Author: semor
Date: Mon Jan 28 17:56:39 2008
New Revision: 4897
URL: http://svn.gna.org/viewcvs/relax?rev=4897&view=rev
Log:
Merged revisions 4854-4856,4858-4860,4886-4888 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r4854 | bugman | 2008-01-18 09:42:02 -0500 (Fri, 18 Jan 2008) | 3 lines
Big refactorisation of the partition_params() and set() functions.
........
r4855 | bugman | 2008-01-18 09:58:10 -0500 (Fri, 18 Jan 2008) | 3 lines
Changed the way the model parameters are set in the set() function.
........
r4856 | bugman | 2008-01-18 10:01:28 -0500 (Fri, 18 Jan 2008) | 6 lines
Reverted r4850 as generic_fns.value.partition_params() has returned to its
previous behaviour.
The command used was:
svn merge -r4850:4849 .
........
r4858 | semor | 2008-01-18 16:41:55 -0500 (Fri, 18 Jan 2008) | 3 lines
Uniformized the format of constants.
........
r4859 | bugman | 2008-01-21 05:15:41 -0500 (Mon, 21 Jan 2008) | 5 lines
When None, the param variable is converted to a list of None with the
length equal to that of val.
This affects the generic_fns.value.set() function when no parameters are
supplied.
........
r4860 | bugman | 2008-01-21 05:19:40 -0500 (Mon, 21 Jan 2008) | 6 lines
Reverted the last change as param needs to be passed to
set_non_spin_params() as None.
The command used was:
svn merge -r4859:4858 .
........
r4886 | bugman | 2008-01-25 08:13:57 -0500 (Fri, 25 Jan 2008) | 9 lines
Bug fix for the generic_fns.value.set() function.
The differentiation between a spin specific parameter and a global
parameter was not working for
specific analyses with no spin specific parameters. The return_data_name()
function was being used
to differentiate, which makes no sense. So instead the is_spin_param()
function has been introduced
to allow the specific code to answer the question explicitly. Note that
this will temporarily break
many things.
........
r4887 | bugman | 2008-01-25 09:31:19 -0500 (Fri, 25 Jan 2008) | 5 lines
Implemented the is_spin_param() base class method.
This function always returns true.
........
r4888 | bugman | 2008-01-25 09:56:06 -0500 (Fri, 25 Jan 2008) | 3 lines
Implemented the model-free specific is_spin_param() method.
........
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/generic_fns/value.py
branches/consistency_tests_1.3/physical_constants.py
branches/consistency_tests_1.3/specific_fns/__init__.py
branches/consistency_tests_1.3/specific_fns/base_class.py
branches/consistency_tests_1.3/specific_fns/model_free/model_free.py
branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py
Propchange: branches/consistency_tests_1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Jan 28 17:56:39 2008
@@ -1,1 +1,1 @@
-/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461,4473,4476-4493,4523-4551,4567-4577,4579,4585-4586,4618-4623,4659,4662-4693,4698-4759,4778-4792,4796-4839,4841-4850
+/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461,4473,4476-4493,4523-4551,4567-4577,4579,4585-4586,4618-4623,4659,4662-4693,4698-4759,4778-4792,4796-4839,4841-4850,4854-4888
Modified: branches/consistency_tests_1.3/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/value.py?rev=4897&r1=4896&r2=4897&view=diff
==============================================================================
--- branches/consistency_tests_1.3/generic_fns/value.py (original)
+++ branches/consistency_tests_1.3/generic_fns/value.py Mon Jan 28 17:56:39
2008
@@ -50,21 +50,49 @@
"""
# Specific functions.
- return_data_name = get_specific_fn('return_data_name',
relax_data_store[relax_data_store.current_pipe].pipe_type)
+ is_spin_param = get_specific_fn('is_spin_param',
relax_data_store[relax_data_store.current_pipe].pipe_type)
# Initialise.
spin_params = []
spin_values = []
other_params = []
other_values = []
- model_values = []
-
- # The parameter has been specified.
- if param:
- # Single parameter.
