[bug #22505] Failure of the structure.create_diff_tensor_pdb user function when no structural data is present. -- August 22, 2014 - 11:14

URL:
  <http://gna.org/bugs/?22505>

                 Summary: Failure of the structure.create_diff_tensor_pdb user
function when no structural data is present.
                 Project: relax
            Submitted by: bugman
            Submitted on: Fri 22 Aug 2014 09:14:43 AM UTC
                Category: relax's source code
Specific analysis category: Model-free analysis
                Priority: 5 - Normal
                Severity: 2 - Minor
                  Status: In Progress
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: 3.2.3
         Discussion Lock: Any
        Operating System: All systems

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Details:

The PDB representation should be created, even if a structure is not present. 
This is now caught by the Structure.test_create_diff_tensor_pdb system test. 
The output of that test is:

$ ./relax -s Structure.test_create_diff_tensor_pdb
Echoing of user function calls has been enabled.


=============================
= System / functional tests =
=============================

E
======================================================================
ERROR: test_create_diff_tensor_pdb
(test_suite.system_tests.structure.Structure)
Test the deletion of non-existent structural data.
----------------------------------------------------------------------

relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)

relax> structure.delete(atom_id=None, verbosity=1, spin_info=True)
No structures are present.
Deleting all spin specific structural info.
Deleting all interatomic vectors.

relax> diffusion_tensor.init(params=(8.5e-09, 1.1, 20.0, 20.0),
time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=2,
spheroid_type=None, fixed=True)
Converting the angles from degrees to radian units.

relax> structure.create_diff_tensor_pdb(scale=1.8e-06, file='prolate.pdb',
dir='/tmp/tmpxe97j1', force=True)
Traceback (most recent call last):
  File "/data/relax/relax-trunk/test_suite/system_tests/structure.py", line
256, in test_create_diff_tensor_pdb
    self.interpreter.structure.create_diff_tensor_pdb(scale=1.8e-06,
file='prolate.pdb', dir=ds.tmpdir, force=True)
  File "/data/relax/relax-trunk/prompt/uf_objects.py", line 223, in __call__
    self._backend(*new_args, **uf_kargs)
  File "/data/relax/relax-trunk/pipe_control/structure/main.py", line 155, in
create_diff_tensor_pdb
    com = pipe_centre_of_mass()
  File "/data/relax/relax-trunk/pipe_control/structure/mass.py", line 48, in
pipe_centre_of_mass
    raise RelaxNoPdbError
RelaxNoPdbError: RelaxError: No PDB file has been loaded.


----------------------------------------------------------------------
Ran 1 test in 0.002s

FAILED (errors=1)




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