 +0100 (Fri, 12 Feb 2010) | 5 lines
Fix for the iso cone frame order order parameter.
The c11^2, c12^2, c21^2 and c22^2 element equations were incorrect.
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r10699 | bugman | 2010-02-16 11:01:35 +0100 (Tue, 16 Feb 2010) | 5 lines
Fix for the Lipari and Szabo reference information.
The classes were not being instantiated.
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r10703 | bugman | 2010-02-16 14:16:23 +0100 (Tue, 16 Feb 2010) | 5 lines
The proper function from the order_parameters module is being called to calc the cone angle.
This allows the code to operate, but the function is not yet implemented.
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r10704 | bugman | 2010-02-16 14:38:47 +0100 (Tue, 16 Feb 2010) | 5 lines
Fix for the cite_html() bibliography method.
The <em> tag was not being closed!
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r10708 | bugman | 2010-02-18 10:47:55 +0100 (Thu, 18 Feb 2010) | 3 lines
Alphabetical ordering of the rotation matrix module functions.
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r10709 | bugman | 2010-02-18 10:59:41 +0100 (Thu, 18 Feb 2010) | 3 lines
Added the tilt and torsion angle convention conversions to and from rotation matrices.
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r10710 | bugman | 2010-02-18 11:41:19 +0100 (Thu, 18 Feb 2010) | 6 lines
Shifted the RDC and PCS Q-factor calculation code.
The methods previously in the N-state model specific code have been converted to functions of the
generic_fns.rdc and generic_fns.pcs modules.
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r10711 | bugman | 2010-02-18 13:24:04 +0100 (Thu, 18 Feb 2010) | 6 lines
The Q-factor calculation functions can now accept a spin_id arg.
As there can now be data problems, the functions check if there is any selected spins looped over,
that the is RDC/PCS data, and that there is back-calculated RDC/PCS data.
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r10712 | bugman | 2010-02-18 13:27:07 +0100 (Thu, 18 Feb 2010) | 5 lines
Created the rdc.calc_q_factors() and pcs.calc_q_factors() user functions.
The back-calculated RDC/PCS data must first be generated by the specific code.
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r10713 | bugman | 2010-02-18 13:27:30 +0100 (Thu, 18 Feb 2010) | 3 lines
Docstring fix for pcs.calc_q_factors().
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r10714 | bugman | 2010-02-18 13:35:14 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a directory for the unit tests of the modules of the auto_analyses package.
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r10715 | bugman | 2010-02-18 13:36:13 +0100 (Thu, 18 Feb 2010) | 3 lines
Copied the __init__.py unit tests module from the _specific_fns directory.
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r10716 | bugman | 2010-02-18 13:38:32 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a __ini__ module to the _auto_analyses unit test package.
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r10717 | bugman | 2010-02-18 13:39:02 +0100 (Thu, 18 Feb 2010) | 3 lines
Modified the _auto_analyses.test___init__ module for the auto_analyses package.
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r10718 | bugman | 2010-02-18 13:51:40 +0100 (Thu, 18 Feb 2010) | 6 lines
Added to the auto_analyses the script for determining relative stereochemistry of organic molecules.
This code corresponds to a paper in press. The script will need to be modified to function as an
auto-analysis, and the actual configuration file turned into the real script.
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r10719 | bugman | 2010-02-18 13:53:39 +0100 (Thu, 18 Feb 2010) | 5 lines
Added the relative stereochemistry analysis configuration file.
This will be converted into a relax script.
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r10720 | bugman | 2010-02-18 13:54:12 +0100 (Thu, 18 Feb 2010) | 3 lines
Renamed the stereochem_analysis_config.py file to the stereochem_analysis.py relax script.
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r10721 | bugman | 2010-02-18 14:04:02 +0100 (Thu, 18 Feb 2010) | 5 lines
Converted stereochem_analysis.py into a true relax script.
This now calls the auto_analyses.stereochem_analysi code.
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r10722 | bugman | 2010-02-18 14:10:07 +0100 (Thu, 18 Feb 2010) | 5 lines
Modified the script so that __init__ sets up the class and run() executes the analysis.
This is not implemented on the other side yet.
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r10723 | bugman | 2010-02-18 14:11:26 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a copyright notice to the stereochem_analysis.py sample script.
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r10724 | bugman | 2010-02-18 14:12:28 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a copyright notice to the stereochem_analysis auto-analysis.
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r10725 | bugman | 2010-02-18 14:12:52 +0100 (Thu, 18 Feb 2010) | 3 lines
Module docstring changes. This is no longer a script!
