relax SVN archive

Created the Structure.test_bug_22861_PDB_writing_chainID_fail system test.

This is to catch bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.

The mol_name argument is now exposed in the structure.add_atom user function.

This has been added as the first argument of the user function to allow new molecules to be created
or to allow the atom to be placed into a specific molecule container. The functionality was already
implemented in the backend, so it has been exposed by simply adding a new argument definition to the
user function.

Merged revisions 26374 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26374 | bugman | 2014-10-23 12:01:49 +0200 (Thu, 23 Oct 2014) | 7 lines

Fix for the structure.com user function.

This fixes bug #22860 (https://gna.org/bugs/?22860), the failure of the structure.com user function
after calling structure.delete. The number of models in cdp.structure is now counted and if set to
zero, RelaxNoPdbError will be raised.
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Merged revisions 26374 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26374 | bugman | 2014-10-23 12:01:49 +0200 (Thu, 23 Oct 2014) | 7 lines

Fix for the structure.com user function.

This fixes bug #22860 (https://gna.org/bugs/?22860), the failure of the structure.com user function
after calling structure.delete. The number of models in cdp.structure is now counted and if set to
zero, RelaxNoPdbError will be raised.
........

Merged revisions 26373 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26373 | bugman | 2014-10-23 12:00:29 +0200 (Thu, 23 Oct 2014) | 6 lines

Modified the Structure.test_bug_22860_CoM_after_deletion system test to expect a RelaxNoPdbError.

This tests that the structure.com user function raises RelaxNoPdbError after deleting all of the
structural information from the current data pipe.
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Merged revisions 26373 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26373 | bugman | 2014-10-23 12:00:29 +0200 (Thu, 23 Oct 2014) | 6 lines

Modified the Structure.test_bug_22860_CoM_after_deletion system test to expect a RelaxNoPdbError.

This tests that the structure.com user function raises RelaxNoPdbError after deleting all of the
structural information from the current data pipe.
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Fix for the structure.com user function.

This fixes bug #22860 (https://gna.org/bugs/?22860), the failure of the structure.com user function
after calling structure.delete. The number of models in cdp.structure is now counted and if set to
zero, RelaxNoPdbError will be raised.

Modified the Structure.test_bug_22860_CoM_after_deletion system test to expect a RelaxNoPdbError.

This tests that the structure.com user function raises RelaxNoPdbError after deleting all of the
structural information from the current data pipe.

Merged revisions 26367-26368 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26367 | bugman | 2014-10-23 11:52:13 +0200 (Thu, 23 Oct 2014) | 5 lines

Fix for the checks in the new Structure.test_load_spins_multi_mol system test.

A spin index was incorrect.
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r26368 | bugman | 2014-10-23 11:54:27 +0200 (Thu, 23 Oct 2014) | 8 lines

Fix for the structure.load_spins user function when the from_mols argument is used.

The load_spins_multi_mol() function of the pipe_control.structure.main module was incorrectly
handling the atomic position returned by the internal structural object atom_loop() method. This
position is a list of lists when multiple models are present. But when only a single model is
present, it returns a simple list.
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Merged revisions 26367-26368 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26367 | bugman | 2014-10-23 11:52:13 +0200 (Thu, 23 Oct 2014) | 5 lines

Fix for the checks in the new Structure.test_load_spins_multi_mol system test.

A spin index was incorrect.
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r26368 | bugman | 2014-10-23 11:54:27 +0200 (Thu, 23 Oct 2014) | 8 lines

Fix for the structure.load_spins user function when the from_mols argument is used.

The load_spins_multi_mol() function of the pipe_control.structure.main module was incorrectly
handling the atomic position returned by the internal structural object atom_loop() method. This
position is a list of lists when multiple models are present. But when only a single model is
present, it returns a simple list.
........