relax SVN archive

Merged revisions 18546 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18546 | bugman | 2013-02-20 18:58:14 +0100 (Wed, 20 Feb 2013) | 5 lines

Epydoc docstring formatting for the generic_fns.structure.pdb_write modules.

These large changes improve the API documentation at http://www.nmr-relax.com/api/.
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Fix for the frame order specific _target_fn_setup() method.

The problem was recently introduced at r18436. Now the checks for missing PCS and RDC data should
function correctly.

Fix for the structure.rmsd user function for the frame order testing branch.

The code needs to be slightly modified to work with this branch.

Epydoc docstring formatting for the generic_fns.structure.pdb_write modules.

These large changes improve the API documentation at http://www.nmr-relax.com/api/.

Merged revisions 18542-18544 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18542 | bugman | 2013-02-20 17:05:25 +0100 (Wed, 20 Feb 2013) | 6 lines

The diffusion tensor PDB files are now conform better to the PDB standard.

The HET records are now correct, only capitalised text is present in the files, and trailing
whitespace to character 80 has been added.
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r18543 | bugman | 2013-02-20 17:17:53 +0100 (Wed, 20 Feb 2013) | 5 lines

Fix for the generic_fns.structure.pdb_write.ter() function.

Whitespace to character 80 is now being added to the TER PDB records.
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r18544 | bugman | 2013-02-20 17:20:17 +0100 (Wed, 20 Feb 2013) | 6 lines

Fix for the creation of the FORMUL PDB records by the internal structural object.

The component number is now set to the index of the hetrogen plus one. This number should have been
a sequential number starting at 1 and is not related to the residue number in any way.
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Fix for the creation of the FORMUL PDB records by the internal structural object.

The component number is now set to the index of the hetrogen plus one. This number should have been
a sequential number starting at 1 and is not related to the residue number in any way.

Fix for the generic_fns.structure.pdb_write.ter() function.

Whitespace to character 80 is now being added to the TER PDB records.

The diffusion tensor PDB files are now conform better to the PDB standard.

The HET records are now correct, only capitalised text is present in the files, and trailing
whitespace to character 80 has been added.

Merged revisions 18533-18540 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18533 | bugman | 2013-02-20 15:52:00 +0100 (Wed, 20 Feb 2013) | 3 lines

Docstring edits for the generic_fns.structure.pdb_* module unit tests.
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r18534 | bugman | 2013-02-20 16:01:07 +0100 (Wed, 20 Feb 2013) | 3 lines

Created a unit test for the generic_fns.structure.pdb_write.het() function.
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r18535 | bugman | 2013-02-20 16:02:44 +0100 (Wed, 20 Feb 2013) | 5 lines

Fix for the generic_fns.structure.pdb_write.helix() function.

The single character PDB record formatting should be %1s, not %s.
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r18536 | bugman | 2013-02-20 16:05:20 +0100 (Wed, 20 Feb 2013) | 5 lines

Fix for the generic_fns.structure.pdb_write.het() function - the record now has trailing whitespace.

The PDB records require trailing whitespace to the 80th character position.
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r18537 | bugman | 2013-02-20 16:23:04 +0100 (Wed, 20 Feb 2013) | 3 lines

Docstring whitespace fixes for the generic_fns.structure.pdb_* modules.
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r18538 | bugman | 2013-02-20 16:40:01 +0100 (Wed, 20 Feb 2013) | 6 lines

Created the generic_fns.structure.pdb_write._handle_text() function.

This private function is used to convert text into PDB suitable format (uppercase and values of None
converted to empty strings).
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r18539 | bugman | 2013-02-20 16:43:29 +0100 (Wed, 20 Feb 2013) | 5 lines

Fixes for many of the generic_fns.structure.pdb_write functions.

The PDB records are now all filled with whitespace up to the 80th character.
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r18540 | bugman | 2013-02-20 16:44:27 +0100 (Wed, 20 Feb 2013) | 5 lines

Fix for the creation of HET PDB records in the internal structural object.

The residue name and chain ID were mixed up.
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Fix for the creation of HET PDB records in the internal structural object.

The residue name and chain ID were mixed up.