bugrelax - 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 codeSpecific analysis category: None
Priority: 3 - LowSeverity: 2 - Minor
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.2.0Operating 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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.

 

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    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Fri 01 Feb 2013 11:42:54 AM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
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