Author: bugman
Date: Thu Mar 3 11:16:29 2011
New Revision: 12759
URL: http://svn.gna.org/viewcvs/relax?rev=12759&view=rev
Log:
Create the specific base class method _sim_pack_relax_data() for packing
relaxation data.
This is the method from specific_fns/model_free/main.py, shifted into
api_common. The J(w) mapping
and consistency testing code now use this base method as well.
Modified:
branches/relax_data/specific_fns/api_common.py
branches/relax_data/specific_fns/consistency_tests.py
branches/relax_data/specific_fns/jw_mapping.py
branches/relax_data/specific_fns/model_free/__init__.py
branches/relax_data/specific_fns/model_free/main.py
Modified: branches/relax_data/specific_fns/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/specific_fns/api_common.py?rev=12759&r1=12758&r2=12759&view=diff
==============================================================================
--- branches/relax_data/specific_fns/api_common.py (original)
+++ branches/relax_data/specific_fns/api_common.py Thu Mar 3 11:16:29 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004, 2006-2009 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -554,6 +554,38 @@
sim_object.append(deepcopy(getattr(spin, object_name)))
+ def _sim_pack_relax_data(self, data_id, sim_data):
+ """Pack the Monte Carlo simulation relaxation data into the
corresponding spin container.
+
+ @param data_id: The spin identification string, as yielded by
the base_data_loop() generator method.
+ @type data_id: str
+ @param sim_data: The Monte Carlo simulation data.
+ @type sim_data: list of float
+ """
+
+ # Get the spin container.
+ spin = return_spin(data_id)
+
+ # Test if the simulation data already exists.
+ if hasattr(spin, 'ri_data_sim'):
+ raise RelaxError("Monte Carlo simulation data already exists.")
+
+ # Initialise the data structure.
+ spin.ri_data_sim = {}
+
+ # Loop over the relaxation data.
+ for i in range(len(cdp.ri_ids)):
+ # The ID.
+ ri_id = cdp.ri_ids[i]
+
+ # Initialise the MC data list.
+ spin.ri_data_sim[ri_id] = []
+
+ # Loop over the simulations.
+ for j in range(cdp.sim_number):
+ spin.ri_data_sim[ri_id].append(sim_data[j][i])
+
+
def _sim_return_chi2_spin(self, model_info, index=None):
"""Return the simulation chi-squared values (spin system specific).
Modified: branches/relax_data/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/specific_fns/consistency_tests.py?rev=12759&r1=12758&r2=12759&view=diff
==============================================================================
--- branches/relax_data/specific_fns/consistency_tests.py (original)
+++ branches/relax_data/specific_fns/consistency_tests.py Thu Mar 3 11:16:29
2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2009 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
# Copyright (C) 2007-2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
@@ -50,6 +50,7 @@
self.return_value = self._return_value_general
self.set_param_values = self._set_param_values_spin
self.set_selected_sim = self._set_selected_sim_spin
+ self.sim_pack_data = self._sim_pack_relax_data
def _set_frq(self, frq=None):
@@ -245,8 +246,7 @@
- 'r', bond length.
- 'csa', CSA value.
- 'heteronuc_type', the heteronucleus type.
- - 'orientation', angle between the 15N-1H vector and the
principal axis of the 15N
- chemical shift tensor.
+ - 'orientation', angle between the 15N-1H vector and the
principal axis of the 15N chemical shift tensor.
- 'tc', correlation time.
- 'j0', spectral density value at 0 MHz (from Farrow et al.
(1995) JBNMR, 6: 153-162).
- 'f_eta', eta-test (from Fushman et al. (1998) JACS, 120:
10947-10952).
@@ -600,23 +600,3 @@
# Multiple spins.
return spin.select_sim
-
-
- def sim_pack_data(self, data_id, sim_data):
- """Pack the Monte Carlo simulation data.
-
- @param data_id: The spin identification string, as yielded by
the base_data_loop() generator method.
- @type data_id: str
- @param sim_data: The Monte Carlo simulation data.
