relax SVN archive

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.

Created the Structure.test_atomic_fluctuations_no_match system test.

This demonstrates a failure in the operation of the structure.atomic_fluctuations user function when
the supplied atom ID matches no atoms.

Merged revisions 27614 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27614 | bugman | 2015-02-10 12:54:17 +0100 (Tue, 10 Feb 2015) | 8 lines

Huge speed up of the internal structural object validate_models() method.

The string formatting to create pseudo-PDB records and the large number of calls to the _translate()
method for atomic information string formatting has been shifted to only be called when atomic
information does not match. Instead the structural information is directly compared within a large
if-else statement.
........

Huge speed up of the internal structural object validate_models() method.

The string formatting to create pseudo-PDB records and the large number of calls to the _translate()
method for atomic information string formatting has been shifted to only be called when atomic
information does not match. Instead the structural information is directly compared within a large
if-else statement.

Merged revisions 27612 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27612 | bugman | 2015-02-10 12:05:01 +0100 (Tue, 10 Feb 2015) | 10 lines

Huge speed up for the assembly of atomic coordinates from a large number of structures.

The internal structural object validate_models() method was being called once for each structure
when assembling the atomic coordinates. This resulted in the _translate() internal structural
object method, which converts all input data to formatted strings, being called hundreds of millions
of times. The problem was in lib.structure.internal.coordinates.assemble_atomic_coordinates(), in
that the one_letter_codes() method, which calls validate_models(), was called for each molecule
encountered. The solution was not to validate models in one_letter_codes().
........

Huge speed up for the assembly of atomic coordinates from a large number of structures.

The internal structural object validate_models() method was being called once for each structure
when assembling the atomic coordinates. This resulted in the _translate() internal structural
object method, which converts all input data to formatted strings, being called hundreds of millions
of times. The problem was in lib.structure.internal.coordinates.assemble_atomic_coordinates(), in
that the one_letter_codes() method, which calls validate_models(), was called for each molecule
encountered. The solution was not to validate models in one_letter_codes().

Bug fix for the frame order specific analysis API base_data_loop() method.

This was looping over non-existent PCS and RDC data. Now the alignment ID is checked for in the
interatomic data container 'rdc' data structure and the spin container 'pcs' data structure, as well
as values of None, before yielding the data.

Implemented the frame order analysis backend for the statistics.model and statistics.aic user functions.

This simply required aliasing the specific analysis API common _get_model_container_cdp() method to
get_model_container().

Modified the frame order system test check_chi2() method to test the statistics.model user function.

This causes all of the Frame_order.test_cam_* system tests to fail, as the user function backend is
not implemented for the frame order analysis.

Merged revisions 27606 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27606 | bugman | 2015-02-09 10:50:36 +0100 (Mon, 09 Feb 2015) | 10 lines

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.
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