Re: r11116 - /branches/bieri_gui/gui_bieri/analyses/auto_model_free.py -- April 27, 2010 - 19:27

Hi Michael,

Actually, now that I think about it, in the future some of these
settings will have to remain as global settings.  For the next
iteration we can set up the auto-analyses to accept a data pipe as
input.  All the set up user functions can then be called directly by
the GUI to allow for maximal flexibility in reading structures, data,
values, etc.  This will allow the tree view of molecules, residues,
and spins to be set up.  The auto-analyses can then copy the data they
require from that GUI-analysis specific data pipe.  Only the
minimisation and later user functions will not be called by the GUI
(results.write(), state.save(), value.write(), etc. can be
exceptions.) so can be passed in as variables.  I think this type of
design, where each GUI analysis frame has its own GUI specific data
pipe which is filled up by the user interacting with the GUI and then
passed to the auto-analyses would be the most powerful design.

This design will also significantly improve the prompt/scripting UI as
well as then the user can do many non-standard things to the data pipe
they create and manipulate before sending it into the auto-analysis.
This would allow RNA people to use the 'full_analysis.py' script for
their analyses.  So I may implement this in the auto-analyses before
it reaches the GUI!

Regards,

Edward



On 22 April 2010 06:33,  <michael.bieri@xxxxxxxxxxxxx> wrote:
> Author: michaelbieri
> Date: Thu Apr 22 06:33:56 2010
> New Revision: 11116
>
> URL: http://svn.gna.org/viewcvs/relax?rev=11116&view=rev
> Log:
> Global relaxGUI parameters are used for model-free analysis.
>
> Imported parameters:
> - hetero nucleus
> - proton
> - increment size
> - min algor
> - number of Monte Carlo simulations
>
> Modified:
>    branches/bieri_gui/gui_bieri/analyses/auto_model_free.py
>
> Modified: branches/bieri_gui/gui_bieri/analyses/auto_model_free.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py?rev=11116&r1=11115&r2=11116&view=diff
> ==============================================================================
> --- branches/bieri_gui/gui_bieri/analyses/auto_model_free.py (original)
> +++ branches/bieri_gui/gui_bieri/analyses/auto_model_free.py Thu Apr 22 
> 06:33:56 2010
> @@ -520,8 +520,27 @@
>         # The sequence data (file name, dir, mol_name_col, res_num_col, 
> res_name_col, spin_num_col, spin_name_col, sep).  These are the arguments 
> to the  sequence.read() user function, for more information please see the 
> documentation for that function.
>         data.seq_args = [ds.relax_gui.sequencefile, None, None, 1, None, 
> None, None, None]
>
> -        # The heteronucleus atom name corresponding to that of the PDB 
> file (used if the spin name is not in the sequence data).
> -        data.het_name = ds.relax_gui.global_setting[2]
> +        # Import golbal settings.
> +        global_settings = ds.relax_gui.global_setting
> +
> +        # Hetero nucleus name.
> +        data.hetnuc = global_settings[2]
> +
> +        # Proton name.
> +        data.proton = global_settings[3]
> +
> +        # Increment size.
> +        data.inc = int(global_settings[4])
> +
> +        # The optimisation technique.
> +        data.min_algor = global_settings[5]
> +
> +        # The number of Monte Carlo simulations to be used for error 
> analysis at the end of the analysis.
> +        data.mc_num = int(global_settings[6])
> +
> +        # The bond length, CSA values.
> +        data.bond_length = 1.02 * 1e-10
> +        data.csa = -172 * 1e-6
>
>         # The relaxation data (data type, frequency label, frequency, file 
> name, dir, mol_name_col, res_num_col, res_name_col, spin_num_col, 
> spin_name_col, data_col, error_col, sep).  These are the arguments to the 
> relax_data.read() user function, please see the documentation for that 
> function for more information.
>         data.relax_data = []
> @@ -546,21 +565,6 @@
>
>         # A file containing a list of spins which can be dynamically 
> excluded at any point within the analysis (when set to None, this variable 
> is not used).
>         data.exclude = None
> -
> -        # The bond length, CSA values, heteronucleus type, and proton type.
> -        data.bond_length = 1.02 * 1e-10
> -        data.csa = -172 * 1e-6
> -        data.hetnuc = '15N'
> -        data.proton = '1H'
> -
> -        # The grid search size (the number of increments per dimension).
> -        data.grid_inc = 11
> -
> -        # The optimisation technique.
> -        data.min_algor = 'newton'
> -
> -        # The number of Monte Carlo simulations to be used for error 
> analysis at the end of the analysis.
> -        data.mc_num = 500
>
>         # Automatic looping over all rounds until convergence (must be a 
> boolean value of True or False).
>         data.conv_loop = True
>
>
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