relax SVN archive

Huge speed up for the superimposition of a large number of structures.

The internal structural object validate_models() method was being called once for each structure
via the selection() method prior performing the translations, and once prior to performing the
rotations, for creating the atomic selection object. This resulted in the _translate() internal
structural object method, which converts all input data to formatted strings, being called hundreds
of millions of times. Therefore selection() method no longer calls validate_models().

This may speed up quite a number of internal structure object methods when large numbers of
structures are present.

Fixes for the Relax_fit.test_inversion_recovery system test.

The wrong equation was used in the calc.py Python script used to calculate the peak intensities in
the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files. The script and Sparky
files have been updated. And the I0 value in the script and system test has been changed from 30 to
-30, so that the curves start as negative.

Bug fix for the inversion recovery equations (sr #3345).

The inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t)
whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).

Fix for bug #24723 (https://gna.org/bugs/?24723).

This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly
calculated - it should be a quadratic mean.

The quadratic mean and quadratic standard deviation are now correctly calculated, and the
structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have
been updated for the fix.

Implemented the per-atom RMSD calculation for the structure.rmsd user function.

Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.

This is for the new option in the structure.rmsd user function.

Addition of the atomic boolean argument to the structure.rmsd user function front end.

This will be used to enable the calculation of per-atom RMSDs.

Small edits for the CHANGES file.

Updated the relax version number to 4.0.2 on the http://www.nmr-relax.com/api/index.html webpage.

Updated the relax API documentation at http://www.nmr-relax.com/api/4.0/ to version 4.0.2.