relax SVN archive

Fix for the Structure.test_pdb_combined_secondary_structure system test.

The SHEET PDB record check was incorrect and was checking for the improperly formatted atom name
field, which has now been fixed in relax.

Bug fix for the SHEET PDB records created by the structure.write_pdb user function.

The current and previous atom parts of the record were not being correctly formatted. This was
simply using the %4s formatting string. However the PDB atom format is rather more complicated. To
handle this, the new _handle_atom_name() helper function has been added to the
lib.structure.pdb_write module. This is now used in the atom() and sheet() functions for
consistently formatting the atom name field.

Fix for the Structure.test_bug_23295_ss_metadata_merge system test and additional printouts.

Added one more check to the Structure.test_bug_23295_ss_metadata_merge system test.

The test would pass if no HELIX or SHEET records were to be written to the PDB file.

Merged revisions 27695 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27695 | bugman | 2015-02-20 11:49:51 +0100 (Fri, 20 Feb 2015) | 8 lines

Created the Structure.test_bug_23295_ss_metadata_merge system test.

This is to catch bug #23295 (https://gna.org/bugs/?23295), the PDB secondary structure HELIX and
SHEET records not updated when merging molecules. This uses the '2BE6_secondary_structure.pdb'
structure file and 'test.py' relax script contents as the test, checking the HELIX and SHEET
records.
........

Merged revisions 27695 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27695 | bugman | 2015-02-20 11:49:51 +0100 (Fri, 20 Feb 2015) | 8 lines

Created the Structure.test_bug_23295_ss_metadata_merge system test.

This is to catch bug #23295 (https://gna.org/bugs/?23295), the PDB secondary structure HELIX and
SHEET records not updated when merging molecules. This uses the '2BE6_secondary_structure.pdb'
structure file and 'test.py' relax script contents as the test, checking the HELIX and SHEET
records.
........

Created the Structure.test_bug_23295_ss_metadata_merge system test.

This is to catch bug #23295 (https://gna.org/bugs/?23295), the PDB secondary structure HELIX and
SHEET records not updated when merging molecules. This uses the '2BE6_secondary_structure.pdb'
structure file and 'test.py' relax script contents as the test, checking the HELIX and SHEET
records.

Merged revisions 27690-27692 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27690 | bugman | 2015-02-20 10:07:31 +0100 (Fri, 20 Feb 2015) | 7 lines

Improved the RelaxWarning for missing atom numbers in the PDB CONECT records.

This is for the structure.read_pdb user function. Now only one warning is given for the entire PDB
file listing all of the missing atom numbers rather than one warning per missing atom. This can
significantly compact the warnings, removing a lot of repetition.
........
r27691 | bugman | 2015-02-20 10:23:44 +0100 (Fri, 20 Feb 2015) | 8 lines

Improved the quality of the printouts from the structure.read_pdb user function.

This also affects the structure.read_gaussian and structure.read_xyz user functions. The messages
about adding new molecules or merging with existing molecules has been significantly improved. The
text with the model information is now only printed if the model number is present in the PDB file
or has been supplied by the user.
........
r27692 | bugman | 2015-02-20 11:26:56 +0100 (Fri, 20 Feb 2015) | 10 lines

Fixes for all of the PDB documentation HTML links in the docstrings.

The PDB have shifted their documentation from http://www.wwpdb.org/documentation/format33/v3.3.html
to http://www.wwpdb.org/documentation/file-format/format33/v3.3.html, stupidly without redirects.
This will create dead links in the relax API documentation at http://www.nmr-relax.com/api/3.3/, as
well as the older API documentation (http://www.nmr-relax.com/api/2.2/,
http://www.nmr-relax.com/api/3.0/, http://www.nmr-relax.com/api/3.1/,
http://www.nmr-relax.com/api/3.2/).
........

Merged revisions 27690-27692 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27690 | bugman | 2015-02-20 10:07:31 +0100 (Fri, 20 Feb 2015) | 7 lines

Improved the RelaxWarning for missing atom numbers in the PDB CONECT records.

This is for the structure.read_pdb user function. Now only one warning is given for the entire PDB
file listing all of the missing atom numbers rather than one warning per missing atom. This can
significantly compact the warnings, removing a lot of repetition.
........
r27691 | bugman | 2015-02-20 10:23:44 +0100 (Fri, 20 Feb 2015) | 8 lines

Improved the quality of the printouts from the structure.read_pdb user function.

This also affects the structure.read_gaussian and structure.read_xyz user functions. The messages
about adding new molecules or merging with existing molecules has been significantly improved. The
text with the model information is now only printed if the model number is present in the PDB file
or has been supplied by the user.
........
r27692 | bugman | 2015-02-20 11:26:56 +0100 (Fri, 20 Feb 2015) | 10 lines

Fixes for all of the PDB documentation HTML links in the docstrings.

The PDB have shifted their documentation from http://www.wwpdb.org/documentation/format33/v3.3.html
to http://www.wwpdb.org/documentation/file-format/format33/v3.3.html, stupidly without redirects.
This will create dead links in the relax API documentation at http://www.nmr-relax.com/api/3.3/, as
well as the older API documentation (http://www.nmr-relax.com/api/2.2/,
http://www.nmr-relax.com/api/3.0/, http://www.nmr-relax.com/api/3.1/,
http://www.nmr-relax.com/api/3.2/).
........

Fixes for all of the PDB documentation HTML links in the docstrings.

The PDB have shifted their documentation from http://www.wwpdb.org/documentation/format33/v3.3.html
to http://www.wwpdb.org/documentation/file-format/format33/v3.3.html, stupidly without redirects.
This will create dead links in the relax API documentation at http://www.nmr-relax.com/api/3.3/, as
well as the older API documentation (http://www.nmr-relax.com/api/2.2/,
http://www.nmr-relax.com/api/3.0/, http://www.nmr-relax.com/api/3.1/,
http://www.nmr-relax.com/api/3.2/).