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r10726 | bugman | 2010-02-18 14:13:49 +0100 (Thu, 18 Feb 2010) | 5 lines
Removed some unused code and comments at the top of the ex-script.
A config file is no longer read.
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r10727 | bugman | 2010-02-18 14:14:16 +0100 (Thu, 18 Feb 2010) | 3 lines
Renamed StereoAnalysis to Stereochem_analysis and added 'relative' to the class docstring.
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r10728 | bugman | 2010-02-18 14:17:07 +0100 (Thu, 18 Feb 2010) | 5 lines
Separated the stereochem_analysis auto-analysis execution into the run() method.
This leaves __init__() with the job of setting up the class.
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r10729 | bugman | 2010-02-18 14:19:13 +0100 (Thu, 18 Feb 2010) | 3 lines
Removed the class instantiation from the auto_analyses.stereochem_analysis module.
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r10730 | bugman | 2010-02-18 14:25:05 +0100 (Thu, 18 Feb 2010) | 3 lines
The __init__() method now accepts all the keyword args and stores them in the class namespace.
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r10731 | bugman | 2010-02-18 14:30:35 +0100 (Thu, 18 Feb 2010) | 3 lines
Converted the all-caps module variables into lower case class variables.
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r10732 | bugman | 2010-02-18 14:31:58 +0100 (Thu, 18 Feb 2010) | 3 lines
Fix for the stereochem_analysis.py sample script - the instantiated class run() method must be run!
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r10733 | bugman | 2010-02-18 14:43:04 +0100 (Thu, 18 Feb 2010) | 3 lines
The interpreter is now imported and set up. User function calls are now passed through this class.
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r10734 | bugman | 2010-02-18 14:43:39 +0100 (Thu, 18 Feb 2010) | 3 lines
Missing import of pi.
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r10735 | bugman | 2010-02-18 15:03:55 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a directory to the test suite data for holding phthalic acid structures.
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r10736 | bugman | 2010-02-18 15:13:23 +0100 (Thu, 18 Feb 2010) | 3 lines
Updated the package __all__ list to include all modules.
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r10737 | bugman | 2010-02-18 15:57:22 +0100 (Thu, 18 Feb 2010) | 3 lines
Shifted the Gromacs phthalic acid structure.
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r10738 | bugman | 2010-02-18 16:32:06 +0100 (Thu, 18 Feb 2010) | 5 lines
A results directory can now be specified in the stereochem_analysis auto-analysis.
This is not being used yet.
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r10739 | bugman | 2010-02-18 16:34:08 +0100 (Thu, 18 Feb 2010) | 3 lines
The cwd is used if no results_dir arg is given.
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r10740 | bugman | 2010-02-18 16:48:48 +0100 (Thu, 18 Feb 2010) | 3 lines
The stereochem_analysis auto-analysis is now placing all generated files into the desired results dir.
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r10741 | bugman | 2010-02-18 16:53:13 +0100 (Thu, 18 Feb 2010) | 5 lines
STDOUT is now being restored after each stage.
STDOUT was being lost if logging was turned on!
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r10742 | bugman | 2010-02-18 17:05:55 +0100 (Thu, 18 Feb 2010) | 5 lines
The Grace plots are now being created.
The sorted results files were not been checked for in the results directory.
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r10743 | bugman | 2010-02-18 17:08:35 +0100 (Thu, 18 Feb 2010) | 5 lines
Added a few Gromacs QM/MM snapshots.
This will be used for a stereochemistry analysis system test.
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r10744 | bugman | 2010-02-18 17:10:22 +0100 (Thu, 18 Feb 2010) | 3 lines
Added the phthalic acid RDC data aligned in a PAN gel.
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r10745 | bugman | 2010-02-18 17:12:26 +0100 (Thu, 18 Feb 2010) | 3 lines
Created a directory for collecting all N-state model system test scripts together.
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r10746 | bugman | 2010-02-18 17:16:25 +0100 (Thu, 18 Feb 2010) | 3 lines
Shifted all the N-state model scripts into their directory.
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r10747 | bugman | 2010-02-18 17:30:01 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a system test script for testing the relative stereochemistry analysis.
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r10748 | bugman | 2010-02-18 17:33:34 +0100 (Thu, 18 Feb 2010) | 5 lines
Fixes for all the N-state model system tests.
The scripts were moved to a sub-directory!
