relax SVN archive

Fixes for the N-state model target functions for the lib.alignment.rdc changes.

The absolute value is now calculated within the target function rather than when back calculating
the RDCs.

Removed the absolute argument for all of the lib.alignment.rdc functions.

This should be performed at the level of the target function, as mathematical operations may be
required prior to taking the absolute value.

Merged revisions 20125-20127 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r20125 | bugman | 2013-06-14 18:05:28 +0200 (Fri, 14 Jun 2013) | 3 lines

Added the j_coupling module to the pipe_control __all__ list.
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r20126 | bugman | 2013-06-14 18:07:44 +0200 (Fri, 14 Jun 2013) | 5 lines

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.
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r20127 | bugman | 2013-06-14 18:12:11 +0200 (Fri, 14 Jun 2013) | 5 lines

Unit test fixes for the N-state model.

This is needed due to the recent package rearrangements.
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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.