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* Added a PDB file and RDC values (and absolute J+D and J) for propylene carbonate. This will be used for testing of pseudo-atoms in the N-state model analysis.
* Renamed the propylene carbonate files to the correct name of pyrotartaric anhydride.
* Created two new system tests based on the new pyrotarctic anhydride long range (1J<sup>1</sup>J, 2J <sup>2</sup>J & 3J<sup>3</sup>J) RDC data. The first (N_state_model.test_pyrotartaric_anhydride_rdcs) optimises an alignment tensor using long range signed RDC data. The second (N_state_model.test_pyrotartaric_anhydride_absT) optimises an alignment tensor using long range absolute T (J+D) data. Both test long range data together with methyl group pseudo-atom data.
* Added all of the pyrotartaric anhydride RDC generation scripts and files. This is simply for reference and reproducibility.
* Modifications for the pyrotartaric anhydride system test script. The grid search now is much quicker, and the RDC correlation plots are now sent to DEVNULL.
* 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.
* 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).
* 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 <sup>1</sup>J methyl RDCs. However this approach is not valid for non-methyl pseudo-atoms or for 2J<sup>2</sup>J, 3J<sup>3</sup>J, etc. data.
* 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.
* 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.
* The stereochemistry auto-analysis can now accept a file of interatomic distances. This is for better pseudo-atom support.
* The N-state model specific check_rdcs() function now properly handles pseudo-atoms.
* The pipe_control.rdc.q_factors() function now properly handles pseudo-atoms. If pseudo-atoms are present, then 2Da^2D<sub>a</sub><sup>2</sup>(4 + 3R)/5 normalised Q factor is skipped.
* Created the N_state_model.test_pyrotartaric_anhydride_mix system test. This is used to demonstrate a bug in the N-state analysis using mixed RDC and long range absolute J+D data.
* Movement of N-state model specific code to the analysis neutral pipe_control package. Many of the functions of the specific_analyses.n_state_model.data module relating to alignment tensors, RDC data and PCS data have been shifted in to the pipe_control package modules align_tensor, rdc, and pcs respectively. This allows these functions to be made more general and allow the code to be shared with the frame order analysis or any future analysis using such data, and hence remove some code duplication.