relax SVN archive

Molecular dynamics by NMR data analysis

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SVN archive Commit Log

Commit	Date
[r7797] by semor Started the implementation of a generic peak intensities file. This follows a thread at: https://mail.gna.org/public/relax-devel/2008-10/msg00026.html (Message ID: 48EE7028.6060409@...)	2008-10-17 17:53:53	Tree
[r7796] by semor Corrected some naming and syntax within docstrings and prints. This follows a post by Edward at: https://mail.gna.org/public/relax-devel/2008-10/msg00068.html (message ID: 7f080ed10810161412j1910a956gd37dbd35eb0584c1@...)	2008-10-16 22:29:26	Tree
[r7795] by bugman Added a class docstring for the main relax class.	2008-10-16 22:18:03	Tree
[r7794] by bugman Method spacing fix.	2008-10-16 22:16:35	Tree
[r7793] by bugman Merged revisions 7528-7791 via svnmerge from svn+ssh://bugman@.../svn/relax/1.3 ........ r7530 \| bugman \| 2008-10-06 22:13:43 +0200 (Mon, 06 Oct 2008) \| 3 lines Changed an MC simulation te value to 200 ns to trigger MC sim failure detection by eliminate(). ........ r7531 \| bugman \| 2008-10-06 22:18:03 +0200 (Mon, 06 Oct 2008) \| 3 lines Added some checks to the test_omp_analysis() system test. ........ r7532 \| bugman \| 2008-10-06 22:26:18 +0200 (Mon, 06 Oct 2008) \| 3 lines Fix for the tests added at r7531. ........ r7533 \| bugman \| 2008-10-06 22:30:06 +0200 (Mon, 06 Oct 2008) \| 3 lines Changed the checks in test_omp_analysis() for the 'select_sim' arrays to lists of Booleans. ........ r7534 \| bugman \| 2008-10-06 22:33:38 +0200 (Mon, 06 Oct 2008) \| 3 lines Converted the 'select_sim' variable to a list of bools. ........ r7535 \| bugman \| 2008-10-06 22:50:26 +0200 (Mon, 06 Oct 2008) \| 5 lines Fix for the loading of a version 1.2 model-free results file. The 'select_sim' array was not being set as a list of booleans but rather an numpy array of bools. ........ r7536 \| bugman \| 2008-10-06 22:52:15 +0200 (Mon, 06 Oct 2008) \| 5 lines Modified the test_omp_analysis() system test to add more MC sim failures. This adds a second failure to the second residue. ........ r7537 \| bugman \| 2008-10-06 23:05:04 +0200 (Mon, 06 Oct 2008) \| 3 lines Docstring fix for setup(). ........ r7538 \| bugman \| 2008-10-06 23:13:50 +0200 (Mon, 06 Oct 2008) \| 6 lines Fix for the 'select_sim' list setting methods. The copy.deepcopy() function is now used to set 'select_sim' so that the lists from different spins are no longer actually exactly the same list. ........ r7539 \| bugman \| 2008-10-06 23:28:44 +0200 (Mon, 06 Oct 2008) \| 3 lines Removed the sconstruct file from the API manual. ........ r7540 \| bugman \| 2008-10-06 23:40:47 +0200 (Mon, 06 Oct 2008) \| 3 lines Converted the linear_gradient() docstring to epytxt format and added a module docstring. ........ r7541 \| bugman \| 2008-10-06 23:56:07 +0200 (Mon, 06 Oct 2008) \| 7 lines Epydoc fixes for the docstrings appended to molmol.write() and pymol.write(). The text appended to the user functions have been shifted to the global variables __molmol_colours_prompt_doc__ and __x11_colours_prompt_doc__. Proper docstrings have been added to the functions of the colour module. ........ r7542 \| bugman \| 2008-10-06 23:59:57 +0200 (Mon, 06 Oct 2008) \| 3 lines Epydoc fixes for the module docstring. ........ r7543 \| bugman \| 2008-10-07 00:09:47 +0200 (Tue, 07 Oct 2008) \| 3 lines Shifted the prompt documentation from docstrings into global variables. ........ r7544 \| bugman \| 2008-10-07 00:17:25 +0200 (Tue, 07 Oct 2008) \| 3 lines Shifted the prompt documentation from docstrings into global variables. ........ r7545 \| bugman \| 2008-10-07 00:22:39 +0200 (Tue, 07 Oct 2008) \| 3 lines Many epydoc docstring fixes. ........ r7546 \| bugman \| 2008-10-07 00:57:18 +0200 (Tue, 07 Oct 2008) \| 3 lines Many eypdoc docstring fixes for the unit test runner. ........ r7547 \| bugman \| 2008-10-07 01:03:06 +0200 (Tue, 07 Oct 2008) \| 3 lines Removed the system tests from the API documentation. ........ r7548 \| bugman \| 2008-10-07 01:15:04 +0200 (Tue, 07 Oct 2008) \| 3 lines A number of epydoc docstring fixes. ........ r7549 \| bugman \| 2008-10-07 21:14:37 +0200 (Tue, 07 Oct 2008) \| 3 lines Fixed the indentation of the prompt interface documentation. ........ r7550 \| bugman \| 2008-10-07 21:17:27 +0200 (Tue, 07 Oct 2008) \| 7 lines Added example Sparky peak lists to the NOE and relaxation curve fitting chapter. This documentation improvement was suggested by Tyler Reddy at https://mail.gna.org/public/relax-users/2008-10/msg00011.html (Message-id: <20081007144810.ab985qup4408wokg@...>). ........ r7551 \| bugman \| 2008-10-07 21:25:09 +0200 (Tue, 07 Oct 2008) \| 3 lines Added a user script for adding a new system test of an NOE analysis. ........ r7552 \| bugman \| 2008-10-07 21:34:11 +0200 (Tue, 07 Oct 2008) \| 3 lines Fixes for the system test NOE analysis script. ........ r7553 \| bugman \| 2008-10-07 21:37:06 +0200 (Tue, 07 Oct 2008) \| 3 lines Added some truncated Sparky peak lists from an NOE analysis. ........ r7554 \| bugman \| 2008-10-07 21:37:24 +0200 (Tue, 07 Oct 2008) \| 3 lines Activated the NOE analysis system test. ........ r7555 \| bugman \| 2008-10-07 21:39:58 +0200 (Tue, 07 Oct 2008) \| 3 lines Shifted the last of the system test data into the test suite common data directory. ........ r7556 \| bugman \| 2008-10-07 21:41:02 +0200 (Tue, 07 Oct 2008) \| 3 lines Removed the empty system test data directory. ........ r7557 \| bugman \| 2008-10-07 21:44:00 +0200 (Tue, 07 Oct 2008) \| 3 lines Fixed all the references to the shifted system test data. ........ r7559 \| bugman \| 2008-10-07 22:46:59 +0200 (Tue, 07 Oct 2008) \| 3 lines Fixed the noe.read() user function. ........ r7560 \| bugman \| 2008-10-07 22:49:53 +0200 (Tue, 07 Oct 2008) \| 5 lines Fix for the noe.py system test script. The spin names needed to be set to 'N'. ........ r7561 \| bugman \| 2008-10-07 22:52:59 +0200 (Tue, 07 Oct 2008) \| 3 lines Converted the assign_function() method to the new design. ........ r7562 \| bugman \| 2008-10-07 22:54:17 +0200 (Tue, 07 Oct 2008) \| 3 lines Added a check to assign_function() for when the spectrum_type arg is incorrect. ........ r7563 \| bugman \| 2008-10-07 22:57:05 +0200 (Tue, 07 Oct 2008) \| 3 lines The spectrum_type arg is now propagated all the way to where it's needed. ........ r7564 \| bugman \| 2008-10-07 22:58:04 +0200 (Tue, 07 Oct 2008) \| 3 lines Added some missing imports. ........ r7565 \| bugman \| 2008-10-07 23:04:49 +0200 (Tue, 07 Oct 2008) \| 3 lines Converted the noe.error() user function front and back-end to the new design. ........ r7566 \| bugman \| 2008-10-07 23:06:41 +0200 (Tue, 07 Oct 2008) \| 5 lines Fixed the calls to noe.error(). The sample script and system test script now use the spin_id arg rather than residue number. ........ r7567 \| bugman \| 2008-10-07 23:09:05 +0200 (Tue, 07 Oct 2008) \| 3 lines Converted the overfit_deselect() method to the new design. ........ r7568 \| bugman \| 2008-10-07 23:09:57 +0200 (Tue, 07 Oct 2008) \| 3 lines Modified overfit_deselect() to set the spin container select flag to False rather than 0. ........ r7569 \| bugman \| 2008-10-07 23:12:08 +0200 (Tue, 07 Oct 2008) \| 5 lines Fixes for the spin container select flag. Now the flag is always set to the bools True or False rather than 1 and 0. ........ r7570 \| bugman \| 2008-10-07 23:14:41 +0200 (Tue, 07 Oct 2008) \| 3 lines Converted the calculate() method to the new design. ........ r7571 \| bugman \| 2008-10-07 23:16:40 +0200 (Tue, 07 Oct 2008) \| 8 lines Deletion of a number of methods no longer used in the 1.3 line. These are: read_columnar_results() write_columnar_line() write_columnar_results() ........ r7572 \| bugman \| 2008-10-07 23:17:46 +0200 (Tue, 07 Oct 2008) \| 3 lines Deleted the write() method as it has never been used!!! ........ r7573 \| bugman \| 2008-10-07 23:21:13 +0200 (Tue, 07 Oct 2008) \| 3 lines Updated the value.write() user function interface to the new design. ........ r7574 \| bugman \| 2008-10-07 23:25:23 +0200 (Tue, 07 Oct 2008) \| 6 lines Fix for the write_data() function. The file arg was missing from the write_header() call, and the docstring has been converted to epydoc format. ........ r7575 \| bugman \| 2008-10-07 23:28:57 +0200 (Tue, 07 Oct 2008) \| 3 lines Set the specific_fns.base_class.Common_functions as the base class of the Noe class. ........ r7576 \| bugman \| 2008-10-07 23:29:38 +0200 (Tue, 07 Oct 2008) \| 3 lines Deleted the return_value() method as the base class method is sufficient. ........ r7577 \| bugman \| 2008-10-07 23:53:40 +0200 (Tue, 07 Oct 2008) \| 3 lines Added the removal of temporary manual file to the 'clean' scons target. ........ r7578 \| bugman \| 2008-10-08 00:00:08 +0200 (Wed, 08 Oct 2008) \| 3 lines Fix for assign_function(), the spectrum_type arg is sent into it! ........ r7579 \| bugman \| 2008-10-08 00:00:51 +0200 (Wed, 08 Oct 2008) \| 5 lines Another fix for assign_function(). The last commit incorrectly set up the function args. ........ r7582 \| bugman \| 2008-10-08 22:29:23 +0200 (Wed, 08 Oct 2008) \| 14 lines Ported the modifications to the CHANGES file from the 1.3.2 tag. The command used was: svn merge -r7580:7581 svn+ssh://bugman@.../svn/relax/tags/1.3.2 ..... r7581 \| bugman \| 2008-10-08 22:27:25 +0200 (Wed, 08 Oct 2008) \| 3 lines Changed paths: M /tags/1.3.2/docs/CHANGES Updated the CHANGES file for relax version 1.3.2. ..... ........ r7592 \| semor \| 2008-10-09 19:37:20 +0200 (Thu, 09 Oct 2008) \| 3 lines Continued the implementation for the reading of a Nmrview peak list. ........ r7593 \| semor \| 2008-10-10 04:23:03 +0200 (Fri, 10 Oct 2008) \| 10 lines Added more for the reading of intensities from a nmrview peak list. There is still a need to fix the reading of the assignments which are of the format number.nucleus (e.g. 22.HN). Moreover, a functionality to chose whether the intensity or volume column is read could be added as proposed in a post at: https://mail.gna.org/public/relax-devel/2008-10/msg00026.html (Message-id: <48EE7028.6060409@...>). ........ r7595 \| bugman \| 2008-10-11 18:15:19 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted all the Dasha class methods into module functions. ........ r7596 \| bugman \| 2008-10-11 18:18:08 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the Dasha user function class prompt interface to the new design. ........ r7597 \| bugman \| 2008-10-11 18:40:20 +0200 (Sat, 11 Oct 2008) \| 3 lines Created 7 arg unit tests for all fns of the dasha user function class. ........ r7598 \| bugman \| 2008-10-11 18:41:47 +0200 (Sat, 11 Oct 2008) \| 5 lines Missing import bug fix. This was identified by the arg unit tests of 7597. ........ r7599 \| bugman \| 2008-10-11 18:43:02 +0200 (Sat, 11 Oct 2008) \| 3 lines Fixes for the Dasha user function print outs. ........ r7600 \| bugman \| 2008-10-11 20:45:03 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create() function to the new design. ........ r7601 \| bugman \| 2008-10-11 21:09:54 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create_script() function to the new design. ........ r7602 \| bugman \| 2008-10-11 21:16:30 +0200 (Sat, 11 Oct 2008) \| 3 lines Created the 2 new API functions: first_residue_num() and last_residue_num(). ........ r7603 \| bugman \| 2008-10-11 21:20:18 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the execute() function to the new design. ........ r7604 \| bugman \| 2008-10-11 21:25:49 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the extract() function to the new design. ........ r7605 \| bugman \| 2008-10-11 22:03:02 +0200 (Sat, 11 Oct 2008) \| 6 lines Fixes for the copy() and read() functions. The specific set() function was destroyed at r4822, well at least shifted to generic_fns.value.set_spin_params(). ........ r7606 \| bugman \| 2008-10-11 22:16:08 +0200 (Sat, 11 Oct 2008) \| 3 lines Fixed the creation of the Dasha script. ........ r7607 \| bugman \| 2008-10-11 22:17:22 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the extract() method. The current data pipe was missing. ........ r7608 \| bugman \| 2008-10-11 22:18:42 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the extract() docstring. ........ r7609 \| bugman \| 2008-10-11 22:35:06 +0200 (Sat, 11 Oct 2008) \| 6 lines Switched to using os.popen3 for executing Dasha. This allows STDOUT and STDERR to be caught and sent to relax's STDOUT and STDERR. Hence Dasha's output is caught by the system tests, etc. ........ r7610 \| bugman \| 2008-10-11 22:36:49 +0200 (Sat, 11 Oct 2008) \| 5 lines Bug fix for the minimisation set() function. The variable 'index' no longer exists as it is replace by the SpinContainer instance. ........ r7611 \| bugman \| 2008-10-11 22:42:51 +0200 (Sat, 11 Oct 2008) \| 3 lines Modified the Dasha system test script to use the temporary directory. ........ r7612 \| bugman \| 2008-10-11 22:46:23 +0200 (Sat, 11 Oct 2008) \| 3 lines The Dasha system test script can now run outside of the system test framework. ........ r7613 \| bugman \| 2008-10-11 22:47:48 +0200 (Sat, 11 Oct 2008) \| 3 lines Fixed the call to results.write() in the Dasha system test script. ........ r7614 \| bugman \| 2008-10-11 22:49:03 +0200 (Sat, 11 Oct 2008) \| 3 lines Comment fix. ........ r7615 \| bugman \| 2008-10-11 23:04:16 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create() args to keyword args and the docstring to epydoc format. ........ r7616 \| bugman \| 2008-10-11 23:04:36 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the constraints flag to a bool. ........ r7617 \| bugman \| 2008-10-11 23:06:13 +0200 (Sat, 11 Oct 2008) \| 3 lines The Modelfree4 execution system test script can now be run outside of the test suite framework. ........ r7618 \| bugman \| 2008-10-11 23:07:00 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the palmer.create() print out. ........ r7619 \| bugman \| 2008-10-11 23:07:51 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the check of the constraints arg in palmer.create(). ........ r7620 \| bugman \| 2008-10-11 23:14:16 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the last pieces of create() to the new design. ........ r7621 \| bugman \| 2008-10-11 23:21:05 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted create_mfin() to the new design. ........ r7622 \| bugman \| 2008-10-11 23:34:53 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted create_mfdata() to the new design. ........ r7623 \| bugman \| 2008-10-11 23:47:44 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create_mfmodel() and create_mfpar() functions to the new design. ........ r7624 \| bugman \| 2008-10-11 23:51:37 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted create_run() to the new design. ........ r7625 \| bugman \| 2008-10-11 23:55:21 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted execute() to the new design. ........ r7626 \| bugman \| 2008-10-12 00:03:01 +0200 (Sun, 12 Oct 2008) \| 5 lines Bug fix for the palmer.py sample script. The model_selection() user function args were wrong. ........ r7627 \| bugman \| 2008-10-12 00:11:52 +0200 (Sun, 12 Oct 2008) \| 3 lines Many fixes for the Modelfree4 execution system test script. ........ r7628 \| bugman \| 2008-10-12 00:51:36 +0200 (Sun, 12 Oct 2008) \| 6 lines Switched from os.spawnlp to os.popen3 for proper IO redirection. This allows the system tests to capture Modelfree4's STDOUT and STDERR streams, as they are fused into relax's. ........ r7629 \| bugman \| 2008-10-12 00:54:20 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the palmer.py sample script. The model selection data pipe is created by the user function so it shouldn't be created beforehand. ........ r7630 \| bugman \| 2008-10-12 01:33:29 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the reset() user function - the generic_fns.reset module was not properly imported. ........ r7631 \| bugman \| 2008-10-12 11:23:07 +0200 (Sun, 12 Oct 2008) \| 3 lines Shifted the pipe creation from setUp() to the script to allow for stand alone execution. ........ r7632 \| bugman \| 2008-10-12 11:40:43 +0200 (Sun, 12 Oct 2008) \| 3 lines Created a system test for the saving, loading, saving, and loading again of the system state. ........ r7633 \| bugman \| 2008-10-12 11:47:14 +0200 (Sun, 12 Oct 2008) \| 5 lines Removed the state loadings which was uncovering a pickling issue. This bug is now caught by its own system test. ........ r7634 \| bugman \| 2008-10-12 11:48:16 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the call to the fix() user function. ........ r7635 \| bugman \| 2008-10-12 11:57:44 +0200 (Sun, 12 Oct 2008) \| 3 lines Updated the ancient palmer.py sample script to the new design. ........ r7636 \| bugman \| 2008-10-12 12:07:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Removed all references to 'run' and removed some useless comments. ........ r7637 \| bugman \| 2008-10-12 12:26:47 +0200 (Sun, 12 Oct 2008) \| 5 lines Created the new specific method model_desc() for returning a human readable model description. This will be used in the model selection printouts. ........ r7638 \| bugman \| 2008-10-12 12:27:23 +0200 (Sun, 12 Oct 2008) \| 3 lines Shifted to the use of the model_loop(). ........ r7639 \| bugman \| 2008-10-12 12:38:48 +0200 (Sun, 12 Oct 2008) \| 8 lines Converted the rest of the model selection to the model_loop() design. The following model-free methods have been converted to using the model_loop(): duplicate_data() model_statistics() skip_function() ........ r7640 \| bugman \| 2008-10-12 12:42:09 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the determination of the global_stats flag in model_statistics(). ........ r7641 \| bugman \| 2008-10-12 12:48:17 +0200 (Sun, 12 Oct 2008) \| 3 lines Renamed the duplicate_data() arg model_info to model_index. ........ r7642 \| bugman \| 2008-10-12 13:00:50 +0200 (Sun, 12 Oct 2008) \| 3 lines Created the model_type() method to determine whether the model is local or global. ........ r7643 \| bugman \| 2008-10-12 13:02:29 +0200 (Sun, 12 Oct 2008) \| 3 lines Activated the specific model_type() method. ........ r7644 \| bugman \| 2008-10-12 13:04:07 +0200 (Sun, 12 Oct 2008) \| 3 lines Removed the model_index arg from model_type(). ........ r7645 \| bugman \| 2008-10-12 13:05:50 +0200 (Sun, 12 Oct 2008) \| 3 lines Used the new model_type() specific method to differentiate between global and local models. ........ r7646 \| bugman \| 2008-10-12 13:24:48 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the setUp() method. The 'palmer' data pipe shouldn't be created! ........ r7647 \| bugman \| 2008-10-12 15:17:44 +0200 (Sun, 12 Oct 2008) \| 3 lines Changes to the model selection print out. ........ r7648 \| bugman \| 2008-10-12 16:09:04 +0200 (Sun, 12 Oct 2008) \| 3 lines Added checks to the Modelfree4 system test. ........ r7649 \| bugman \| 2008-10-12 16:12:49 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the extract() function. ........ r7650 \| bugman \| 2008-10-12 16:30:32 +0200 (Sun, 12 Oct 2008) \| 5 lines Removed the 'format' arg from results.write() and results.display(). This is no longer used as the only supported format is now XML. ........ r7651 \| bugman \| 2008-10-12 17:05:21 +0200 (Sun, 12 Oct 2008) \| 7 lines Fixes for the relax data store singleton 'add()', 'to_xml()', and 'from_xml()' methods. These were referring to the contents of the singleton as self, whereas in reality with the current temporary implementation it is stored in self.instance. Hence the singleton wasn't operating on itself. ........ r7652 \| bugman \| 2008-10-12 17:07:57 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the extraction of mfout file data in the Modelfree4 system test. ........ r7653 \| bugman \| 2008-10-12 17:09:00 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the Modelfree4 controlling sample script. This matches the fixes of r7652. ........ r7654 \| bugman \| 2008-10-12 17:22:45 +0200 (Sun, 12 Oct 2008) \| 3 lines Fixes for the checks of the test_palmer() system test. ........ r7655 \| bugman \| 2008-10-12 17:30:11 +0200 (Sun, 12 Oct 2008) \| 3 lines Added some checks for the final mfout file. ........ r7656 \| bugman \| 2008-10-12 17:40:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Fixes for the checks of the final mfout reading. ........ r7657 \| bugman \| 2008-10-12 17:47:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Added checks for the global chi2 and tm value. ........ r7658 \| bugman \| 2008-10-12 18:22:02 +0200 (Sun, 12 Oct 2008) \| 3 lines The global chi2 and tm value are now extracted from the mfout file. ........ r7659 \| bugman \| 2008-10-12 18:23:12 +0200 (Sun, 12 Oct 2008) \| 3 lines Removed a debugging print out. ........ r7660 \| bugman \| 2008-10-12 18:33:46 +0200 (Sun, 12 Oct 2008) \| 6 lines Fix for the loading of global data from the mfout file. This only happens when a global model is optimised. The parameters and chi2 value are in the mfout file but are fixed or the sum of individual chi2 vals. ........ r7661 \| bugman \| 2008-10-12 18:35:17 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for a typo in the global chi2 check. ........ r7662 \| bugman \| 2008-10-12 18:37:04 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the check of the optimised tm value. ........ r7663 \| bugman \| 2008-10-12 18:43:27 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for running Modelfree4 - the structure is properly copied in the create_run() method. ........ r7664 \| bugman \| 2008-10-12 18:45:21 +0200 (Sun, 12 Oct 2008) \| 3 lines More fixes for create_run(). ........ r7665 \| bugman \| 2008-10-12 18:46:27 +0200 (Sun, 12 Oct 2008) \| 3 lines Modified the Modelfree4 system test to use a PDB file and spheroid diffusion tensor. ........ r7666 \| bugman \| 2008-10-12 18:46:57 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the execute() method when a PDB file is being used. ........ r7667 \| bugman \| 2008-10-12 18:57:33 +0200 (Sun, 12 Oct 2008) \| 3 lines Created a new script to test out the handling of Modelfree4 with PDB files and spheroid diffusion. ........ r7668 \| bugman \| 2008-10-12 18:58:28 +0200 (Sun, 12 Oct 2008) \| 5 lines Removed the reading of the PDB file and setting of a spheroid tensor. This will be tested in a second system test. ........ r7669 \| bugman \| 2008-10-12 19:00:13 +0200 (Sun, 12 Oct 2008) \| 5 lines Created a system test for Modelfree4 with the OMP data. This runs the palmer_omp.py system test script. ........ r7670 \| bugman \| 2008-10-12 19:03:26 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the create() method. Deselected spins should be skipped. ........ r7671 \| bugman \| 2008-10-12 19:22:42 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the test_palmer_omp() system test. The PDB file has no models in it! ........ r7672 \| bugman \| 2008-10-12 19:26:35 +0200 (Sun, 12 Oct 2008) \| 5 lines Created a truncated OMP PDB file with only NH vectors of the first 15 residues. The molmol residue name syntax has also been fixed to allow Modelfree4 to be happy. ........ r7673 \| bugman \| 2008-10-12 19:28:06 +0200 (Sun, 12 Oct 2008) \| 3 lines The Modelfree4 system test using the OMP data now uses the truncated and more standard PDB file. ........ r7674 \| bugman \| 2008-10-12 19:35:56 +0200 (Sun, 12 Oct 2008) \| 3 lines Updated the checks of the test_palmer_omp() system test to be specific to that test. ........ r7675 \| bugman \| 2008-10-12 19:38:10 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the spin names in the test_palmer_omp() system test checks. ........ r7676 \| bugman \| 2008-10-12 19:48:55 +0200 (Sun, 12 Oct 2008) \| 3 lines The spheroidal diffusion tensor from the mfout file is now read and loaded into the relax data store. ........ r7677 \| bugman \| 2008-10-12 19:59:03 +0200 (Sun, 12 Oct 2008) \| 8 lines Important bug fix!! The theta angle of the spheroidal diffusion tensor was being improperly wrapped between 0 and pi. This was causing the glide reflection symmetry to be broken, hence the tensor was incorrect. The result would be longer optimisation times for the spheroid tensors and more iterations than necessary in the full_analysis.py script. ........ r7678 \| bugman \| 2008-10-12 21:34:09 +0200 (Sun, 12 Oct 2008) \| 3 lines Fixes for the OpenDX code to handle mapping of the global parameter space (diff tensor, etc.). ........ r7679 \| bugman \| 2008-10-12 21:37:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the dx.execute() user function - the correct args now are used. ........ r7680 \| bugman \| 2008-10-12 21:40:22 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the backend of the dx.execute() user function. The file arg was at some point renamed to file_prefix. The code now uses this name change. ........ r7681 \| bugman \| 2008-10-12 22:00:14 +0200 (Sun, 12 Oct 2008) \| 6 lines Reverted r7677. This was a false alarm! The command used was: svn merge -r7677:7676 . ........ r7682 \| bugman \| 2008-10-12 22:14:47 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the setting of the theta and phi diff tensor angles from the Modelfree4 mfout file. The angles need to be passed in in radian units. ........ r7683 \| bugman \| 2008-10-12 22:15:26 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the theta and phi angle checks in the test_palmer_omp() system test. ........ r7684 \| bugman \| 2008-10-12 22:23:16 +0200 (Sun, 12 Oct 2008) \| 6 lines Fix for bug #12437 (https://gna.org/bugs/?12437). The problem was that the 'from_xml' and 'to_xml' methods needed to be blacklisted to prevent them from being restored from the pickled state. ........ r7685 \| semor \| 2008-10-13 17:10:52 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the name of the NMRView program. ........ r7686 \| semor \| 2008-10-13 17:32:25 +0200 (Mon, 13 Oct 2008) \| 5 lines Added a system test for the reading of a Sparky peak list. This will help find the problems specific to NMRView peak list support... ........ r7687 \| semor \| 2008-10-13 17:37:17 +0200 (Mon, 13 Oct 2008) \| 5 lines Fixed a problem raised when the number 0 would be given as relaxation delay. A delay of 0.0 is now given for the intensities associated with the Sparky peak list. ........ r7688 \| semor \| 2008-10-13 18:03:23 +0200 (Mon, 13 Oct 2008) \| 3 lines Added the function for the NMRView peak list header handling. ........ r7689 \| semor \| 2008-10-13 19:44:02 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the extraction of the residue number, nucleus name and heteronucleus name. ........ r7690 \| semor \| 2008-10-13 19:44:38 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the column number for the intensity. ........ r7691 \| semor \| 2008-10-13 20:24:28 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the test for the setting of Sparky and NMRView intensities. ........ r7692 \| semor \| 2008-10-13 20:47:19 +0200 (Mon, 13 Oct 2008) \| 3 lines Added the framework for a XEasy system test. ........ r7693 \| bugman \| 2008-10-14 12:27:56 +0200 (Tue, 14 Oct 2008) \| 3 lines Modified the test_palmer_omp() system test to take into account the bugs fixed in Modelfree 4.20. ........ r7694 \| semor \| 2008-10-14 18:10:16 +0200 (Tue, 14 Oct 2008) \| 7 lines Added the support for when a nmrview peak list contains unassigned peaks. These peaks have an assignment field as '{}' in the peak list and are now excluded. Complemented the peak list sample accordingly. ........ r7695 \| semor \| 2008-10-14 18:50:59 +0200 (Tue, 14 Oct 2008) \| 7 lines Added the support of unassigned peaks in Sparky formatted peak lists. The unassigned peak show up as '?-?'. Thanks to Ryan Hoffman and his bug report (https://gna.org/bugs/?11913). ........ r7696 \| bugman \| 2008-10-14 21:10:31 +0200 (Tue, 14 Oct 2008) \| 3 lines Added an XEasy peak list, with peak heights as volumes, into the test suite data store. ........ r7697 \| semor \| 2008-10-14 21:25:20 +0200 (Tue, 14 Oct 2008) \| 7 lines Corrected two typos. These were discovered by Edward d'Auvergne in a post at: https://mail.gna.org/public/relax-devel/2008-10/msg00041.html (message ID: 7f080ed10810141215r72940a18hc09456a02d3f69ce@...) ........ r7698 \| bugman \| 2008-10-14 22:06:17 +0200 (Tue, 14 Oct 2008) \| 5 lines Added a RelaxError to tell the user that the Modelfree4 version being used is buggy. It also tells them that they must upgrade! ........ r7699 \| bugman \| 2008-10-14 22:42:18 +0200 (Tue, 14 Oct 2008) \| 6 lines The relaxation curve time point can now be an integer to allow the time of '0'. See the post at https://mail.gna.org/public/relax-devel/2008-10/msg00040.html (Message-id: <7f080ed10810141213s2211d36fre56906e0ae5903e2@...>). ........ r7700 \| bugman \| 2008-10-14 22:43:20 +0200 (Tue, 14 Oct 2008) \| 3 lines Made sure that the relaxation curve fitting time point is stored as a float. ........ r7701 \| semor \| 2008-10-14 23:33:38 +0200 (Tue, 14 Oct 2008) \| 3 lines Corrected the formatting of a few lines... ........ r7702 \| semor \| 2008-10-15 00:01:04 +0200 (Wed, 15 Oct 2008) \| 5 lines Continued the implementation of the XEasy support system test. Much more work is needed, though. ........ r7703 \| semor \| 2008-10-15 00:20:08 +0200 (Wed, 15 Oct 2008) \| 3 lines Grouped the three peak list support tests into a single one. ........ r7704 \| bugman \| 2008-10-15 00:43:39 +0200 (Wed, 15 Oct 2008) \| 7 lines Modified the Modelfree4 system tests to work with the Portland C compiler Linux version. The modelfree4 Linux binary compiled with Gnu gcc gives different results, sometimes quite large, to the Linux binary compiled with the Portland C compiler. The tests now catch this. There may be problems with the Mac OS X Modelfree4 binary still. ........ r7705 \| semor \| 2008-10-15 04:23:33 +0200 (Wed, 15 Oct 2008) \| 8 lines Placed the setting of the 'H_dim' variable before the call to the intensity_xeasy() function. The 'H_dim' variable was undefined otherwise... This fix may break the handling of peak lists when the w1 and w2 dimensions are inverted. Can these peak lists exist in XEasy ? ........ r7706 \| semor \| 2008-10-15 04:30:55 +0200 (Wed, 15 Oct 2008) \| 6 lines Set the default 'H_dim' variable in the intensity_xeasy() function. Passing the variable to the intensity_xeasy() funciton the way it was done before could not have worked... ........ r7707 \| bugman \| 2008-10-15 17:40:15 +0200 (Wed, 15 Oct 2008) \| 3 lines Replaced all references to 'residue' by 'spin' in the relax_fit.mean_and_error() user fn docstring. ........ r7728 \| semor \| 2008-10-15 23:18:55 +0200 (Wed, 15 Oct 2008) \| 5 lines Passed the 'file_data' variable to the det_dimensions() function and removed some 'self.' instances. The system test for XEasy peak list support now goes further... However, more work is still needed. ........ r7730 \| semor \| 2008-10-16 00:13:40 +0200 (Thu, 16 Oct 2008) \| 3 lines Added a missing 'cdp' definition... ........ r7731 \| semor \| 2008-10-16 00:14:47 +0200 (Thu, 16 Oct 2008) \| 3 lines Added a missing import. ........ r7733 \| semor \| 2008-10-16 00:17:00 +0200 (Thu, 16 Oct 2008) \| 3 lines Changed a normalization force flag to boolean. ........ r7741 \| semor \| 2008-10-16 04:28:28 +0200 (Thu, 16 Oct 2008) \| 9 lines Corrected a name clash. This originates from a post by Edward at: https://mail.gna.org/public/relax-devel/2008-10/msg00060.html (message ID: 7f080ed10810151446p58ab78f1u93cb1bc4afbeb202@...). I hope this fixes the problem... ........ r7742 \| semor \| 2008-10-16 04:32:10 +0200 (Thu, 16 Oct 2008) \| 6 lines Passed more arguments to the det_dimensions() function and removed 'self.' instances. The test for the support of a XEasy peak list now passes, although there still may be some bugs present... ........ r7743 \| semor \| 2008-10-16 05:02:11 +0200 (Thu, 16 Oct 2008) \| 10 lines Added more to the XEasy support test. Now, the test fails when reaching the first residue with a non HN/N assignment. In fact, the reading of this residue is fine, but no intensity is extracted... hence the failure of the test. Now, what do we want to do ? Do we want to support side chain assignments mixed with backbone assignments ? In other words, do we want to support multiuple assignment types in a single analysis ? ........ r7744 \| semor \| 2008-10-16 05:47:31 +0200 (Thu, 16 Oct 2008) \| 3 lines Updated some copyrights. ........ r7784 \| bugman \| 2008-10-16 21:22:02 +0200 (Thu, 16 Oct 2008) \| 7 lines Fix for bug #12456 (https://gna.org/bugs/?12456). When calculating the errors from replicate spectra, the standard deviations of all spins were being averaged rather than the variance. The same error occurred when averaging across spectra - when not all are duplicated, triplicated, etc. ........ r7787 \| semor \| 2008-10-16 22:07:30 +0200 (Thu, 16 Oct 2008) \| 7 lines Set the peak intensity as the default for the reading of NMRView peak list. The volume was being used. Now, the volume can be used with the use of the 'int_col' variable. Moreover, the docstrings are now more complete for the of NMRView peak lists. ........ r7789 \| semor \| 2008-10-16 22:47:52 +0200 (Thu, 16 Oct 2008) \| 3 lines Corrected the passing of the 'int_col' variable to the intensity extraction functions. ........ r7790 \| semor \| 2008-10-16 23:12:10 +0200 (Thu, 16 Oct 2008) \| 7 lines Corrected an argument. This was pointed out by Edward in a post at : https://mail.gna.org/public/relax-devel/2008-10/msg00067.html (message ID: 7f080ed10810161357h418d386bi4d2dd5851d7a4575@...) ........	2008-10-16 21:58:02	Tree
[r7792] by bugman Merged revisions 7594-7791 via svnmerge from svn+ssh://bugman@.../svn/relax/1.3 ........ r7595 \| bugman \| 2008-10-11 18:15:19 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted all the Dasha class methods into module functions. ........ r7596 \| bugman \| 2008-10-11 18:18:08 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the Dasha user function class prompt interface to the new design. ........ r7597 \| bugman \| 2008-10-11 18:40:20 +0200 (Sat, 11 Oct 2008) \| 3 lines Created 7 arg unit tests for all fns of the dasha user function class. ........ r7598 \| bugman \| 2008-10-11 18:41:47 +0200 (Sat, 11 Oct 2008) \| 5 lines Missing import bug fix. This was identified by the arg unit tests of 7597. ........ r7599 \| bugman \| 2008-10-11 18:43:02 +0200 (Sat, 11 Oct 2008) \| 3 lines Fixes for the Dasha user function print outs. ........ r7600 \| bugman \| 2008-10-11 20:45:03 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create() function to the new design. ........ r7601 \| bugman \| 2008-10-11 21:09:54 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create_script() function to the new design. ........ r7602 \| bugman \| 2008-10-11 21:16:30 +0200 (Sat, 11 Oct 2008) \| 3 lines Created the 2 new API functions: first_residue_num() and last_residue_num(). ........ r7603 \| bugman \| 2008-10-11 21:20:18 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the execute() function to the new design. ........ r7604 \| bugman \| 2008-10-11 21:25:49 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the extract() function to the new design. ........ r7605 \| bugman \| 2008-10-11 22:03:02 +0200 (Sat, 11 Oct 2008) \| 6 lines Fixes for the copy() and read() functions. The specific set() function was destroyed at r4822, well at least shifted to generic_fns.value.set_spin_params(). ........ r7606 \| bugman \| 2008-10-11 22:16:08 +0200 (Sat, 11 Oct 2008) \| 3 lines Fixed the creation of the Dasha script. ........ r7607 \| bugman \| 2008-10-11 22:17:22 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the extract() method. The current data pipe was missing. ........ r7608 \| bugman \| 2008-10-11 22:18:42 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the extract() docstring. ........ r7609 \| bugman \| 2008-10-11 22:35:06 +0200 (Sat, 11 Oct 2008) \| 6 lines Switched to using os.popen3 for executing Dasha. This allows STDOUT and STDERR to be caught and sent to relax's STDOUT and STDERR. Hence Dasha's output is caught by the system tests, etc. ........ r7610 \| bugman \| 2008-10-11 22:36:49 +0200 (Sat, 11 Oct 2008) \| 5 lines Bug fix for the minimisation set() function. The variable 'index' no longer exists as it is replace by the SpinContainer instance. ........ r7611 \| bugman \| 2008-10-11 22:42:51 +0200 (Sat, 11 Oct 2008) \| 3 lines Modified the Dasha system test script to use the temporary directory. ........ r7612 \| bugman \| 2008-10-11 22:46:23 +0200 (Sat, 11 Oct 2008) \| 3 lines The Dasha system test script can now run outside of the system test framework. ........ r7613 \| bugman \| 2008-10-11 22:47:48 +0200 (Sat, 11 Oct 2008) \| 3 lines Fixed the call to results.write() in the Dasha system test script. ........ r7614 \| bugman \| 2008-10-11 22:49:03 +0200 (Sat, 11 Oct 2008) \| 3 lines Comment fix. ........ r7615 \| bugman \| 2008-10-11 23:04:16 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create() args to keyword args and the docstring to epydoc format. ........ r7616 \| bugman \| 2008-10-11 23:04:36 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the constraints flag to a bool. ........ r7617 \| bugman \| 2008-10-11 23:06:13 +0200 (Sat, 11 Oct 2008) \| 3 lines The Modelfree4 execution system test script can now be run outside of the test suite framework. ........ r7618 \| bugman \| 2008-10-11 23:07:00 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the palmer.create() print out. ........ r7619 \| bugman \| 2008-10-11 23:07:51 +0200 (Sat, 11 Oct 2008) \| 3 lines Fix for the check of the constraints arg in palmer.create(). ........ r7620 \| bugman \| 2008-10-11 23:14:16 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the last pieces of create() to the new design. ........ r7621 \| bugman \| 2008-10-11 23:21:05 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted create_mfin() to the new design. ........ r7622 \| bugman \| 2008-10-11 23:34:53 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted create_mfdata() to the new design. ........ r7623 \| bugman \| 2008-10-11 23:47:44 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted the create_mfmodel() and create_mfpar() functions to the new design. ........ r7624 \| bugman \| 2008-10-11 23:51:37 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted create_run() to the new design. ........ r7625 \| bugman \| 2008-10-11 23:55:21 +0200 (Sat, 11 Oct 2008) \| 3 lines Converted execute() to the new design. ........ r7626 \| bugman \| 2008-10-12 00:03:01 +0200 (Sun, 12 Oct 2008) \| 5 lines Bug fix for the palmer.py sample script. The model_selection() user function args were wrong. ........ r7627 \| bugman \| 2008-10-12 00:11:52 +0200 (Sun, 12 Oct 2008) \| 3 lines Many fixes for the Modelfree4 execution system test script. ........ r7628 \| bugman \| 2008-10-12 00:51:36 +0200 (Sun, 12 Oct 2008) \| 6 lines Switched from os.spawnlp to os.popen3 for proper IO redirection. This allows the system tests to capture Modelfree4's STDOUT and STDERR streams, as they are fused into relax's. ........ r7629 \| bugman \| 2008-10-12 00:54:20 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the palmer.py sample script. The model selection data pipe is created by the user function so it shouldn't be created beforehand. ........ r7630 \| bugman \| 2008-10-12 01:33:29 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the reset() user function - the generic_fns.reset module was not properly imported. ........ r7631 \| bugman \| 2008-10-12 11:23:07 +0200 (Sun, 12 Oct 2008) \| 3 lines Shifted the pipe creation from setUp() to the script to allow for stand alone execution. ........ r7632 \| bugman \| 2008-10-12 11:40:43 +0200 (Sun, 12 Oct 2008) \| 3 lines Created a system test for the saving, loading, saving, and loading again of the system state. ........ r7633 \| bugman \| 2008-10-12 11:47:14 +0200 (Sun, 12 Oct 2008) \| 5 lines Removed the state loadings which was uncovering a pickling issue. This bug is now caught by its own system test. ........ r7634 \| bugman \| 2008-10-12 11:48:16 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the call to the fix() user function. ........ r7635 \| bugman \| 2008-10-12 11:57:44 +0200 (Sun, 12 Oct 2008) \| 3 lines Updated the ancient palmer.py sample script to the new design. ........ r7636 \| bugman \| 2008-10-12 12:07:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Removed all references to 'run' and removed some useless comments. ........ r7637 \| bugman \| 2008-10-12 12:26:47 +0200 (Sun, 12 Oct 2008) \| 5 lines Created the new specific method model_desc() for returning a human readable model description. This will be used in the model selection printouts. ........ r7638 \| bugman \| 2008-10-12 12:27:23 +0200 (Sun, 12 Oct 2008) \| 3 lines Shifted to the use of the model_loop(). ........ r7639 \| bugman \| 2008-10-12 12:38:48 +0200 (Sun, 12 Oct 2008) \| 8 lines Converted the rest of the model selection to the model_loop() design. The following model-free methods have been converted to using the model_loop(): duplicate_data() model_statistics() skip_function() ........ r7640 \| bugman \| 2008-10-12 12:42:09 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the determination of the global_stats flag in model_statistics(). ........ r7641 \| bugman \| 2008-10-12 12:48:17 +0200 (Sun, 12 Oct 2008) \| 3 lines Renamed the duplicate_data() arg model_info to model_index. ........ r7642 \| bugman \| 2008-10-12 13:00:50 +0200 (Sun, 12 Oct 2008) \| 3 lines Created the model_type() method to determine whether the model is local or global. ........ r7643 \| bugman \| 2008-10-12 13:02:29 +0200 (Sun, 12 Oct 2008) \| 3 lines Activated the specific model_type() method. ........ r7644 \| bugman \| 2008-10-12 13:04:07 +0200 (Sun, 12 Oct 2008) \| 3 lines Removed the model_index arg from model_type(). ........ r7645 \| bugman \| 2008-10-12 13:05:50 +0200 (Sun, 12 Oct 2008) \| 3 lines Used the new model_type() specific method to differentiate between global and local models. ........ r7646 \| bugman \| 2008-10-12 13:24:48 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the setUp() method. The 'palmer' data pipe shouldn't be created! ........ r7647 \| bugman \| 2008-10-12 15:17:44 +0200 (Sun, 12 Oct 2008) \| 3 lines Changes to the model selection print out. ........ r7648 \| bugman \| 2008-10-12 16:09:04 +0200 (Sun, 12 Oct 2008) \| 3 lines Added checks to the Modelfree4 system test. ........ r7649 \| bugman \| 2008-10-12 16:12:49 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the extract() function. ........ r7650 \| bugman \| 2008-10-12 16:30:32 +0200 (Sun, 12 Oct 2008) \| 5 lines Removed the 'format' arg from results.write() and results.display(). This is no longer used as the only supported format is now XML. ........ r7651 \| bugman \| 2008-10-12 17:05:21 +0200 (Sun, 12 Oct 2008) \| 7 lines Fixes for the relax data store singleton 'add()', 'to_xml()', and 'from_xml()' methods. These were referring to the contents of the singleton as self, whereas in reality with the current temporary implementation it is stored in self.instance. Hence the singleton wasn't operating on itself. ........ r7652 \| bugman \| 2008-10-12 17:07:57 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the extraction of mfout file data in the Modelfree4 system test. ........ r7653 \| bugman \| 2008-10-12 17:09:00 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the Modelfree4 controlling sample script. This matches the fixes of r7652. ........ r7654 \| bugman \| 2008-10-12 17:22:45 +0200 (Sun, 12 Oct 2008) \| 3 lines Fixes for the checks of the test_palmer() system test. ........ r7655 \| bugman \| 2008-10-12 17:30:11 +0200 (Sun, 12 Oct 2008) \| 3 lines Added some checks for the final mfout file. ........ r7656 \| bugman \| 2008-10-12 17:40:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Fixes for the checks of the final mfout reading. ........ r7657 \| bugman \| 2008-10-12 17:47:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Added checks for the global chi2 and tm value. ........ r7658 \| bugman \| 2008-10-12 18:22:02 +0200 (Sun, 12 Oct 2008) \| 3 lines The global chi2 and tm value are now extracted from the mfout file. ........ r7659 \| bugman \| 2008-10-12 18:23:12 +0200 (Sun, 12 Oct 2008) \| 3 lines Removed a debugging print out. ........ r7660 \| bugman \| 2008-10-12 18:33:46 +0200 (Sun, 12 Oct 2008) \| 6 lines Fix for the loading of global data from the mfout file. This only happens when a global model is optimised. The parameters and chi2 value are in the mfout file but are fixed or the sum of individual chi2 vals. ........ r7661 \| bugman \| 2008-10-12 18:35:17 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for a typo in the global chi2 check. ........ r7662 \| bugman \| 2008-10-12 18:37:04 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the check of the optimised tm value. ........ r7663 \| bugman \| 2008-10-12 18:43:27 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for running Modelfree4 - the structure is properly copied in the create_run() method. ........ r7664 \| bugman \| 2008-10-12 18:45:21 +0200 (Sun, 12 Oct 2008) \| 3 lines More fixes for create_run(). ........ r7665 \| bugman \| 2008-10-12 18:46:27 +0200 (Sun, 12 Oct 2008) \| 3 lines Modified the Modelfree4 system test to use a PDB file and spheroid diffusion tensor. ........ r7666 \| bugman \| 2008-10-12 18:46:57 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the execute() method when a PDB file is being used. ........ r7667 \| bugman \| 2008-10-12 18:57:33 +0200 (Sun, 12 Oct 2008) \| 3 lines Created a new script to test out the handling of Modelfree4 with PDB files and spheroid diffusion. ........ r7668 \| bugman \| 2008-10-12 18:58:28 +0200 (Sun, 12 Oct 2008) \| 5 lines Removed the reading of the PDB file and setting of a spheroid tensor. This will be tested in a second system test. ........ r7669 \| bugman \| 2008-10-12 19:00:13 +0200 (Sun, 12 Oct 2008) \| 5 lines Created a system test for Modelfree4 with the OMP data. This runs the palmer_omp.py system test script. ........ r7670 \| bugman \| 2008-10-12 19:03:26 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the create() method. Deselected spins should be skipped. ........ r7671 \| bugman \| 2008-10-12 19:22:42 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the test_palmer_omp() system test. The PDB file has no models in it! ........ r7672 \| bugman \| 2008-10-12 19:26:35 +0200 (Sun, 12 Oct 2008) \| 5 lines Created a truncated OMP PDB file with only NH vectors of the first 15 residues. The molmol residue name syntax has also been fixed to allow Modelfree4 to be happy. ........ r7673 \| bugman \| 2008-10-12 19:28:06 +0200 (Sun, 12 Oct 2008) \| 3 lines The Modelfree4 system test using the OMP data now uses the truncated and more standard PDB file. ........ r7674 \| bugman \| 2008-10-12 19:35:56 +0200 (Sun, 12 Oct 2008) \| 3 lines Updated the checks of the test_palmer_omp() system test to be specific to that test. ........ r7675 \| bugman \| 2008-10-12 19:38:10 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the spin names in the test_palmer_omp() system test checks. ........ r7676 \| bugman \| 2008-10-12 19:48:55 +0200 (Sun, 12 Oct 2008) \| 3 lines The spheroidal diffusion tensor from the mfout file is now read and loaded into the relax data store. ........ r7677 \| bugman \| 2008-10-12 19:59:03 +0200 (Sun, 12 Oct 2008) \| 8 lines Important bug fix!! The theta angle of the spheroidal diffusion tensor was being improperly wrapped between 0 and pi. This was causing the glide reflection symmetry to be broken, hence the tensor was incorrect. The result would be longer optimisation times for the spheroid tensors and more iterations than necessary in the full_analysis.py script. ........ r7678 \| bugman \| 2008-10-12 21:34:09 +0200 (Sun, 12 Oct 2008) \| 3 lines Fixes for the OpenDX code to handle mapping of the global parameter space (diff tensor, etc.). ........ r7679 \| bugman \| 2008-10-12 21:37:28 +0200 (Sun, 12 Oct 2008) \| 3 lines Bug fix for the dx.execute() user function - the correct args now are used. ........ r7680 \| bugman \| 2008-10-12 21:40:22 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the backend of the dx.execute() user function. The file arg was at some point renamed to file_prefix. The code now uses this name change. ........ r7681 \| bugman \| 2008-10-12 22:00:14 +0200 (Sun, 12 Oct 2008) \| 6 lines Reverted r7677. This was a false alarm! The command used was: svn merge -r7677:7676 . ........ r7682 \| bugman \| 2008-10-12 22:14:47 +0200 (Sun, 12 Oct 2008) \| 5 lines Fix for the setting of the theta and phi diff tensor angles from the Modelfree4 mfout file. The angles need to be passed in in radian units. ........ r7683 \| bugman \| 2008-10-12 22:15:26 +0200 (Sun, 12 Oct 2008) \| 3 lines Fix for the theta and phi angle checks in the test_palmer_omp() system test. ........ r7684 \| bugman \| 2008-10-12 22:23:16 +0200 (Sun, 12 Oct 2008) \| 6 lines Fix for bug #12437 (https://gna.org/bugs/?12437). The problem was that the 'from_xml' and 'to_xml' methods needed to be blacklisted to prevent them from being restored from the pickled state. ........ r7685 \| semor \| 2008-10-13 17:10:52 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the name of the NMRView program. ........ r7686 \| semor \| 2008-10-13 17:32:25 +0200 (Mon, 13 Oct 2008) \| 5 lines Added a system test for the reading of a Sparky peak list. This will help find the problems specific to NMRView peak list support... ........ r7687 \| semor \| 2008-10-13 17:37:17 +0200 (Mon, 13 Oct 2008) \| 5 lines Fixed a problem raised when the number 0 would be given as relaxation delay. A delay of 0.0 is now given for the intensities associated with the Sparky peak list. ........ r7688 \| semor \| 2008-10-13 18:03:23 +0200 (Mon, 13 Oct 2008) \| 3 lines Added the function for the NMRView peak list header handling. ........ r7689 \| semor \| 2008-10-13 19:44:02 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the extraction of the residue number, nucleus name and heteronucleus name. ........ r7690 \| semor \| 2008-10-13 19:44:38 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the column number for the intensity. ........ r7691 \| semor \| 2008-10-13 20:24:28 +0200 (Mon, 13 Oct 2008) \| 3 lines Fixed the test for the setting of Sparky and NMRView intensities. ........ r7692 \| semor \| 2008-10-13 20:47:19 +0200 (Mon, 13 Oct 2008) \| 3 lines Added the framework for a XEasy system test. ........ r7693 \| bugman \| 2008-10-14 12:27:56 +0200 (Tue, 14 Oct 2008) \| 3 lines Modified the test_palmer_omp() system test to take into account the bugs fixed in Modelfree 4.20. ........ r7694 \| semor \| 2008-10-14 18:10:16 +0200 (Tue, 14 Oct 2008) \| 7 lines Added the support for when a nmrview peak list contains unassigned peaks. These peaks have an assignment field as '{}' in the peak list and are now excluded. Complemented the peak list sample accordingly. ........ r7695 \| semor \| 2008-10-14 18:50:59 +0200 (Tue, 14 Oct 2008) \| 7 lines Added the support of unassigned peaks in Sparky formatted peak lists. The unassigned peak show up as '?-?'. Thanks to Ryan Hoffman and his bug report (https://gna.org/bugs/?11913). ........ r7696 \| bugman \| 2008-10-14 21:10:31 +0200 (Tue, 14 Oct 2008) \| 3 lines Added an XEasy peak list, with peak heights as volumes, into the test suite data store. ........ r7697 \| semor \| 2008-10-14 21:25:20 +0200 (Tue, 14 Oct 2008) \| 7 lines Corrected two typos. These were discovered by Edward d'Auvergne in a post at: https://mail.gna.org/public/relax-devel/2008-10/msg00041.html (message ID: 7f080ed10810141215r72940a18hc09456a02d3f69ce@...) ........ r7698 \| bugman \| 2008-10-14 22:06:17 +0200 (Tue, 14 Oct 2008) \| 5 lines Added a RelaxError to tell the user that the Modelfree4 version being used is buggy. It also tells them that they must upgrade! ........ r7699 \| bugman \| 2008-10-14 22:42:18 +0200 (Tue, 14 Oct 2008) \| 6 lines The relaxation curve time point can now be an integer to allow the time of '0'. See the post at https://mail.gna.org/public/relax-devel/2008-10/msg00040.html (Message-id: <7f080ed10810141213s2211d36fre56906e0ae5903e2@...>). ........ r7700 \| bugman \| 2008-10-14 22:43:20 +0200 (Tue, 14 Oct 2008) \| 3 lines Made sure that the relaxation curve fitting time point is stored as a float. ........ r7701 \| semor \| 2008-10-14 23:33:38 +0200 (Tue, 14 Oct 2008) \| 3 lines Corrected the formatting of a few lines... ........ r7702 \| semor \| 2008-10-15 00:01:04 +0200 (Wed, 15 Oct 2008) \| 5 lines Continued the implementation of the XEasy support system test. Much more work is needed, though. ........ r7703 \| semor \| 2008-10-15 00:20:08 +0200 (Wed, 15 Oct 2008) \| 3 lines Grouped the three peak list support tests into a single one. ........ r7704 \| bugman \| 2008-10-15 00:43:39 +0200 (Wed, 15 Oct 2008) \| 7 lines Modified the Modelfree4 system tests to work with the Portland C compiler Linux version. The modelfree4 Linux binary compiled with Gnu gcc gives different results, sometimes quite large, to the Linux binary compiled with the Portland C compiler. The tests now catch this. There may be problems with the Mac OS X Modelfree4 binary still. ........ r7705 \| semor \| 2008-10-15 04:23:33 +0200 (Wed, 15 Oct 2008) \| 8 lines Placed the setting of the 'H_dim' variable before the call to the intensity_xeasy() function. The 'H_dim' variable was undefined otherwise... This fix may break the handling of peak lists when the w1 and w2 dimensions are inverted. Can these peak lists exist in XEasy ? ........ r7706 \| semor \| 2008-10-15 04:30:55 +0200 (Wed, 15 Oct 2008) \| 6 lines Set the default 'H_dim' variable in the intensity_xeasy() function. Passing the variable to the intensity_xeasy() funciton the way it was done before could not have worked... ........ r7707 \| bugman \| 2008-10-15 17:40:15 +0200 (Wed, 15 Oct 2008) \| 3 lines Replaced all references to 'residue' by 'spin' in the relax_fit.mean_and_error() user fn docstring. ........ r7728 \| semor \| 2008-10-15 23:18:55 +0200 (Wed, 15 Oct 2008) \| 5 lines Passed the 'file_data' variable to the det_dimensions() function and removed some 'self.' instances. The system test for XEasy peak list support now goes further... However, more work is still needed. ........ r7730 \| semor \| 2008-10-16 00:13:40 +0200 (Thu, 16 Oct 2008) \| 3 lines Added a missing 'cdp' definition... ........ r7731 \| semor \| 2008-10-16 00:14:47 +0200 (Thu, 16 Oct 2008) \| 3 lines Added a missing import. ........ r7733 \| semor \| 2008-10-16 00:17:00 +0200 (Thu, 16 Oct 2008) \| 3 lines Changed a normalization force flag to boolean. ........ r7741 \| semor \| 2008-10-16 04:28:28 +0200 (Thu, 16 Oct 2008) \| 9 lines Corrected a name clash. This originates from a post by Edward at: https://mail.gna.org/public/relax-devel/2008-10/msg00060.html (message ID: 7f080ed10810151446p58ab78f1u93cb1bc4afbeb202@...). I hope this fixes the problem... ........ r7742 \| semor \| 2008-10-16 04:32:10 +0200 (Thu, 16 Oct 2008) \| 6 lines Passed more arguments to the det_dimensions() function and removed 'self.' instances. The test for the support of a XEasy peak list now passes, although there still may be some bugs present... ........ r7743 \| semor \| 2008-10-16 05:02:11 +0200 (Thu, 16 Oct 2008) \| 10 lines Added more to the XEasy support test. Now, the test fails when reaching the first residue with a non HN/N assignment. In fact, the reading of this residue is fine, but no intensity is extracted... hence the failure of the test. Now, what do we want to do ? Do we want to support side chain assignments mixed with backbone assignments ? In other words, do we want to support multiuple assignment types in a single analysis ? ........ r7744 \| semor \| 2008-10-16 05:47:31 +0200 (Thu, 16 Oct 2008) \| 3 lines Updated some copyrights. ........ r7784 \| bugman \| 2008-10-16 21:22:02 +0200 (Thu, 16 Oct 2008) \| 7 lines Fix for bug #12456 (https://gna.org/bugs/?12456). When calculating the errors from replicate spectra, the standard deviations of all spins were being averaged rather than the variance. The same error occurred when averaging across spectra - when not all are duplicated, triplicated, etc. ........ r7787 \| semor \| 2008-10-16 22:07:30 +0200 (Thu, 16 Oct 2008) \| 7 lines Set the peak intensity as the default for the reading of NMRView peak list. The volume was being used. Now, the volume can be used with the use of the 'int_col' variable. Moreover, the docstrings are now more complete for the of NMRView peak lists. ........ r7789 \| semor \| 2008-10-16 22:47:52 +0200 (Thu, 16 Oct 2008) \| 3 lines Corrected the passing of the 'int_col' variable to the intensity extraction functions. ........ r7790 \| semor \| 2008-10-16 23:12:10 +0200 (Thu, 16 Oct 2008) \| 7 lines Corrected an argument. This was pointed out by Edward in a post at : https://mail.gna.org/public/relax-devel/2008-10/msg00067.html (message ID: 7f080ed10810161357h418d386bi4d2dd5851d7a4575@...) ........	2008-10-16 21:57:25	Tree
[r7791] by bugman Merged revisions 7739-7790 via svnmerge from svn+ssh://bugman@.../svn/relax/1.3 ........ r7741 \| semor \| 2008-10-16 04:28:28 +0200 (Thu, 16 Oct 2008) \| 9 lines Corrected a name clash. This originates from a post by Edward at: https://mail.gna.org/public/relax-devel/2008-10/msg00060.html (message ID: 7f080ed10810151446p58ab78f1u93cb1bc4afbeb202@...). I hope this fixes the problem... ........ r7742 \| semor \| 2008-10-16 04:32:10 +0200 (Thu, 16 Oct 2008) \| 6 lines Passed more arguments to the det_dimensions() function and removed 'self.' instances. The test for the support of a XEasy peak list now passes, although there still may be some bugs present... ........ r7743 \| semor \| 2008-10-16 05:02:11 +0200 (Thu, 16 Oct 2008) \| 10 lines Added more to the XEasy support test. Now, the test fails when reaching the first residue with a non HN/N assignment. In fact, the reading of this residue is fine, but no intensity is extracted... hence the failure of the test. Now, what do we want to do ? Do we want to support side chain assignments mixed with backbone assignments ? In other words, do we want to support multiuple assignment types in a single analysis ? ........ r7744 \| semor \| 2008-10-16 05:47:31 +0200 (Thu, 16 Oct 2008) \| 3 lines Updated some copyrights. ........ r7784 \| bugman \| 2008-10-16 21:22:02 +0200 (Thu, 16 Oct 2008) \| 7 lines Fix for bug #12456 (https://gna.org/bugs/?12456). When calculating the errors from replicate spectra, the standard deviations of all spins were being averaged rather than the variance. The same error occurred when averaging across spectra - when not all are duplicated, triplicated, etc. ........ r7787 \| semor \| 2008-10-16 22:07:30 +0200 (Thu, 16 Oct 2008) \| 7 lines Set the peak intensity as the default for the reading of NMRView peak list. The volume was being used. Now, the volume can be used with the use of the 'int_col' variable. Moreover, the docstrings are now more complete for the of NMRView peak lists. ........ r7789 \| semor \| 2008-10-16 22:47:52 +0200 (Thu, 16 Oct 2008) \| 3 lines Corrected the passing of the 'int_col' variable to the intensity extraction functions. ........ r7790 \| semor \| 2008-10-16 23:12:10 +0200 (Thu, 16 Oct 2008) \| 7 lines Corrected an argument. This was pointed out by Edward in a post at : https://mail.gna.org/public/relax-devel/2008-10/msg00067.html (message ID: 7f080ed10810161357h418d386bi4d2dd5851d7a4575@...) ........	2008-10-16 21:54:42	Tree
[r7790] by semor Corrected an argument. This was pointed out by Edward in a post at : https://mail.gna.org/public/relax-devel/2008-10/msg00067.html (message ID: 7f080ed10810161357h418d386bi4d2dd5851d7a4575@...)	2008-10-16 21:12:10	Tree
[r7789] by semor Corrected the passing of the 'int_col' variable to the intensity extraction functions.	2008-10-16 20:47:52	Tree
[r7788] by bugman Updated the dependency list for relax 1.3 to include numpy. This was pointed out by Christophe Farès.	2008-10-16 20:30:17	Tree

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