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* Fixes for the Frame_order.test_generate_rotor2_distribution system test. The test_suite/shared_data/frame_order/cam/generate_base.py script now saves the program state files into the self.save_path directory, preventing the system test from attempting to save files into the relax test suite directories.
* Another fix for the Frame_order.test_generate_rotor2_distribution system test. The test_suite/shared_data/frame_order/cam/generate_base.py script no longer prints its progress indicator to sys.__stderr__ but to sys.stderr instead. This avoids the progress text from appearing during the relax test suite execution.
* Created the Structure.test_bug_21522_master_record_atom_count system test. This is designed to catch bug #21522 ([https://gna.org/bugs/?21522)bug #21522, the structure.write_pdb user function creating an incorrect MASTER record]. This hence also catches bug #21520 ([https://gna.org/bugs/?21520)bug #21520, the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present]. The test simply creates two structural models, adds one atom, and writes out a PDB file, checking its contents.
* The structure.write_pdb user function can now handle a file instance for the file argument. This is for the Structure.test_bug_21522_master_record_atom_count system test, to allow a dummy file object to be used. This can also be useful for power users.
* Created the lib.geometry.vectors.unit_vector_from_2point() function. This is used to quickly calculate the unit vector between two points.
* The behaviour of the rdc.write user function has been changed to output spin ID strings in single quotes. This is to avoid problems with the '#' molecule identifier and the '#' comment character.
* Fix for the diffusion_tensor.init user function reference in the intro chapter of the manual. This was using a very old and now non-functional syntax.
* Created the Diffusion_tensor.test_bug_21561_tensor_pdb_failure system test. This is to catch bug #21561 ([https://gna.org/bugs/?21561)bug #21561], as reported by Martin Ballaschk ([https://gna.org/users/mab)Martin Ballaschk]. This catches the failure of the structure.create_diff_tensor_pdb user function for non-spherical diffusion tensors when no Monte Carlo simulations are present.* Added the truncated data for creating a system test to catch bug #21562. This bug ([https://gna.org/bugs/?21562) bug #21562]. This bug was reported by Dhanas Muthu ([https://gna.org/users/dhanas) Dhanas Muthu] and is the failure of the NOE analysis when spectra are replicated. This consists of the Sparky peak lists attached to the bug report and the modified 2AT7 PDB file. The data has been truncated to only include residues :12, :13, and :14.
* Shifted the NOE system test script into the new 'noe' directory.
* Created the Noe.test_bug_21562_noe_replicate_fail system test. This is to catch bug #21562 ([https://gna.org/bugs/?21562)bug #21562], reported by Dhanas Muthu ([https://gna.org/users/dhanas)Dhanas Muthu]. This is the failure of the NOE analysis when spectra are replicated. This uses the truncated data taken from the files attached to the bug report. The NOE output file is checked to see if the contents are correct.
* Better support for replicated spectra in the NOE analysis. The saturated and reference peak intensity and error are now properly averaged. Previously averaging was not used as the number of replicates N are cancelled in the ratios used for the NOE and error calculation. However this fails when the number of replicates for the saturated spectrum does not match the number of replicates for the reference spectrum. Now any data combination is possible.
* Another fix for the NOE analysis for when replicated spectra have been collected. Variance averaging rather than error averaging is now used for the peak intensity errors. This is important if the errors for each replicated spectra are different - a case which is rarely encountered as the replicates are almost always used to determine one error for all the replicates.
== Bugfixes ==
* Fix for bug #21499 ([https://gna.org/bugs/?21499)bug #21499, the failure of the rdc.write user function]. The rdc.write user function fails for back-calculated RDC data. The fix was to handle the missing interatom.rdc_data_types variable.* Fix for bug #21522 ([https://gna.org/bugs/?21522) and bug #21520 (21522, the structure.write_pdb user function creating an incorrect MASTER record] and [https://gna.org/bugs/?21520). These bugs are the structure.write_pdb user function creating an incorrect MASTER record and bug #21520, the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present]. The counts for the ATOM, HETATM, and TER records are now only for a single model, rather than being the sum for all models together.* Fix for [https://gna.org/bugs/?21561 bug #21561, the structure.create_diff_tensor_pdb user function failure with no simulations]. Bug #21561 (https://gna.org/bugs/?21561) This was reported by Martin Ballaschk ([https://gna.org/users/mab)Martin Ballaschk]. The problem was that the simulation axes of the tensor PDB file were not being initialised correctly when no Monte Carlo simulations had been run.* Fix for [https://gna.org/bugs/?21562 bug #21562, the failure of the NOE analysis when spectra are replicated]. This bug (https://gna.org/bugs/?21562) was reported by Dhanas Muthu ([https://gna.org/users/dhanas)Dhanas Muthu]. The problem was that the NOE overfit_deselect() method was deselecting all spins which do not have exactly 2 intensity values. This is incompatible with replicated spectra as the number will be greater than two. The check has been modified to deselect spins only when the number of intensity values are zero or one.
