[bug #22069] Failure of the structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'". -- May 22, 2014 - 14:25

URL:
  <http://gna.org/bugs/?22069>

                 Summary: Failure of the structure.delete user function with
"AttributeError: Internal instance has no attribute 'helices'".
                 Project: relax
            Submitted by: bugman
            Submitted on: Thu 22 May 2014 12:25:24 PM UTC
                Category: relax's source code
Specific analysis category: None
                Priority: 5 - Normal
                Severity: 3 - Normal
                  Status: None
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: 3.2.0
         Discussion Lock: Any
        Operating System: All systems

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Details:

The following user function calls, when running relax in the prompt UI mode
from the base directory, will cause the failure:

pipe.create('structure.delete fail', 'N-state')
structure.read_pdb('1J7P_1st_NH_rot.pdb',
dir='test_suite/shared_data/frame_order/cam/')
structure.delete(atom_id='@CA')

The error is:

relax> structure.delete(atom_id='@CA', verbosity=1, spin_info=True)
Deleting structural data from the current pipe.
Traceback (most recent call last):
  File "/data/relax/relax-trunk/multi/processor.py", line 494, in run
    self.callback.init_master(self)
  File "/data/relax/relax-trunk/multi/__init__.py", line 318, in
default_init_master
    self.master.run()
  File "/data/relax/relax-trunk/relax.py", line 194, in run
    self.interpreter.run(self.script_file)
  File "/data/relax/relax-trunk/prompt/interpreter.py", line 275, in run
    return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
  File "/data/relax/relax-trunk/prompt/interpreter.py", line 569, in
run_script
    return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/data/relax/relax-trunk/prompt/interpreter.py", line 468, in
interact_script
    exec_script(script_file, local)
  File "/data/relax/relax-trunk/prompt/interpreter.py", line 347, in
exec_script
    runpy.run_module(module, globals)
  File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
    fname, loader, pkg_name)
  File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/data/relax/relax-trunk/fail.py", line 10, in <module>
    structure.delete(atom_id='@CA')
  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 314, in
delete
    cdp.structure.delete(atom_id=atom_id, verbosity=verbosity)
  File "/data/relax/relax-trunk/lib/structure/internal/object.py", line 1583,
in delete
    for i in range(len(self.helices)):
AttributeError: Internal instance has no attribute 'helices'




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