relax SVN archive

Updated the menthol long range RDC data file to include pseudo-atom member distances.

An RDC error of 0.0 will now deselect the corresponding interatomic data container.

This can be used for simpler pseudo-atom handling.

The N_state_model.test_pyrotartaric_anhydride_absT system test now uses simplex optimisation to pass.

The Newton algorithm cannot be used as the gradients for T = J+D type data have not been implemented.

A RelaxError is now raised for the N-state model optimisation with gradients when T = J+D data is used.

The gradients for this data type are not implemented yet, so it is better to prevent the user from
using this.

Reverted r21420 as the spin containers and interatomic data containers should be handled separately.

The command used was:
svn merge -r21420:r21419 .

This is important to allow interatomic containers with good RDC data to be selected while one of the
spin pairs deselected (for example if its PCS data is bad).

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r21420 | bugman | 2013-11-13 14:58:54 +0100 (Wed, 13 Nov 2013) | 3 lines
Changed paths:
M /trunk/pipe_control/interatomic.py

The interatomic loop now skips the element if either of the spin systems are deselected.
.....

Eliminated the old pseudo-atom handling in the N-state model specific return_rdc_data() function.

This was multiplying the RDCs by -3 to handle the tetrahedral geometry of the 1J methyl RDCs.
However this approach is not valid for non-methyl pseudo-atoms or for 2J, 3J, etc. data.

The interatomic loop now skips the element if either of the spin systems are deselected.

Fix for the pyrotartaric_anhydride.py N-state model system test script.

This is used in two system tests. The user function call for reading the inter-spin distances was
instead reading the J couplings as the distance.

J couplings for the N-state analysis are now properly handled for pseudo-atoms.

The measured J couplings for the members of the pseudo-atom should not be used, but rather that of
the pseudo-atom spin itself (as the former does not exist).

Added proper pseudo-atom support for the RDCs in the N-state model analysis.

This involves a number of changes. The pseudo-atom specific functions ave_rdc_tensor_pseudoatom()
and ave_rdc_tensor_pseudoatom_dDij_dAmn() have been added to the lib.alignment.rdc module. These
simply average the values from the equivalent non-pseudo-atom functions. The return_rdc_data()
function in the specific_analyses.n_state_model.data module has been modified to assemble the RDC
constants and unit vectors for all members of the pseudo-atom and add these to the returned
structures, as well as a new list of flags specifying if the interatom pair contains pseudo-atoms.
The N-state model target function and gradient have been updated to send the pseudo-atom data to the
new lib.alignment.rdc module functions.