Author: bugman
Date: Thu Jan 28 13:14:25 2010
New Revision: 10496
URL: http://svn.gna.org/viewcvs/relax?rev=10496&view=rev
Log:
Completed assemble_data().
All the data used by the dAuvernge_protocol class is now gleaned from the
relax data store. This
code is very similar, though highly modified, to that in
gui_bieri.execution.calc_modelfree. Code
comments have been taken directly from sample_scripts/full_analysis.py.
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=10496&r1=10495&r2=10496&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
13:14:25 2010
@@ -520,7 +520,7 @@
def assemble_data(self):
"""Assemble the data required for the dAuvernge_protocol class.
- See the docstring for auto_analyses.dauvernge_protocol for details.
+ 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.
@rtype: class instance
@@ -528,6 +528,66 @@
# The data container.
data = Container()
+
+ # The model-free models (do not change these unless absolutely
necessary).
+ data.mf_models = []
+ data.local_mf_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_mf_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
+ else:
+ data.structure_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]
+
+ # 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_settings[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 = []
+ for i in range(3):
+ # The objects.
+ frq = getattr(self.data, 'nmrfreq%i' % i)
+ files = getattr(self.data, 'paramfiles%i' % i)
+
+ # Data has not been given, so skip this entry.
+ if frq == '':
+ 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]
+
+ # 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'
+
+ # 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
# Return the container.
return data
r10496 - /branches/bieri_gui/gui_bieri/analyses/auto_model_free.py