relax SVN archive

Merged revisions 26379 via svnmerge from
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r26379 | bugman | 2014-10-23 14:17:31 +0200 (Thu, 23 Oct 2014) | 8 lines

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.
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Merged revisions 26379 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26379 | bugman | 2014-10-23 14:17:31 +0200 (Thu, 23 Oct 2014) | 8 lines

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.
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Fix for the structure.delete user function for molecule metadata once no more data exists.

This relates to 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 metadata, when it exists, is now deleted for the molecule once no more data is present.

Small modification of the Structure.test_bug_22861_PDB_writing_chainID_fail system test.

File metadata is now being set to demonstrate that the structure.delete user function does not
remove this once there is no more data left for the molecule.

The structure.write_pdb user function can now handle empty molecules.

This fixes 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.

To handle this consistently, the internal structural object ModelContainer.mol_loop() generator
method has been created. This loops over the molecules, yielding those that are not empty. The
MolContainer.is_empty() method has been fixed by not checking for the molecule name, as that remains
after the structure.delete user function call while all other information has been removed. And
finally the write_pdb() structural object method has been modified to use the mol_loop() method
rather than performing the loop itself.

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.
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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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