- if type(param) == str:
+
+ # Single parameter.
+ if type(param) == str:
+ # Spin specific parameter.
+ if is_spin_param(param):
+ params = spin_params
+ values = spin_values
+
+ # Other parameters.
+ else:
+ params = other_params
+ values = other_values
+
+ # List of values.
+ if type(val) == list or isinstance(val, ndarray):
+ # Parameter name.
+ for i in xrange(len(val)):
+ params.append(param)
+
+ # Parameter value.
+ values = val
+
+ # Single value.
+ else:
+ # Parameter name.
+ params.append(param)
+
+ # Parameter value.
+ values.append(val)
+
+ # Multiple parameters.
+ elif type(param) == list:
+ # Loop over all parameters.
+ for i in xrange(len(param)):
# Spin specific parameter.
- if return_data_name(param):
+ if is_spin_param(param[i]):
params = spin_params
values = spin_values
@@ -73,59 +101,18 @@
params = other_params
values = other_values
- # List of values.
+ # Parameter name.
+ params.append(param[i])
+
+ # Parameter value.
if type(val) == list or isinstance(val, ndarray):
- # Parameter name.
- for i in xrange(len(val)):
- params.append(param)
-
- # Parameter value.
- values = val
-
- # Single value.
+ values.append(val[i])
else:
- # Parameter name.
- params.append(param)
-
- # Parameter value.
values.append(val)
- # Multiple parameters.
- elif type(param) == list:
- # Loop over all parameters.
- for i in xrange(len(param)):
- # Spin specific parameter.
- if return_data_name(param[i]):
- params = spin_params
- values = spin_values
-
- # Other parameters.
- else:
- params = other_params
- values = other_values
-
- # Parameter name.
- params.append(param[i])
-
- # Parameter value.
- if type(val) == list or isinstance(val, ndarray):
- values.append(val[i])
- else:
- values.append(val)
-
-
- # No parameter name supplied, so these must be the model parameter
values.
- else:
- # List of values.
- if type(val) == list or isinstance(val, ndarray):
- model_values = val
-
- # Single value.
- elif val:
- model_values = [val]
# Return the partitioned parameters and values.
- return spin_params, spin_values, other_params, other_values, model_values
+ return spin_params, spin_values, other_params, other_values
def set(val=None, param=None, spin_id=None, force=False):
@@ -149,52 +136,70 @@
return_value = get_specific_fn('return_value',
relax_data_store[relax_data_store.current_pipe].pipe_type)
set_non_spin_params = get_specific_fn('set_non_spin_params',
relax_data_store[relax_data_store.current_pipe].pipe_type)
- # Partition the parameters into those which are spin specific and those
which are not.
- spin_params, spin_values, other_params, other_values, model_values =
partition_params(val, param)
-
-
- # Spin specific parameters.
- ###########################
-
- if spin_params:
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # First test if parameter value already exists, prior to setting any
params.
- if not force:
+ # The parameters have been specified.
+ if param:
+ # Partition the parameters into those which are spin specific and
those which are not.
+ spin_params, spin_values, other_params, other_values =
partition_params(val, param)
+
+ # Spin specific parameters.
+ if spin_params:
+ # Test if the sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # First test if parameter value already exists, prior to setting
any params.
+ if not force:
+ # Loop over the spins.
+ for spin in spin_loop(spin_id):
+ # Skip unselected spins.
+ if not spin.select:
+ continue
+
+ # Loop over the parameters.
+ for param in spin_params:
+ # Get the value and error.
+ temp_value, temp_error = return_value(spin, param)
+
+ # Data exists.
+ if temp_value != None or temp_error != None:
+ raise RelaxValueError, (param)
+
+ # Loop over the spins.
+ for spin in spin_loop(spin_id):
+ # Skip unselected residues.
+ if not spin.select:
+ continue
+
+ # Set the individual parameter values.
+ for j in xrange(len(spin_params)):
+ set_spin_params(value=spin_values[j], error=None,
spin=spin, param=spin_params[j])
+
+
+ # All other parameters.
