relax SVN archive

The stereochemistry auto-analysis can now accept a file of interatomic distances.

This is for better pseudo-atom support.

Updated the value checking for the N_state_model.test_absolute_rdc_menthol system test.

The pseudo-atoms are now properly handled so the result is now much better.

The interatom.unit_vectors user function now calculates the unit vectors for deselected containers.

This is useful for pseudo-atom handling where the interatomic containers to the pseudo-atom members
have already been deselected.

Renamed the interatomic_loop() function 'selected' argument to 'skip_desel'.

This is to match the spin_loop() function arguments.

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).

.....
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.