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→Bugfixes: Copied the bugfix list from the CHANGES file.
<section begin=bugfixes/>
* Big bug fix for the N-state model num_data_points() function. This is from the specific_analyses.n_state_model.data module. This code was very much out of date. It was expecting an ancient behaviour where the spin container 'pcs' variable and interatomic data container 'rdc' where lists of floats. However these were converted many years ago to dictionaries with keys set to the alignment IDs. The result was that no RDCs nor PCSs were counted as a base data point, so the function would in most cases return a value of zero.
* Fixes for the printout from the pipe_control.pcs.return_pcs_data() function. The number of PCSs printed out was including values of None when data was missing for one alignment. These values of None are no longer counted.
* Fixes for the printout from the pipe_control.rdc.return_rdc_data() function. The number of RDCs printed out was including values of None when data was missing for one alignment. These values of None are no longer counted.
* More fixes for the RDC and PCS count printouts from the corresponding data assembly functions. Sometimes the RDC or PCS value could be present as None. This is now detected and the count is not incremented.
* More fixes for the PCS count printout from the pipe_control.pcs.return_pcs_data() function. The check for None values was incorrect.
* Fixes for the N-state model num_data_points() function. The deselected interatomic data containers are no longer used for counting RDC data. And the skipping of deselected spin containers for the PCS is now via the spin_loop() skip_desel argument.
* Fix for bug #23259 (https://gna.org/bugs/?23259). This is the broken user functions in the prompt UI with the RelaxError: The user function 'X' has been renamed to 'Y'. The problem was that the only the first part of the user function name, for example 'minimise' from 'minimise.calculate' was being checked in the user function name translation table. As the minimise user function has been renamed to minimise.execute, 'minimise' is in the translation table and hence minimise.calculate was being identified as the minimise user function. Now the full user function name is reconstructed before checking the translation table.
* Fixes for the lib.structure.internal.coordinates.assemble_coord_array() function. The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The function can now handle no data being passed in.
* Fixes for the pipe_control.structure.main.assemble_structural_coordinates() function. The function will now raise a RelaxError if no structural data matching the atom ID can be found. The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The fix affects the structure.atomic_fluctuations, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose, and structure.web_of_motion user functions.
* Fix for bug #23265 (https://gna.org/bugs/?23265). This is the failure of the edit buttons in the user function GUI windows. The problem was that the column titles of the window opened by the edit button were being incorrectly handled if the dimensions of the window were not supplied.
* Fix for bug #23288 (https://gna.org/bugs/?23288). This is the failure of the structure.read_pdb user function when simultaneously merging multiple molecules from one file. The set_mol_name and set_model_num arguments are now converted to lists equal to the length of the read_mol and read_model arguments simultaneously, if supplied.
* Small fix for the structure.write_pdb user function for handling old relax state and results files.
* Fix for bug #23293 (https://gna.org/bugs/?23293). This is the PDB HETATM loading error whereby the last HETATM record is sometimes not read from the PDB file. The problem was two-fold. Firstly the internal structural object _parse_mols_pdb() method for separating a PDB file into distinct molecules was terminating too early when a new molecule is found, so that the last PDB record is not appended to the records list for the molecule. Secondly the write_pdb() method was not handling the PDB sequential serial number correctly.
* Fix for bug #23294 (https://gna.org/bugs/?23294). This is the automatic merging of PDB molecules resulting in an IndexError. Now if only a single molecule name is supplied, this will be used for all molecules in the PDB file. The result is that the structural data will all be automatically merged into a single molecule. This merging is communicated to the user via the current printouts.
* Bug fix for the SHEET PDB records created by the structure.write_pdb user function. The current and previous atom parts of the record were not being correctly formatted. This was simply using the %4s formatting string. However the PDB atom format is rather more complicated. To handle this, the new _handle_atom_name() helper function has been added to the lib.structure.pdb_write module. This is now used in the atom() and sheet() functions for consistently formatting the atom name field.
* Fix for bug #23295 (https://gna.org/bugs/?23295). This is the PDB secondary structure HELIX and SHEET records not updating when merging molecules. The problem was that the algorithm for changing the molecule numbers for the helix and sheet metadata when calling the structure.read_pdb user function was far too simplistic. Therefore the logic has been completely rewritten. Now the helix and sheet metadata are stored in temporary data structures in the _parse_pdb_ss() method. As the molecules are being read from the PDB records, new data structures containing the original molecule numbers and new molecule numbers are created. The helix and sheet metadata is then stored in the internal structural object via the pack_structs() method, and the molecule indices of the metadata changed based on the two molecule number remapping data structures.
* Python 3 fix for the new internal structural object MolContainer._sort() method. The list() builtin function is required to convert the output of the range() function into a true list in Python 3, so that the list.sort() method can be accessed.
* Python 3 fix for the Test_msa.test_central_star unit test. This is from the _lib._sequence_alignment.test_msa unit test module. The logic of range() + range() does not work in Python 3, so the range function calls are now wrapped in list() function calls to convert to the correct data structure type.
* Python 3 fix for the internal structural object MolContainer._sort_key() method. This method is used as the key for the sort() function. However in Python 3, the key cannot be None. So now if the residue number is None, the value of 0 is returned instead.
* Python 3 fix for the pipe_control.structure.main.assemble_structural_coordinates() function. This affects most of the structure user functions. This was another case of requiring the list() built in function to create a list object from an iterator.
* Another Python 3 list() fix for the structure user functions. This time the problem was in the pipe_control.structure.main.sequence_alignment() function.
* Fix for a RelaxError message from the internal structural object when validating models.
* Bug fix for the results.write user function when loading relax state files. The results.write user function can load not only the results file consisting of a single data pipe, but also relax state files if only a single pipe is present. However this was causing the current data pipe and other pipe-independent data (sequence alignments and the GUI) to be overwritten, just as when loading a state file. Now only the data from the data pipe will be loaded and the pipe independent data in the state file will be ignored.
* Fix for the rdc.write user function. The check for the missing rdc_data_types variable in the interatomic containers is now more comprehensive and checks for the presence of the alignment ID.
* Big bug fix for the pipe_control.interatomic.interatomic_loop() function. This was identified in the Rdc.test_rdc_copy_different_spins system test. The problem was that the pipe argument was being ignored when looking up the spin containers. Hence if the pipe being worked on was not the current data pipe, and the spin sequences were not identical, the function would fail. This mainly affects the rdc.copy user function.
* Fix for the pcs.read user function. The problem was caught by the new Pcs.test_pcs_copy_different_spins system test. If the spin system does not exist in the current data pipe, but data for it is present in the PCS file, the pcs.read user function would terminate in a TypeError.
* Fixes for the rdc.calc_q_factors user function for when no alignment tensor is present. This was caught by the Rdc.test_calc_q_factors_no_tensor system test. Now if no tensor is present, a warning is given and the 2Da^2(4 + 3R)/5 normalised Q factor is skipped. Also, if present but no spin isotope information is present, then RelaxSpinTypeError errors are raised.
* Fix for the pcs.corr_plot user function when the spin containers have no element information.
* Fix for bug #23372 (https://gna.org/bugs/?23372), the sequence.read failure with CSV files. The problem was that the sep argument was not being passed all the way to the backend lib.io.extract_data() function.
* Fix for the lib.sequence.check_sequence checking object. Although rarely used, the check for the spin number was incorrect and half of the checks were instead for the residue number. This is a classic copy and paste error where the residue name and number checks were copied but not completely converted to spin name and numbers.
<section end=bugfixes/>
