relax SVN archive

Fix for bug #20471 (https://gna.org/bugs/?20471).

The problem was that the data pipe is_empty() method was not handling structural data correctly.
The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the
object cdp.structure is not always present.

Created the Bmrb.test_bug_20471_structure_present to catch bug #20471 (https://gna.org/bugs/?20471).

Merged revisions 18355-18356 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18355 | bugman | 2013-02-01 15:55:17 +0100 (Fri, 01 Feb 2013) | 3 lines

Removed a debugging print out.
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r18356 | bugman | 2013-02-01 15:59:02 +0100 (Fri, 01 Feb 2013) | 7 lines

Fix for the Mf.test_bug_20213_asn_sidechain system test.

The file test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb contains
alternate location indicators! Therefore the structure.read_pdb user function call requires the
alt_loc argument.
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Fix for the Mf.test_bug_20213_asn_sidechain system test.

The file test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb contains
alternate location indicators! Therefore the structure.read_pdb user function call requires the
alt_loc argument.

Removed a debugging print out.

Merged revisions 18350-18352 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18350 | bugman | 2013-02-01 15:23:45 +0100 (Fri, 01 Feb 2013) | 6 lines

Created the Structure.test_alt_loc_missing system test.

This is to test that the internal relax PDB reader raises an error when a PDB file is encountered
with alternate location indicators but the alt_loc argument has not been specified.
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r18351 | bugman | 2013-02-01 15:27:36 +0100 (Fri, 01 Feb 2013) | 7 lines

Fix for bug #20470 (https://gna.org/bugs/?20470).

The structure.read_pdb user function now accepts the alt_loc argument for specifying the alternate
location indicator to read. This is used by the internal PDB reader. The bug was caught by the
Structure.test_bug_20470_alternate_location_indicator system test.
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r18352 | bugman | 2013-02-01 15:37:30 +0100 (Fri, 01 Feb 2013) | 5 lines

Fix for the checking of the alternate location indicator in the internal PDB reader.

These checks now only occur for the ATOM and HETATM records.
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Merged revisions 18349 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18349 | bugman | 2013-02-01 13:08:27 +0100 (Fri, 01 Feb 2013) | 5 lines

Created the Structure.test_bug_20470_alternate_location_indicator system test to catch bug #20470.

This report is at https://gna.org/bugs/?20470.
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Fix for the checking of the alternate location indicator in the internal PDB reader.

These checks now only occur for the ATOM and HETATM records.

Fix for bug #20470 (https://gna.org/bugs/?20470).

The structure.read_pdb user function now accepts the alt_loc argument for specifying the alternate
location indicator to read. This is used by the internal PDB reader. The bug was caught by the
Structure.test_bug_20470_alternate_location_indicator system test.

Created the Structure.test_alt_loc_missing system test.

This is to test that the internal relax PDB reader raises an error when a PDB file is encountered
with alternate location indicators but the alt_loc argument has not been specified.