relax SVN archive

Unit test _lib/test_ns_cpmg_2site_expanded.py copied to _/test_lm63.py.

They are both of CPMG type.

Merged revisions 23340 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23340 | bugman | 2014-05-22 17:21:05 +0200 (Thu, 22 May 2014) | 11 lines

Important bug fix for the structure.delete user function when multiple models are present.

This is to fix bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with structure.delete.

The problem is that structure.delete was removing the atoms from the first model but none of the
others. This is because it was using the structural object atom_loop() method to find the atoms to
be deleted, but this method operates on the first model. So when the second model is reached, the
atoms are already gone.
........

Important bug fix for the structure.delete user function when multiple models are present.

This is to fix bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with structure.delete.

The problem is that structure.delete was removing the atoms from the first model but none of the
others. This is because it was using the structural object atom_loop() method to find the atoms to
be deleted, but this method operates on the first model. So when the second model is reached, the
atoms are already gone.

Merged revisions 23336-23337 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23336 | bugman | 2014-05-22 15:39:21 +0200 (Thu, 22 May 2014) | 6 lines

Created the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

This is to catch bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with structure.delete.
........
r23337 | bugman | 2014-05-22 16:09:50 +0200 (Thu, 22 May 2014) | 6 lines

Added some checks to the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

These tests reveal the real problem - that the atoms of the second model have not been removed by
the structure.delete user function.
........

Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'DPL94'.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.

Added some checks to the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

These tests reveal the real problem - that the atoms of the second model have not been removed by
the structure.delete user function.

Created the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

This is to catch bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with structure.delete.

Merged revisions 23327-23329,23331 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23327 | bugman | 2014-05-22 14:05:01 +0200 (Thu, 22 May 2014) | 17 lines

Added 7 unit tests demonstrating edge case 'no Rex' failures of the 'NS CPMG 2-site expanded' model.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.

Such tests should be replicated for all dispersion models.
........
r23328 | bugman | 2014-05-22 14:30:58 +0200 (Thu, 22 May 2014) | 6 lines

Created the Structure.test_bug_22069_structure_delete_helix_attribute system test.

This is to catch bug #22069 (https://gna.org/bugs/index.php?22069), the failure of the
structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'".
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r23329 | bugman | 2014-05-22 14:37:09 +0200 (Thu, 22 May 2014) | 6 lines

Fix for bug #22069 by only deleting helix and sheet data with structure.delete when it exists.

This is bug #22069 (https://gna.org/bugs/index.php?22069), the failure of the structure.delete user
function with "AttributeError: Internal instance has no attribute 'helices'".
........
r23331 | bugman | 2014-05-22 14:52:08 +0200 (Thu, 22 May 2014) | 10 lines

Fix for all edge case 'no Rex' failures of the 'NS CPMG 2-site expanded' model.

This uses the no exchange checking idea, modified to function in the relax trunk, from
http://article.gmane.org/gmane.science.nmr.relax.devel/5847. This is importantly on line 1 of the
function.

The recently introduced set of 7 unit tests (r23327) comprehensively showing these failures now all
pass. This commit is mainly for demonstration purposes.
........

Modified unit tests demonstrating edge case 'no Rex' failures of the model 'NS CPMG 2-site expanded'.

This is to align with the current return of data in the disp_speed branch.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.

Align math-domain catching for model NS CPMG 2-site expanded with trunk implementation.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

The catching of errors have to be more careful.