relax version 2.2.1.
Posted by Edward d'Auvergne on February 02, 2013 - 09:36:
This is a quick bugfix release solving a number of issues uncovered
since the release of relax 2.2.0 last week. Upgrading to this newest
version is highly recommended.
The new relax versions can be downloaded from
http://www.nmr-relax.com/download.html. If binary distributions are
not yet available for your platform and you manage to compile the
binary modules, please consider contributing these to the relax
project (described in section 3.6 of the relax manual,
The full list of changes is:
* Replaced a reference to freshmeat with Freecode in the
Release checklist document. Freshmeat no longer exists and is now
called Freecode (http://freecode.com/projects/nmr-relax).
* Created the Mf.test_bug_20464_missing_ri_data system test to
catch bug #20464. The data comes from the bug report submitted by
Stanislava Panova (stpanova att gmail dot com) at
* Created the Structure.test_bug_sr_2998_broken_conect_records
system test. This is to catch the bug reported as service request
#2998 (https://gna.org/support/?2998) and is for corrupted PDB files
with broken CONECT records.
* Created the
Structure.test_bug_20469_scientific_parser_xray_records system test.
This is to catch bug #20469 (https://gna.org/bugs/?20469).
* Created the
Structure.test_bug_20470_alternate_location_indicator system test to
catch bug #20470. This report is at https://gna.org/bugs/?20470.
* 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 Bmrb.test_bug_20471_structure_present to catch
bug #20471 (https://gna.org/bugs/?20471).
* Modified the bmrb.read documentation to make it clearer that
the data pipe must be empty.
* Python 3 fix for a print statement in the metal_pos_opt.py
N-state model system test script.
* Python 3 fix for the part of ScientificPython distributed
with relax (for the PDB parser).
* Python 3 import fixes for the GUI.
* Python 3 fixes for the list sort() method - this has been
replaced by the builtin sorted() function.
* Fix for bug #20464 (https://gna.org/bugs/?20464) - the
model-free analysis failure with missing relaxation data. The problem
was the previously missing data had a value of None whereas now the
dictionary element can be missing. Checks have been added to make
sure the spin specific relaxation data structures have the key
corresponding to the data.
* Fix for the N_state_model.test_monte_carlo_sims system test.
On certain systems, the chi2 check is too stringent.
* Fix for the bug reported as the support request #2998
(https://gna.org/support/?2998). CONECT records pointing to
non-existent atoms can now be handled.
* 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
* 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.
* Fix for bug #20471 (https://gna.org/bugs/?20471) - the
is_empty() AttributeError when reading BMRB files. 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
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, Updated Thu Feb 14 01:40:03 2013