[bug #23294] Automatic merging of PDB molecules results in an IndexError. -- February 20, 2015 - 09:21

URL:
  <http://gna.org/bugs/?23294>

                 Summary: Automatic merging of PDB molecules results in an
IndexError.
                 Project: relax
            Submitted by: bugman
            Submitted on: Fri 20 Feb 2015 08:21:01 AM UTC
                Category: relax's source code
Specific analysis category: All analyses
                Priority: 3 - Low
                Severity: 2 - Minor
                  Status: None
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: 3.3.6
         Discussion Lock: Any
        Operating System: All systems

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Details:

When reading a PDB file using the structure.read_pdb user function
<http://www.nmr-relax.com/manual/structure_read_pdb.html> and multiple
molecules are present (i.e. multiple chain IDs) and only one molecule name is
given, the following error is seen:

Internal relax PDB parser.
Opening the file 'in.pdb' for reading.
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 199, in run
    self.interpreter.run(self.script_file)
  File "/data/relax/relax-trunk/prompt/interpreter.py", line 279, 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 585, 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 484, in
interact_script
    exec_script(script_file, local)
  File "/data/relax/relax-trunk/prompt/interpreter.py", line 363, 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/debugging/bug_x_multi_mol_automerge/test.py", line 3, in
<module>
    structure.read_pdb('in.pdb', read_model=1, set_mol_name='merged mol')
  File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__
    self._backend(*new_args, **uf_kargs)
  File "/data/relax/relax-trunk/pipe_control/structure/main.py", line 1099, in
read_pdb
    cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num,
alt_loc=alt_loc, verbosity=verbosity, merge=merge)
  File "/data/relax/relax-trunk/lib/structure/internal/object.py", line 2085,
in load_pdb
    new_mol_name.append(set_mol_name[mol_index])
IndexError: list index out of range


This should not happen!  Instead either a RelaxError should be raised to point
out the problem, or the molecules should be automatically merged.  The
attached minimal 'in.pdb' structure and 'test.py' relax script demonstrate
this problem.



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File Attachments:


-------------------------------------------------------
Date: Fri 20 Feb 2015 08:21:01 AM UTC  Name: in.pdb  Size: 652B   By: bugman

<http://gna.org/bugs/download.php?file_id=23873>
-------------------------------------------------------
Date: Fri 20 Feb 2015 08:21:01 AM UTC  Name: test.py  Size: 172B   By: bugman

<http://gna.org/bugs/download.php?file_id=23874>

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