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r10749 | bugman | 2010-02-18 17:44:15 +0100 (Thu, 18 Feb 2010) | 3 lines
Fixes for the NOE restraint system tests as these involve the N-state model.
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r10750 | bugman | 2010-02-18 18:04:59 +0100 (Thu, 18 Feb 2010) | 3 lines
Enabled the relative stereochemistry analysis system test.
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r10751 | bugman | 2010-02-18 18:05:15 +0100 (Thu, 18 Feb 2010) | 3 lines
Bug fix for the snapshot paths.
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r10752 | bugman | 2010-02-18 18:06:27 +0100 (Thu, 18 Feb 2010) | 3 lines
Another fix for the stereochem_analysis system test, the results dir is now in ds.tmpdir.
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r10753 | bugman | 2010-02-18 18:24:33 +0100 (Thu, 18 Feb 2010) | 3 lines
Fixes for STDOUT control in the auto_analyses.stereochem_analysis module.
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r10754 | bugman | 2010-02-18 18:43:29 +0100 (Thu, 18 Feb 2010) | 3 lines
Added checks for all of the results files being present in the tmp directory.
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r10766 | bugman | 2010-02-19 11:09:06 +0100 (Fri, 19 Feb 2010) | 3 lines
Converted write_multi_header() to write_xy_header() and simplified the args by expecting [X, Y] pairs.
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r10767 | bugman | 2010-02-19 11:43:22 +0100 (Fri, 19 Feb 2010) | 6 lines
Clean up of write_xy_header().
Labels are now not overwritten if supplied, all file.write() operations are collected together, and
the X and Y-axis settings have been merged.
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r10768 | bugman | 2010-02-19 11:46:25 +0100 (Fri, 19 Feb 2010) | 3 lines
write_xy_header() now has a sets arg for specifying the number of data sets in the graph G0.
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r10769 | bugman | 2010-02-19 14:11:57 +0100 (Fri, 19 Feb 2010) | 7 lines
More changes to write_xy_header().
The return_units() and return_grace_string() analysis specific methods are no longer passed in as
args but are set up in the method itself. Many simplifications have been made. And now spin data
has been made axis independent - it can be X or Y data.
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r10770 | bugman | 2010-02-19 14:43:19 +0100 (Fri, 19 Feb 2010) | 3 lines
Bug fix for write_xy_header(), a statement typo was stopping relax from running.
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r10771 | bugman | 2010-02-19 14:46:26 +0100 (Fri, 19 Feb 2010) | 3 lines
Added symbol formatting to the individual graph sets in write_xy_header().
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r10772 | bugman | 2010-02-19 14:47:42 +0100 (Fri, 19 Feb 2010) | 5 lines
Deletion of the write_header() function.
This is now redundant due to the improvements in write_xy_header().
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r10773 | bugman | 2010-02-19 14:51:15 +0100 (Fri, 19 Feb 2010) | 5 lines
Fix for the call to write_xy_header().
This is now independent of the number of data sets, and is called correctly.
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r10774 | bugman | 2010-02-19 14:54:39 +0100 (Fri, 19 Feb 2010) | 3 lines
Added the axis_min and axis_max args to write_xy_header() for specifying the graph ranges.
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r10775 | bugman | 2010-02-19 14:56:10 +0100 (Fri, 19 Feb 2010) | 5 lines
Typo fix in write_xy_header().
axis_label should have been axis_labels!
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r10776 | bugman | 2010-02-19 15:09:10 +0100 (Fri, 19 Feb 2010) | 5 lines
Spin ids are no longer passed into write_xy_header().
Instead the new args seq_type and set_names are passed in.
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r10777 | bugman | 2010-02-19 15:13:32 +0100 (Fri, 19 Feb 2010) | 3 lines
Fix for the counting of the number of graph sets.
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r10778 | bugman | 2010-02-19 15:33:40 +0100 (Fri, 19 Feb 2010) | 5 lines
Shifted to using write_xy_data().
This was the write_multi_data() function, and write_data() function has been deleted.
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r10779 | bugman | 2010-02-19 15:52:28 +0100 (Fri, 19 Feb 2010) | 7 lines
Changed the format of the data arg to write_xy_data().
This is a huge simplification and makes the function more usable for any type of data thrown at it.
The structure is now expected to be a 4D list/array corresponding to Gx, Sx, data point, data point
info.
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r10780 | bugman | 2010-02-19 17:03:42 +0100 (Fri, 19 Feb 2010) | 7 lines
Redesign of get_data() and deletion of determine_graph_type().
get_data() determines the graph type in a few lines of code, so determine_graph_type() is not
necessary. get_data() now returns the 4D grace graph data structure, the labels for the data sets,
and the graph_type.
