[bug #12409] Failure of the final stage of the 'full_analysis.py' script. -- October 05, 2008 - 13:09

URL:
  <http://gna.org/bugs/?12409>

                 Summary: Failure of the final stage of the
'full_analysis.py' script.
                 Project: relax
            Submitted by: bugman
            Submitted on: Sunday 10/05/2008 at 11:09
                Category: relax's source code
                Severity: 4 - Important
                Priority: 7 - High
                  Status: None
                 Privacy: Public
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: 1.3.1
        Operating System: All systems

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Details:

When attempting the 'final' stage, an error occurs when loading the PDB file
upon reading of the results file.  The error message is:

relax> results.read(file='results', dir='prolate/round_6/opt')
Opening the file 'prolate/round_6/opt/results.bz2' for reading.
Traceback (most recent call last):
  File "/media/disk/relax/relax-1.3/relax", line 408, in <module>
    Relax()
  File "/media/disk/relax/relax-1.3/relax", line 125, in __init__
    self.interpreter.run(self.script_file)
  File "/media/disk/relax/relax-1.3/prompt/interpreter.py", line 270, in run
    return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
  File "/media/disk/relax/relax-1.3/prompt/interpreter.py", line 531, in
run_script
    return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/media/disk/relax/relax-1.3/prompt/interpreter.py", line 427, in
interact_script
    execfile(script_file, local)
  File "full_analysis_final.py", line 642, in <module>
    Main(self.relax)
  File "full_analysis_final.py", line 325, in __init__
    results.read(file='results', dir=model + '/round_' + `self.round` +
'/opt')
  File "/media/disk/relax/relax-1.3/prompt/results.py", line 102, in read
    results.read(file=file, directory=dir)
  File "/media/disk/relax/relax-1.3/generic_fns/results.py", line 114, in
read
    read_function = ds.from_xml(file, dir=directory)
  File "/media/disk/relax/relax-1.3/data/__init__.py", line 185, in from_xml
    self[self.current_pipe].from_xml(relax_node, dir=dir)
  File "/media/disk/relax/relax-1.3/data/pipe_container.py", line 164, in
from_xml
    self.structure.from_xml(str_nodes[0], dir=dir)
  File "/media/disk/relax/relax-1.3/generic_fns/structure/api_base.py", line
269, in from_xml
    loaded = self.load_pdb(file_path=self.file[i], model=None,
struct_index=i)
  File "/media/disk/relax/relax-1.3/generic_fns/structure/scientific.py",
line 561, in load_pdb
    self.add_struct(name=name, model=model, file=file, path=path,
str=data_pipe.structure.structural_data[i], struct_index=struct_index)
IndexError: list index out of range


This problem has also been caught by the new test_load_scientific_results()
system test.  Its output when failing is:

======================================================================
FAIL: Load the PDB file using the information in a results file (using the
Scientific python structural object).
----------------------------------------------------------------------

relax> pipe.create(pipe_name='mf', pipe_type='mf')

relax> results.read(file='str_scientific',
dir='/data/relax/relax-1.3/test_suite/shared_data/structures')
Opening the file
'/data/relax/relax-1.3/test_suite/shared_data/structures/str_scientific.bz2'
for reading.
RelaxWarning: The structure file 'Ap4Aase_res1-12.pdb' cannot be found in the
current directory or the directory of the results file.
Traceback (most recent call last):
  File "/data/relax/relax-1.3/test_suite/system_tests/structure.py", line
113, in test_load_scientific_results
    self.assert_(len(cdp.structure.structural_data))
AssertionError

----------------------------------------------------------------------


This is specific to the Scientific python structural object and doesn't
affect the alternative internal structural object.




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