Re: r11347 - /branches/bieri_gui/auto_analyses/relax_fit.py -- July 27, 2010 - 09:29

Hi,

For this change, you have hardcoded the loading of @N spins - this is
not acceptable.  To fix this, please add the 'load_spin_ids=None'
argument to the function and then have the GUI pass in the correct
spin name.

Cheers,

Edward


On 27 July 2010 03:46,  <michael.bieri@xxxxxxxxxxxxx> wrote:
> Author: michaelbieri
> Date: Tue Jul 27 03:46:13 2010
> New Revision: 11347
>
> URL: http://svn.gna.org/viewcvs/relax?rev=11347&view=rev
> Log:
> Sequence can be read from PDB 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=11347&r1=11346&r2=11347&view=diff
> ==============================================================================
> --- branches/bieri_gui/auto_analyses/relax_fit.py (original)
> +++ branches/bieri_gui/auto_analyses/relax_fit.py Tue Jul 27 03:46:13 2010
> @@ -29,7 +29,7 @@
>
>
>  class Relax_fit:
> -    def __init__(self, filename='rx', pipe_name='rx', seq_args=None, 
> file_names=None, relax_times=None, view_plots=True, int_method='height', 
> mc_num=500):
> +    def __init__(self, filename='rx', pipe_name='rx', seq_args=None, 
> file_names=None, relax_times=None, pdb_file=None, view_plots=True, 
> int_method='height', mc_num=500):
>         """Perform relaxation curve fitting.
>
>         @keyword filename:      Name of the output file.
> @@ -42,6 +42,8 @@
>         @type file_names:       list of str
>         @keyword relax_times:   The list of relaxation times corresponding 
> to file_names.  These two lists must be of the same size.
>         @type relax_times:      list of float
> +        @keyword pdb_file:      Name of the PDB file.
> +        @type pdb_file:         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'.
> @@ -56,6 +58,7 @@
>         self.seq_args = seq_args
>         self.file_names = file_names
>         self.relax_times = relax_times
> +        self.pdb_file = pdb_file
>         self.view_plots = view_plots
>         self.int_method = int_method
>         self.mc_num = mc_num
> @@ -79,7 +82,12 @@
>         self.interpreter.pipe.create(self.pipe_name, 'relax_fit')
>
>         # Load the sequence.
> -        self.interpreter.sequence.read(file=self.seq_args[0], 
> dir=self.seq_args[1], mol_name_col=self.seq_args[2], 
> res_num_col=self.seq_args[3], res_name_col=self.seq_args[4], 
> spin_num_col=self.seq_args[5], spin_name_col=self.seq_args[6], 
> sep=self.seq_args[7])
> +        if self.pdb_file:   # load PDB File
> +            self.interpreter.structure.read_pdb(self.pdb_file)
> +            generic_fns.structure.main.load_spins(spin_id='@N')
> +
> +        else:
> +            self.interpreter.sequence.read(file=self.seq_args[0], 
> dir=self.seq_args[1], mol_name_col=self.seq_args[2], 
> res_num_col=self.seq_args[3], res_name_col=self.seq_args[4], 
> spin_num_col=self.seq_args[5], spin_name_col=self.seq_args[6], 
> sep=self.seq_args[7])
>
>         # Loop over the spectra.
>         for i in xrange(len(self.file_names)):
>
>
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