relax SVN archive

Unit test fixes for the N-state model.

This is needed due to the recent package rearrangements.

Fix for the pipe_control.rdc.q_factors() for T = J+D type data.

The Q factor normalisation was incorrect, as the J coupling should be subtracted from T first.

Added the j_coupling module to the pipe_control __all__ list.

Merged revisions 20123 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r20123 | bugman | 2013-06-14 17:37:05 +0200 (Fri, 14 Jun 2013) | 3 lines

Another fix similar to that of r20120, this time for the _minimise_setup_rdcs() method.
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Another fix similar to that of r20120, this time for the _minimise_setup_rdcs() method.

Merged revisions 20111-20121 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r20111 | bugman | 2013-06-14 10:48:59 +0200 (Fri, 14 Jun 2013) | 3 lines

Removed some now irrelevant information from the rdc.read user function docstring.
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r20112 | bugman | 2013-06-14 10:52:12 +0200 (Fri, 14 Jun 2013) | 3 lines

Removed a false prompt example from the rdc.read user function docstring.
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r20113 | bugman | 2013-06-14 11:22:07 +0200 (Fri, 14 Jun 2013) | 6 lines

Created an entire new user function class for handling J couplings in the relax data store.

This derives from the RDC user function modules. The following functions have been created:
j_coupling.copy, j_coupling.delete, j_coupling.display, j_coupling.read, and j_coupling.write.
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r20114 | bugman | 2013-06-14 11:39:19 +0200 (Fri, 14 Jun 2013) | 3 lines

Added a check for the RDC data type to the rdc.read user function.
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r20115 | bugman | 2013-06-14 11:44:55 +0200 (Fri, 14 Jun 2013) | 5 lines

The rdc.read user function can now handle T = J+D type data.

Support for this in the specific analyses is yet to be added.
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r20116 | bugman | 2013-06-14 13:44:25 +0200 (Fri, 14 Jun 2013) | 6 lines

Fixed for the rdc.read, j_coupling.read and interatomic.read_dist user functions.

Comment lines are no longer removed, as it is impossible to tell a comment line from a spin ID
string.
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r20117 | bugman | 2013-06-14 13:50:30 +0200 (Fri, 14 Jun 2013) | 6 lines

Split up the specific_analyses.n_state_model package into modules.

The new data and parameter modules have been created by shifting out method from the __init__ module
and converting them into functions of the two new modules. This is to simplify the package.
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r20118 | bugman | 2013-06-14 13:54:21 +0200 (Fri, 14 Jun 2013) | 3 lines

Shifted another method from the N_state_model class to the specific_analyses.n_state_model.data module.
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r20119 | bugman | 2013-06-14 16:00:46 +0200 (Fri, 14 Jun 2013) | 7 lines

Added support for the T = J+D RDC data type to the N-state model target function.

The J couplings are sent into the target function class when the 'T' RDC data type is encountered.
These measured values are then added to the back-calculated RDC values to produced T(theta) which
is then compared to T via the chi-squared function.
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r20120 | bugman | 2013-06-14 16:54:48 +0200 (Fri, 14 Jun 2013) | 5 lines

Fix for the new specific_analyses.n_state_model.data.opt_uses_j_couplings() function.

The cdp.rdc_data_types appears not to have all alignments IDs within it.
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r20121 | bugman | 2013-06-14 16:55:53 +0200 (Fri, 14 Jun 2013) | 6 lines

Removed the check for Numeric Python in the dep_check module.

This Python module not been used within relax for the better part of a decade. This check is not
needed.
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Removed the check for Numeric Python in the dep_check module.

This Python module not been used within relax for the better part of a decade. This check is not
needed.

Fix for the new specific_analyses.n_state_model.data.opt_uses_j_couplings() function.

The cdp.rdc_data_types appears not to have all alignments IDs within it.

Added support for the T = J+D RDC data type to the N-state model target function.

The J couplings are sent into the target function class when the 'T' RDC data type is encountered.
These measured values are then added to the back-calculated RDC values to produced T(theta) which
is then compared to T via the chi-squared function.

Shifted another method from the N_state_model class to the specific_analyses.n_state_model.data module.