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Commit Date  
[r26328] by bugman

Modified the N_state_model.test_populations system test to test the grid search code paths.

This performs a grid search of one increment after minimisation, then switches to the 'fixed'
N-state model and performs a second grid search of one increment. This now tests currently untested
code paths in the grid_search() API method behind the minimise.grid_search user function. The test
demonstrates a bug in the N-state model which was not uncovered in the test suite.

2014-10-21 15:03:49 Tree
[r26327] by bugman

Implemented the multiple molecule merging functionality of the structure.load_spins user function.

The argument has been added to the user function frontend and a description added for this new
functionality. In the backend, the pipe_control.structure.main.load_spins() function will now call
the load_spins_multi_mol() function if from_mols is supplied. This alternative function is required
to handle missing atoms and differential atom numbering.

2014-10-21 13:58:31 Tree
[r26326] by bugman

Fixes for the Structure.test_load_spins_multi_mol system test.

The call to the structure.load_spins user function has also been modified so that all 3 spins are
loaded at the same time.

2014-10-21 13:55:05 Tree
[r26325] by bugman

Created the Structure.test_load_spins_multi_mol system test.

This is to test yet to be implemented functionality of the structure.load_spins user function. This
is the loading of spin information similar, but not necessarily identical molecules all loaded into
the same structural model. For this, the from_mols argument will be added.

2014-10-21 12:43:36 Tree
[r26324] by bugman

Modified the internal structural object backend for the structure.read_pdb user function.

The MolContainer._det_pdb_element() method for handling PDB files with missing element information
has been updated to use the Periodic_table.has_element() method to check if the PDB atom name
corresponds to any atoms in the periodic table. This allows for far greater support for HETATOMS
and all of the metals.

2014-10-21 12:17:49 Tree
[r26323] by bugman

Added 4 unit tests to the _lib.test_periodic_table module for the Periodic_table.has_element() method.

2014-10-21 11:57:05 Tree
[r26322] by bugman

Created the Periodic_table.has_element() method for the lib.periodic_table module.

This is used to simply check if a given symbol exists as an atom in the periodic table.

2014-10-21 11:52:10 Tree
[r26321] by bugman

Bug fix for the structure.align user function for when no data pipes are supplied.

2014-10-21 06:58:14 Tree
[r26320] by bugman

The compression level for results files can now be set in the frame order auto-analysis.

This is via the new argument results_compress_type, which is used to set the compress_type argument
of the results.write user function. The results reading parts of the auto-analysis have been
updated to allow uncompressed, bzip2 compressed, and gzip compressed files to be handled.

2014-10-20 14:45:49 Tree
[r26319] by bugman

The intermediate results are no longer stored in the Frame_order.test_auto_analysis system test.

This drops the test timing on one system from ~190 seconds to ~50 seconds.

2014-10-20 14:24:11 Tree
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