Re: r11353 - /branches/bieri_gui/auto_analyses/relax_fit.py -- July 27, 2010 - 09:53

Hi,

This change is confusing, why did you switch from
self.interpreter.deselect.read() to selection.desel_read() and add a
print statement.  This is not necessary at all, the
self.interpreter.deselect.read() user function provides all that is
needed.  The print statement should not be there.  If I rename
deselect.read() to select.load(), allowing for the deselection in the
args, then this print statement will be wrong!  As it is not in the
standard place for the printouts from the user functions, this print
statement will probably not be changed.

I would suggest (i.e. this needs to be done) not hardcoding that the
residue number is in column 1.  This prevents me from working with
multi-spin per residue systems, or systems with no residues.  This was
no problem in the script, as the user could modify the script for
their system.  But now that it is an auto-analysis, this is no longer
the case.  Therefore for the deselection, an argument like that for
seq_args can be used where the argument is a fixed list of (file name,
dir, mol_name_col, res_num_col, res_name_col, spin_num_col,
spin_name_col, sep).  It would be best if you do this so that the
change does not break the GUI ;)

Cheers,

Edward


On 27 July 2010 04:19,  <michael.bieri@xxxxxxxxxxxxx> wrote:
> Author: michaelbieri
> Date: Tue Jul 27 04:19:00 2010
> New Revision: 11353
>
> URL: http://svn.gna.org/viewcvs/relax?rev=11353&view=rev
> Log:
> File containing unresolved residues can be a relax dummy file.
>
> Modified:
>    branches/bieri_gui/auto_analyses/relax_fit.py
>
> Modified: branches/bieri_gui/auto_analyses/relax_fit.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/relax_fit.py?rev=11353&r1=11352&r2=11353&view=diff
> ==============================================================================
> --- branches/bieri_gui/auto_analyses/relax_fit.py (original)
> +++ branches/bieri_gui/auto_analyses/relax_fit.py Tue Jul 27 04:19:00 2010
> @@ -25,12 +25,13 @@
>
>  # relax module imports.
>  import generic_fns.structure.main
> +from generic_fns import selection
>  from prompt.interpreter import Interpreter
>
>
>
>  class Relax_fit:
> -    def __init__(self, filename='rx', pipe_name='rx', results_directory = 
> None, seq_args=None, file_names=None, relax_times=None, pdb_file=None, 
> view_plots=True, int_method='height', heteronuc = 'N', proton = 'H', 
> mc_num=500, inc = '11'):
> +    def __init__(self, filename='rx', pipe_name='rx', results_directory = 
> None, seq_args=None, file_names=None, relax_times=None, pdb_file=None, 
> unresolved='unresolved', view_plots=True, int_method='height', heteronuc = 
> 'N', proton = 'H', mc_num=500, inc = '11'):
>         """Perform relaxation curve fitting.
>
>         @keyword filename:      Name of the output file.
> @@ -47,6 +48,8 @@
>         @type relax_times:      list of float
>         @keyword pdb_file:      Name of the PDB file.
>         @type pdb_file:         str
> +        @keyword unresolved:    Filename of the unresolved spin list.
> +        @type unresolved:       str
>         @keyword view_plots:    Flag to automatically viu grace plots after 
> calculation.
>         @type view_plots:       boolean
>         @keyword int_method:    The integration method, one of 'height', 
> 'point sum' or 'other'.
> @@ -73,6 +76,7 @@
>         self.file_names = file_names
>         self.relax_times = relax_times
>         self.pdb_file = pdb_file
> +        self.unresolved = unresolved
>         self.view_plots = view_plots
>         self.int_method = int_method
>         self.heteronuc = heteronuc
> @@ -125,7 +129,8 @@
>         self.interpreter.spectrum.error_analysis()
>
>         # Deselect unresolved spins.
> -        self.interpreter.deselect.read(file=self.unresolved)
> +        selection.desel_read(file=self.unresolved, dir=None, 
> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, 
> spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, 
> boolean='AND', change_all=None)
> +        print 'relax> deselect.read(selected residues)'
>
>         # Set the relaxation curve type.
>         self.interpreter.relax_fit.select_model('exp')
>
>
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