relax SVN archive

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.

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.

Merged revisions 27687 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27687 | bugman | 2015-02-20 09:35:07 +0100 (Fri, 20 Feb 2015) | 8 lines

Fix for bug #23294 (https://gna.org/bugs/?23294).

This is the automatic merging of PDB molecules resulting in an IndexError. Now if only a single
molecule name is supplied, this will be used for all molecules in the PDB file. The result is that
the structural data will all be automatically merged into a single molecule. This merging is
communicated to the user via the current printouts.
........

Merged revisions 27687 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27687 | bugman | 2015-02-20 09:35:07 +0100 (Fri, 20 Feb 2015) | 8 lines

Fix for bug #23294 (https://gna.org/bugs/?23294).

This is the automatic merging of PDB molecules resulting in an IndexError. Now if only a single
molecule name is supplied, this will be used for all molecules in the PDB file. The result is that
the structural data will all be automatically merged into a single molecule. This merging is
communicated to the user via the current printouts.
........

Fix for bug #23294 (https://gna.org/bugs/?23294).

This is the automatic merging of PDB molecules resulting in an IndexError. Now if only a single
molecule name is supplied, this will be used for all molecules in the PDB file. The result is that
the structural data will all be automatically merged into a single molecule. This merging is
communicated to the user via the current printouts.

Merged revisions 27683-27684 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27683 | bugman | 2015-02-20 09:31:15 +0100 (Fri, 20 Feb 2015) | 3 lines

Added the PDB file to the repository for the Structure.test_bug_23294_multi_mol_automerge system test.
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r27684 | bugman | 2015-02-20 09:32:09 +0100 (Fri, 20 Feb 2015) | 6 lines

Fix for the Structure.test_bug_23294_multi_mol_automerge system test.

The MASTER PDB record has been added to the data to check for, as this will be produced by the
structure.write_pdb user function.
........

Merged revisions 27683-27684 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27683 | bugman | 2015-02-20 09:31:15 +0100 (Fri, 20 Feb 2015) | 3 lines

Added the PDB file to the repository for the Structure.test_bug_23294_multi_mol_automerge system test.
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r27684 | bugman | 2015-02-20 09:32:09 +0100 (Fri, 20 Feb 2015) | 6 lines

Fix for the Structure.test_bug_23294_multi_mol_automerge system test.

The MASTER PDB record has been added to the data to check for, as this will be produced by the
structure.write_pdb user function.
........

Fix for the Structure.test_bug_23294_multi_mol_automerge system test.

The MASTER PDB record has been added to the data to check for, as this will be produced by the
structure.write_pdb user function.

Added the PDB file to the repository for the Structure.test_bug_23294_multi_mol_automerge system test.

Merged revisions 27680 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27680 | bugman | 2015-02-20 09:26:57 +0100 (Fri, 20 Feb 2015) | 9 lines

Created the Structure.test_bug_23294_multi_mol_automerge system test.

This is used to catch bug #2329 (https://gna.org/bugs/?23294), the automatic merging of PDB
molecules resulting in an IndexError. It reads in the 'in.pdb' PDB file attached to the bug report,
now named 'bug_23294_multi_mol_automerge.pdb', to show the IndexError. The test also checks the
structure.write_pdb user function to make sure that the output PDB file contains a single merged
molecule.
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