Re: latex script on final results -- November 10, 2008 - 03:51

Right, it's opening the file now and procuding a .tex file as well, but 
there is
still this output:

RelaxWarning: The structure file 'PDB_file.pdb' cannot be found in the current
directory or the directory of the results file.

Which seems odd because I have a copy of this PDB file in the same 
directory as
the script and in the directory with the results.bz2 file, just in case. Also,
what is the normal way to view a .tex file like this one?

Tyler


Quoting Douglas Kojetin <douglas.kojetin@xxxxxxxxx>:

> Are you certain your RESULTS variable points towards 'final/ 
> results.bz2'?  The output from your job below differs vs. mine, in  
> particular these lines in the output:
>
> relax> results.read(file='final/results.bz2', dir=None)
> Opening the file 'final/results.bz2' for reading.
>
> Perhaps you should attach the input script text as well as the output  text?
>
> Doug
>
>
> On Nov 9, 2008, at 5:45 PM, Tyler Reddy wrote:
>
> > It looks like both problems were already fixed in my script, so it  must be
> > something else?
> >
> >
> > Quoting Douglas Kojetin <douglas.kojetin@xxxxxxxxx>:
> >
> > > I made the following changes to the distributed latex_mf_table.py   
> > > file, and it seemed to work OK.
> > >
> > > % diff updated_latex_mf_table.py old_latex_mf_table.py
> > > 42c42
> > > < RESULTS_FILE = 'final/results.bz2'
> > > ---
> > > > RESULTS_FILE = 'final'
> > > 171c171
> > > <         for spin, spin_id in spin_loop(return_id=True):
> > > ---
> > > >         for spin, spin_id in spin_loop(return_id=True)
> > >
> > > I think your error might be caused by the change on line 42, but  
> > > an  error will popup for the change on line 171 (the for statement  
> > > is  missing a semi-colon ).
> > >
> > > Doug
> > >
> > >
> > >
> > > On Nov 9, 2008, at 7:55 AM, Tyler Reddy wrote:
> > >
> > > > Hi,
> > > >
> > > > My model-free results from the full analysis python script have   
> > > > converged and
> > > > the 'final' run is complete. I moved the latex table script into  
> > > > the  'final'
> > > > directory, but when I execute the script I get the output below.  
> > > > I  think Edward
> > > > mentioned this script might need some work. Has anyone used it   
> > > > successfully?
> > > >
> > > > Tyler
> > > >
> > > > Output:
> > > >
> > > > Latex()
> > > > ----------------------------------------------------------------------------------------------------
> > > >
> > > > relax> pipe.create(pipe_name='results', pipe_type='mf')
> > > >
> > > > relax> results.read(file='results', dir=None)
> > > > Opening the file 'results' for reading.
> > > > Traceback (most recent call last):
> > > > File "/Applications/relax-1.3.1/relax-1.3/relax", line 422, in   <module>
> > > >   Relax()
> > > > File "/Applications/relax-1.3.1/relax-1.3/relax", line 131, in   __init__
> > > >   self.interpreter.run(self.script_file)
> > > > File "/Applications/relax-1.3.1/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 "/Applications/relax-1.3.1/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 "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py",  
> > > >  line 427, in
> > > > interact_script
> > > >   execfile(script_file, local)
> > > > File "latex_mf_table.py", line 220, in <module>
> > > >   Latex()
> > > > File "latex_mf_table.py", line 53, in __init__
> > > >   results.read(RESULTS_FILE, dir=None)
> > > > File "/Applications/relax-1.3.1/relax-1.3/prompt/results.py",  
> > > > line  99, in read
> > > >   results.read(file=file, directory=dir)
> > > > File "/Applications/relax-1.3.1/relax-1.3/generic_fns/ 
> > > > results.py",  line 98, in
> > > > read
> > > >   read_function = ds.from_xml(file, dir=directory)
> > > > File "/Applications/relax-1.3.1/relax-1.3/data/__init__.py", line  
> > > >  185, in
> > > > from_xml
> > > >   self[self.instance.current_pipe].from_xml(relax_node, dir=dir)
> > > > File "/Applications/relax-1.3.1/relax-1.3/data/ 
> > > > pipe_container.py",  line 164,
> > > > in from_xml
> > > >   self.structure.from_xml(str_nodes[0], dir=dir)
> > > > File "/Applications/relax-1.3.1/relax-1.3/generic_fns/structure/  
> > > > api_base.py",
> > > > line 276, in from_xml
> > > >   loaded = self.load_pdb(file_path=dir + sep + self.file[i],   model=None,
> > > > struct_index=i)
> > > > TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
> > > >
> > > >
> > > >
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