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r10781 | bugman | 2010-02-19 17:08:23 +0100 (Fri, 19 Feb 2010) | 3 lines
Clean up of the write() function for the new get_data() design.
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r10782 | bugman | 2010-02-19 18:18:44 +0100 (Fri, 19 Feb 2010) | 3 lines
Fixes for get_data() for when the analysis specific return_value() fn returns a list of values!
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r10783 | bugman | 2010-02-19 18:22:23 +0100 (Fri, 19 Feb 2010) | 3 lines
Fix for the graph type determination in get_data().
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r10784 | bugman | 2010-02-19 18:23:34 +0100 (Fri, 19 Feb 2010) | 3 lines
Removed the linestyle setting in write_xy_header() that made the line invisible.
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r10785 | bugman | 2010-02-19 18:35:57 +0100 (Fri, 19 Feb 2010) | 5 lines
Fix for the write_xy_header() method.
The args are now explicitly reset as they are lists and are persistent!
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r10786 | bugman | 2010-02-19 18:37:59 +0100 (Fri, 19 Feb 2010) | 5 lines
Another fix for write_xy_header().
The "world xmax" and "world xmax" were being set as the minimums!
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r10787 | bugman | 2010-02-19 18:40:42 +0100 (Fri, 19 Feb 2010) | 5 lines
Another fix for write_xy_header().
This time, "(normalised)" is not added to the X-axis label for normalised plots.
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r10788 | bugman | 2010-02-19 19:00:30 +0100 (Fri, 19 Feb 2010) | 5 lines
Fix for the test_bug_12670_12679() system test.
The Grace file lines are now not hardcoded!!!
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r10789 | bugman | 2010-02-21 15:44:45 +0100 (Sun, 21 Feb 2010) | 5 lines
Bug fix for the test_R_to_axis_angle_180_complex() for MS Windows.
self.assertAlmostEquals() has to be used do to precision issues.
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r10794 | bugman | 2010-02-22 10:13:04 +0100 (Mon, 22 Feb 2010) | 3 lines
Args after the flags -x, -u, -s are now considered to be the tests performed and not a script.
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r10795 | bugman | 2010-02-22 10:14:15 +0100 (Mon, 22 Feb 2010) | 3 lines
Test_suite_runner now has an __init__() method and stores the list of tests.
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r10796 | bugman | 2010-02-22 10:20:14 +0100 (Mon, 22 Feb 2010) | 3 lines
Finished the __init__() docstring and passed the tests arg into the system tests.
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r10797 | bugman | 2010-02-22 10:22:27 +0100 (Mon, 22 Feb 2010) | 3 lines
Passed self.tests into the run() method instead of the class __init__() method.
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r10798 | bugman | 2010-02-22 10:32:27 +0100 (Mon, 22 Feb 2010) | 3 lines
Individual system tests can now be executed through the relax test suite.
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r10799 | bugman | 2010-02-22 10:33:34 +0100 (Mon, 22 Feb 2010) | 3 lines
The tests list is now optional.
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r10800 | bugman | 2010-02-22 10:39:03 +0100 (Mon, 22 Feb 2010) | 3 lines
The paper size of A4 can now be set in write_xy_header().
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r10801 | bugman | 2010-02-22 10:43:28 +0100 (Mon, 22 Feb 2010) | 5 lines
Changed the handling of the [None, None] format args.
These now default to None and are converted to [None, None] inside the function.
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r10802 | bugman | 2010-02-22 10:47:27 +0100 (Mon, 22 Feb 2010) | 3 lines
In write_xy_header(), the legend box can be now turned on or off and can have its position set.
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r10803 | bugman | 2010-02-22 10:50:42 +0100 (Mon, 22 Feb 2010) | 3 lines
Set colours can now be specified in write_xy_header().
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r10804 | bugman | 2010-02-22 10:52:36 +0100 (Mon, 22 Feb 2010) | 3 lines
The symbols are now also coloured in write_xy_header().
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r10805 | bugman | 2010-02-22 11:00:12 +0100 (Mon, 22 Feb 2010) | 5 lines
Much finer control of the set appearance in write_xy_header().
The symbol style, sizes, and line linestyle can now all be specified.
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r10806 | bugman | 2010-02-22 11:10:18 +0100 (Mon, 22 Feb 2010) | 5 lines
Fix for the colour setting in write_xy_header().