- @type sim_data: list of float
- """
-
- # Get the spin container.
- spin = return_spin(data_id)
-
- # Test if the simulation data already exists.
- if hasattr(spin, 'ri_data_sim'):
- raise RelaxError("Monte Carlo simulation data already exists.")
-
- # Create the data structure.
- spin.ri_data_sim = sim_data
Modified: branches/relax_data/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/specific_fns/jw_mapping.py?rev=12759&r1=12758&r2=12759&view=diff
==============================================================================
--- branches/relax_data/specific_fns/jw_mapping.py (original)
+++ branches/relax_data/specific_fns/jw_mapping.py Thu Mar 3 11:16:29 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2009 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -49,6 +49,7 @@
self.return_value = self._return_value_general
self.set_param_values = self._set_param_values_spin
self.set_selected_sim = self._set_selected_sim_spin
+ self.sim_pack_data = self._sim_pack_relax_data
def _set_frq(self, frq=None):
@@ -512,26 +513,6 @@
spin.jwh_err = error
- def sim_pack_data(self, data_id, sim_data):
- """Pack the Monte Carlo simulation data.
-
- @param data_id: The spin identification string, as yielded by
the base_data_loop() generator method.
- @type data_id: str
- @param sim_data: The Monte Carlo simulation data.
- @type sim_data: list of float
- """
-
- # Get the spin container.
- spin = return_spin(data_id)
-
- # Test if the simulation data already exists.
- if hasattr(spin, 'relax_sim_data'):
- raise RelaxError("Monte Carlo simulation data already exists.")
-
- # Create the data structure.
- spin.relax_sim_data = sim_data
-
-
def sim_return_param(self, model_info, index):
"""Return the array of simulation parameter values.
Modified: branches/relax_data/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/specific_fns/model_free/__init__.py?rev=12759&r1=12758&r2=12759&view=diff
==============================================================================
--- branches/relax_data/specific_fns/model_free/__init__.py (original)
+++ branches/relax_data/specific_fns/model_free/__init__.py Thu Mar 3
11:16:29 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2009 Edward d'Auvergne
#
+# Copyright (C) 2007-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -52,4 +52,5 @@
self.base_data_loop = self._base_data_loop_spin
self.return_error = self._return_error_relax_data
self.return_value = self._return_value_general
+ self.sim_pack_data = self._sim_pack_relax_data
self.test_grid_ops = self._test_grid_ops_general
Modified: branches/relax_data/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/specific_fns/model_free/main.py?rev=12759&r1=12758&r2=12759&view=diff
==============================================================================
--- branches/relax_data/specific_fns/model_free/main.py (original)
+++ branches/relax_data/specific_fns/model_free/main.py Thu Mar 3 11:16:29
2011
@@ -2780,38 +2780,6 @@
sim_object.append(deepcopy(getattr(spin,
object_name)))
- def sim_pack_data(self, data_id, sim_data):
- """Pack the Monte Carlo simulation data.
-
- @param data_id: The spin identification string, as yielded by
the base_data_loop() generator method.
- @type data_id: str
- @param sim_data: The Monte Carlo simulation data.
- @type sim_data: list of float
- """
-
- # Get the spin container.
- spin = return_spin(data_id)
-
- # Test if the simulation data already exists.
- if hasattr(spin, 'ri_data_sim'):
- raise RelaxError("Monte Carlo simulation data already exists.")
-
- # Initialise the data structure.
- spin.ri_data_sim = {}
-
- # Loop over the relaxation data.
- for i in range(len(cdp.ri_ids)):
- # The ID.
- ri_id = cdp.ri_ids[i]
-
- # Initialise the MC data list.
- spin.ri_data_sim[ri_id] = []
-
- # Loop over the simulations.
- for j in range(cdp.sim_number):
- spin.ri_data_sim[ri_id].append(sim_data[j][i])
-
-
def sim_return_chi2(self, model_info, index=None):
"""Return the simulation chi-squared values.
r12759 - in /branches/relax_data/specific_fns: ./ model_free/