relax SVN archive

Merged revisions 18349 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
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.
........

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.

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

This report is at https://gna.org/bugs/?20470.

Merged revisions 18346 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18346 | bugman | 2013-02-01 12:42:22 +0100 (Fri, 01 Feb 2013) | 3 lines

Python 3 print statement fixes for the Geometry.Transformation ScientificPython module.
........

Merged revisions 18345 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18345 | bugman | 2013-02-01 12:39:47 +0100 (Fri, 01 Feb 2013) | 17 lines

Python 3 fixes for the newly included Geometry.Transformation ScientificPython module.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
/data/relax/relax-trunk/extern/scientific_python/Geometry/Transformation.py
........

Python 3 print statement fixes for the Geometry.Transformation ScientificPython module.

Python 3 fixes for the newly included Geometry.Transformation ScientificPython module.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
/data/relax/relax-trunk/extern/scientific_python/Geometry/Transformation.py

Merged revisions 18343 via svnmerge from
svn+ssh://bugman@.../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.
........