The arg is called set_colours, not colours!
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r10807 | bugman | 2010-02-22 11:15:09 +0100 (Mon, 22 Feb 2010) | 3 lines
The graph title and subtitle can be specified in write_xy_header().
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r10808 | bugman | 2010-02-22 11:18:28 +0100 (Mon, 22 Feb 2010) | 3 lines
Fix for write_xy_header(), axis limits are now set when the value is 0.
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r10809 | bugman | 2010-02-22 11:21:03 +0100 (Mon, 22 Feb 2010) | 3 lines
The 'Spin ' text is now prepended to the legend only in get_data(), and not write_xy_header().
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r10810 | bugman | 2010-02-22 11:23:04 +0100 (Mon, 22 Feb 2010) | 3 lines
The grace version of the write_xy_header() header is not output.
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r10811 | bugman | 2010-02-22 13:07:36 +0100 (Mon, 22 Feb 2010) | 3 lines
The graph view port size can now be changes and defaults to a larger value.
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r10812 | bugman | 2010-02-22 13:21:51 +0100 (Mon, 22 Feb 2010) | 3 lines
The symbol fill style can now be specified in write_xy_header().
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r10813 | bugman | 2010-02-22 13:26:50 +0100 (Mon, 22 Feb 2010) | 3 lines
The linewidth for all graph elements can now be set in write_xy_header().
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r10814 | bugman | 2010-02-22 13:38:09 +0100 (Mon, 22 Feb 2010) | 3 lines
The line type for each set can now be specified in write_xy_header().
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r10815 | bugman | 2010-02-22 13:39:46 +0100 (Mon, 22 Feb 2010) | 3 lines
Stereochem_analysis.grace_plots() now uses the new write_xy_header() & write_xy_data() fns.
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r10816 | bugman | 2010-02-22 14:31:21 +0100 (Mon, 22 Feb 2010) | 5 lines
The number of ensembles string is now more nicely formatted in the subtitle.
This is in Stereochem_analysis.grace_plots().
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r10817 | bugman | 2010-02-22 15:10:11 +0100 (Mon, 22 Feb 2010) | 3 lines
Fix for the write_xy_header() function for when the data_type arg is not supplied.
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r10818 | bugman | 2010-02-22 16:13:55 +0100 (Mon, 22 Feb 2010) | 3 lines
Added an NOE normalisation variable to the stereochem_analysis.py sample script.
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r10819 | bugman | 2010-02-22 16:19:10 +0100 (Mon, 22 Feb 2010) | 3 lines
Scaled NOE violation correlation plots (RDC Q vs. NOE Q) are now being created.
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r10820 | bugman | 2010-02-22 16:20:45 +0100 (Mon, 22 Feb 2010) | 3 lines
The noe_norm arg is now accepted by the Stereochem_analysis class.
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r10821 | bugman | 2010-02-22 16:21:22 +0100 (Mon, 22 Feb 2010) | 3 lines
Whitespace fixes for the storage of all the Stereochem_analysis args.
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r10822 | bugman | 2010-02-22 16:36:13 +0100 (Mon, 22 Feb 2010) | 3 lines
Completed the Stereochem_analysis.__init__() docstring, adding all the epydoc tags.
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r10823 | bugman | 2010-02-22 16:45:27 +0100 (Mon, 22 Feb 2010) | 3 lines
Fixed the x-axis label for the scaled Q-factor vs. Q-factor correlation plot.
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r10824 | bugman | 2010-02-22 17:03:21 +0100 (Mon, 22 Feb 2010) | 3 lines
Changed the axis ranges for the RDC Q-factor vs. NOE Q-factor correlation plot.
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r10825 | bugman | 2010-02-22 18:04:14 +0100 (Mon, 22 Feb 2010) | 6 lines
Added the -i or --info option to relax.
This causes all of the information about relax and Python to be printed by calling
Info_box.print_sys_info(). This option will be useful for determining issues with relax installs!
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r10826 | bugman | 2010-02-22 18:10:52 +0100 (Mon, 22 Feb 2010) | 3 lines
Shifted the relax intro string (written to STDOUT) from the interpreter module to the Info_box.
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r10827 | bugman | 2010-02-22 18:17:12 +0100 (Mon, 22 Feb 2010) | 5 lines
Renamed Info_box.print_sys_info() to Info_box.sys_info().
The method now returns the info string, and this is printed later.
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r10828 | bugman | 2010-02-22 18:19:09 +0100 (Mon, 22 Feb 2010) | 3 lines
Replaced the relax version line with the full relax intro when using the -i cmdline flag.
