relax - Bugs: bug #20469, Failure in reading X-ray PDB files... [Gna!]

relax - Bugs: bug #20469, Failure in reading X-ray PDB files...

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bug #20469: Failure in reading X-ray PDB files using the ScientificPython parser.

Submitted by:	Edward d Auvergne <bugman>
Submitted on:	Fri 01 Feb 2013 10:53:32 AM UTC

Category:	relax's source code	Severity:	2 - Minor
Priority:	3 - Low	Status:	Fixed
Privacy:	Public	Assigned to:	Edward d Auvergne <bugman>
Originator Name:		Open/Closed:	Closed
Release:	2.2.0	Operating System:	All systems

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Fri 01 Feb 2013 11:37:48 AM UTC, SVN revision 18344: Merged revisions 18343 via svnmerge from svn+ssh://bugman@svn.gna.org/svn/relax/trunk ........ r18343 \| bugman \| 2013-02-01 12:37:16 +0100 (Fri, 01 Feb 2013) \| 7 lines Fix for bug #20469 (https://gna.org/bugs/?20469). This is the Failure in reading X-ray PDB files using the ScientificPython parser. The ScientificPython Geometry.Transformation module is now distributed with relax. Some linear algebra imports in the Geometry.TensorModule in newly used code paths have been fixed as well. ........ (Browse SVN revision 18344)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 11:37:16 AM UTC, SVN revision 18343: Fix for bug #20469 (https://gna.org/bugs/?20469). This is the Failure in reading X-ray PDB files using the ScientificPython parser. The ScientificPython Geometry.Transformation module is now distributed with relax. Some linear algebra imports in the Geometry.TensorModule in newly used code paths have been fixed as well. (Browse SVN revision 18343)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 10:56:42 AM UTC, SVN revision 18342: Merged revisions 18341 via svnmerge from svn+ssh://bugman@svn.gna.org/svn/relax/trunk ........ r18341 \| bugman \| 2013-02-01 11:56:06 +0100 (Fri, 01 Feb 2013) \| 5 lines Created the Structure.test_bug_20469_scientific_parser_xray_records system test. This is to catch bug #20469 (https://gna.org/bugs/?20469). ........ (Browse SVN revision 18342)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 10:56:06 AM UTC, SVN revision 18341: Created the Structure.test_bug_20469_scientific_parser_xray_records system test. This is to catch bug #20469 (https://gna.org/bugs/?20469). (Browse SVN revision 18341)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 10:53:32 AM UTC, original submission: The presence of PDB crystallographic unit cell records triggers the following bug: Scientific Python PDB parser. Traceback (most recent call last): File "test_suite/system_tests/structure.py", line 63, in test_bug_sr_2998_broken_conect_records self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path, parser='scientific') File "prompt/uf_objects.py", line 219, in _call_ self._backend(new_args, uf_kargs) File "generic_fns/structure/main.py", line 504, in read_pdb cdp.structure.load_pdb(file_path, read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num, verbosity=verbosity) File "generic_fns/structure/scientific.py", line 602, in load_pdb model = PDB.Structure(file_path, model_num) File "extern/scientific_python/IO/PDB.py", line 1160, in _init_* self.parseFile(PDBFile(file_or_filename)) File "extern/scientific_python/IO/PDB.py", line 1381, in parseFile from extern.scientific_python.Geometry.Transformation \ ImportError: No module named Transformation	Edward d Auvergne <bugman>

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Date	Changed By	Updated Field	Previous Value	=>	Replaced By
Fri 01 Feb 2013 11:42:54 AM UTC	bugman	Status	None		Fixed
		Open/Closed	Open		Closed

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