Author: bugman
Date: Thu Jan 28 14:16:24 2010
New Revision: 10514
URL: http://svn.gna.org/viewcvs/relax?rev=10514&view=rev
Log:
The object returned by assemble_data() is now a dictionary.
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=10514&r1=10513&r2=10514&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/analyses/auto_model_free.py (original)
+++ branches/bieri_gui/gui_bieri/analyses/auto_model_free.py Thu Jan 28
14:16:24 2010
@@ -38,7 +38,6 @@
# relax GUI module imports.
from gui_bieri.analyses.results_analysis import model_free_results,
see_results
from gui_bieri.analyses.select_model_calc import Select_tensor
-from gui_bieri.base_classes import Container
from gui_bieri.controller import Redirect_text, Thread_container
from gui_bieri.derived_wx_classes import StructureTextCtrl
from gui_bieri.filedialog import opendir, openfile
@@ -524,35 +523,35 @@
See the docstring for auto_analyses.dauvernge_protocol for details.
All data is taken from the relax data store, so data upload from the GUI to
there must have been previously performed.
- @return: A container with all the data required for
dAuvernge_protocol, i.e. its keyword arguments mf_models, local_tm_models,
pdb_file, seq_args, het_name, relax_data, unres, exclude, bond_length, csa,
hetnuc, proton, grid_inc, min_algor, mc_num, conv_loop.
+ @return: A dictionary with all the data required for
dAuvernge_protocol, i.e. its keyword arguments mf_models, local_tm_models,
pdb_file, seq_args, het_name, relax_data, unres, exclude, bond_length, csa,
hetnuc, proton, grid_inc, min_algor, mc_num, conv_loop.
@rtype: class instance
"""
# The data container.
- data = Container()
+ data = {}
# The model-free models (do not change these unless absolutely
necessary).
- data.mf_models = []
- data.local_tm_models = []
+ data['mf_models'] = []
+ data['local_tm_models'] = []
for i in range(len(self.data.model_toggle)):
if self.data.model_toggle[i]:
- data.mf_models.append('m%i' % i)
- data.local_tm_models.append('tm%i' % i)
+ data['mf_models'].append('m%i' % i)
+ data['local_tm_models'].append('tm%i' % i)
# The PDB file (set this to None if no structure is available).
if self.data.structure_file == '':
- data.structure_file = None
+ data['pdb_file'] = None
else:
- data.structure_file = self.data.structure_file
+ data['pdb_file'] = self.data.structure_file
# 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 = [self.data.paramfiles1[0], None, None, 2, 3, 4, 5,
None]
+ data['seq_args'] = [self.data.paramfiles1[0], None, None, 2, 3, 4,
5, 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]
+ data['het_name'] = ds.relax_gui.global_setting[2]
# 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 = []
+ data['relax_data'] = []
for i in range(3):
# The objects.
frq = getattr(self.data, 'nmrfreq%i' % (i+1))
@@ -563,33 +562,33 @@
continue
# Append the relaxation data.
- data.relax_data.append(['R1', str(frq), float(frq)*1e6,
files[1], None, None, 2, 3, 4, 5, 6, 7, None])
- data.relax_data.append(['R2', str(frq), float(frq)*1e6,
files[2], None, None, 2, 3, 4, 5, 6, 7, None])
- data.relax_data.append(['NOE', str(frq), float(frq)*1e6,
files[0], None, None, 2, 3, 4, 5, 6, 7, None])
+ data['relax_data'].append(['R1', str(frq), float(frq)*1e6,
files[1], None, None, 2, 3, 4, 5, 6, 7, None])
+ data['relax_data'].append(['R2', str(frq), float(frq)*1e6,
files[2], None, None, 2, 3, 4, 5, 6, 7, None])
+ data['relax_data'].append(['NOE', str(frq), float(frq)*1e6,
files[0], None, None, 2, 3, 4, 5, 6, 7, None])
# The file containing the list of unresolved spins to exclude from
the analysis (set this to None if no spin is to be excluded).
- data.unres = self.data.results_dir_model + sep + 'unresolved'
+ data['unres'] = self.data.results_dir_model + sep + 'unresolved'
# 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
+ 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'
+ 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
+ data['grid_inc'] = 11
# The optimisation technique.
- data.min_algor = 'newton'
+ 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
+ data['mc_num'] = 500
# Automatic looping over all rounds until convergence (must be a
boolean value of True or False).
- data.conv_loop = True
+ data['conv_loop'] = True
# Return the container.
return data
@@ -797,6 +796,9 @@
# Assemble all the data needed for the dAuvergne_protocol class.
data = self.assemble_data()
+ # Add the global model.
+ data['diff_model'] = global_model
+
# The thread object storage.
self.gui.calc_threads.append(Thread_container())
thread_cont = self.gui.calc_threads[-1]
@@ -814,7 +816,7 @@
time.sleep(0.5)
# Start the thread.
- id = thread.start_new_thread(dAuvergne_protocol, (global_model,
data.mf_models, data.local_tm_models, data.structure_file, data.seq_args,
data.het_name, data.relax_data, data.unres, data.exclude, data.bond_length,
data.csa, data.hetnuc, data.proton, data.grid_inc, data.min_algor,
data.mc_num, data.conv_loop), ('diff_model', 'mf_models', 'local_tm_models',
'pdb_file', 'seq_args', 'het_name', 'relax_data', 'unres', 'exclude',
'bond_length', 'csa', 'hetnuc', 'proton', 'grid_inc', 'min_algor', 'mc_num',
'conv_loop'))
+ id = thread.start_new_thread(dAuvergne_protocol, (), data)
# Add the thread info to the container.
thread_cont.id = id
r10514 - /branches/bieri_gui/gui_bieri/analyses/auto_model_free.py