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r10829 | bugman | 2010-02-22 19:59:57 +0100 (Mon, 22 Feb 2010) | 14 lines
The Info_box.package_info() has been added to provide package information.
This is show with the -i cmdline option. The following packages are currently reported:
minfx
bmrblib
numpy
Numeric
ScientificPython
wxPython
mpi4py
scons
epydoc
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r10838 | bugman | 2010-02-23 02:41:04 +0100 (Tue, 23 Feb 2010) | 3 lines
Fixes for the N_state_model.test_stereochem_analysis system test for the new normalised NOE plots.
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r10841 | bugman | 2010-02-23 02:52:08 +0100 (Tue, 23 Feb 2010) | 3 lines
Fix for the Info_box.package_info() method for when a package is not installed.
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r10842 | bugman | 2010-02-23 02:55:39 +0100 (Tue, 23 Feb 2010) | 3 lines
Info_box.sys_info() no longer prints the computer's URL!
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r10845 | bugman | 2010-02-23 11:15:31 +0100 (Tue, 23 Feb 2010) | 5 lines
Added a 6th stage to the stereochemistry analysis script.
This is the ordering of all ensembles using a combined Q-factor.
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r10846 | bugman | 2010-02-23 11:18:32 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a check for the stage number in the stereochemistry auto analysis.
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r10847 | bugman | 2010-02-23 11:43:47 +0100 (Tue, 23 Feb 2010) | 5 lines
Stage 6, the combined Q-factor and final ordering is now complete.
The combined_q() method was written to perform this last analysis.
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r10848 | bugman | 2010-02-23 13:29:04 +0100 (Tue, 23 Feb 2010) | 5 lines
The modules are no longer deleted after import from dep_check.
This will allow dep_check to be used for extracting package information by the Info_box.
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r10849 | bugman | 2010-02-23 13:44:08 +0100 (Tue, 23 Feb 2010) | 3 lines
Added checks for the bmrblib and Numeric packages.
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r10850 | bugman | 2010-02-23 13:49:32 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a specific import check for Scientific - the other checking the PDB module import.
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r10851 | bugman | 2010-02-23 13:52:53 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a check for the wx module.
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r10852 | bugman | 2010-02-23 13:54:49 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a check for the mpi4py module.
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r10853 | bugman | 2010-02-23 13:55:24 +0100 (Tue, 23 Feb 2010) | 3 lines
Made the mpi4py import flag more consistent.
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r10854 | bugman | 2010-02-23 14:05:49 +0100 (Tue, 23 Feb 2010) | 3 lines
Added an import check for epydoc.
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r10855 | bugman | 2010-02-23 14:20:57 +0100 (Tue, 23 Feb 2010) | 3 lines
Imported os in the os.devnull import check, and deleted devnull.
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r10856 | bugman | 2010-02-23 14:23:45 +0100 (Tue, 23 Feb 2010) | 5 lines
Redesigned package_info() to remove the dependence on the pkg_resources module.
This was a problem in many old python versions. The package info is now presented in a table.
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r10857 | bugman | 2010-02-23 14:27:27 +0100 (Tue, 23 Feb 2010) | 3 lines
Added the relax C module compilation info.
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r10858 | bugman | 2010-02-23 14:28:33 +0100 (Tue, 23 Feb 2010) | 3 lines
The version-less modules now have an empty string for the version printed.
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r10859 | bugman | 2010-02-23 14:34:47 +0100 (Tue, 23 Feb 2010) | 6 lines
Made Info_box.sys_info() fault tolerant.
All the contents of the platform module are checked before added the text, allowing for older python
versions.
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r10860 | bugman | 2010-02-23 16:06:48 +0100 (Tue, 23 Feb 2010) | 17 lines
A python 3.0 fix for the grace module.
The command used was:
2to3 -w \
> -f buffer \
> -f idioms \
> -f set_literal \
> -f ws_comma \
> -x except \
> -x import \
> -x imports \
> -x long \
> -x numliterals \
> -x xrange \
> relax .
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r10862 | bugman | 2010-02-23 18:20:45 +0100 (Tue, 23 Feb 2010) | 5 lines
Converted the Info_box into a singleton.
This will allow for execution specific info to be placed in here and accessed by all.
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r10865 | bugman | 2010-02-23 18:31:03 +0100 (Tue, 23 Feb 2010) | 5 lines
The Info_box is now really a singleton - a bug in __new__() has been eliminated.
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