+ if other_params:
+ set_non_spin_params(value=other_values, param=other_params)
+
+
+ # All model parameters (i.e. no parameters have been supplied).
+ else:
+ # Convert val to a list if necessary.
+ if type(val) != list or not isinstance(val, ndarray):
+ val = [val]
+
+ # Spin specific models.
+ if exists_mol_res_spin_data():
# Loop over the spins.
for spin in spin_loop(spin_id):
# Skip unselected spins.
if not spin.select:
continue
- # Loop over the parameters.
- for param in spin_params:
- # Get the value and error.
- temp_value, temp_error = return_value(spin, param)
-
- # Data exists.
- if temp_value != None or temp_error != None:
- raise RelaxValueError, (param)
-
- # Loop over the spins.
- for spin in spin_loop(spin_id):
- # Skip unselected residues.
- if not spin.select:
- continue
-
- # Go to the specific code.
- for j in xrange(len(spin_params)):
- set_spin_params(value=spin_values[j], error=None, spin=spin,
param=spin_params[j])
-
-
- # All other parameters.
- #######################
-
- if other_params:
- set_non_spin_params(value=other_values, param=other_params)
-
+ # Set the individual parameter values.
+ for j in xrange(len(val)):
+ set_spin_params(value=val[j], error=None, spin=spin,
param=None)
+
+ # Set the non-spin specific parameters.
+ set_non_spin_params(value=val, param=param)
# Reset all minimisation statistics.
reset_min_stats()
Modified: branches/consistency_tests_1.3/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/physical_constants.py?rev=4897&r1=4896&r2=4897&view=diff
==============================================================================
--- branches/consistency_tests_1.3/physical_constants.py (original)
+++ branches/consistency_tests_1.3/physical_constants.py Mon Jan 28 17:56:39
2008
@@ -25,10 +25,10 @@
# Planck's constant.
-h = 6.62606876e-34
+h = 6.62606876 * 1e-34
# Dirac's constant.
-h_bar = h / (2.0*pi)
+h_bar = h / (2.0 * pi)
# The magnetic constant or the permeability of vacuum.
mu0 = 4.0 * pi * 1e-7
@@ -41,16 +41,16 @@
# The 13C gyromagnetic ratio.
-g13C = 6.728e7
+g13C = 6.728 * 1e7
# The 1H gyromagnetic ratio.
-g1H = 26.7522212e7
+g1H = 26.7522212 * 1e7
# The 15N gyromagnetic ratio.
-g15N = -2.7126e7
+g15N = -2.7126 * 1e7
# The 17O gyromagnetic ratio.
-g17O = -3.628e7
+g17O = -3.628 * 1e7
# The 31P gyromagnetic ratio.
-g31P = 1.0841e8
+g31P = 10.841 * 1e7
Modified: branches/consistency_tests_1.3/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/__init__.py?rev=4897&r1=4896&r2=4897&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/__init__.py (original)
+++ branches/consistency_tests_1.3/specific_fns/__init__.py Mon Jan 28
17:56:39 2008
@@ -106,6 +106,10 @@
if eqi == 'init_sim_values':
function = inst.sim_init_values
+ # Spin specific parameter determining function.
+ if eqi == 'is_spin_param':
+ function = inst.is_spin_param
+
# Map bounds function.
if eqi == 'map_bounds':
function = inst.map_bounds
Modified: branches/consistency_tests_1.3/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/base_class.py?rev=4897&r1=4896&r2=4897&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/base_class.py (original)
+++ branches/consistency_tests_1.3/specific_fns/base_class.py Mon Jan 28
17:56:39 2008
@@ -66,6 +66,22 @@
# No errors found.
return False
+
+
+ def is_spin_param(self, name):
+ """Determine whether the given parameter is spin specific.
+
+ This base class method always returns true, hence all parameters
will be considered
+ residents of a SpinContainer object unless this method is
overwritten.
+
+ @param name: The name of the parameter.
+ @type name: str
+ @return: True
+ @rtype: bool
+ """
+
+ # Return the default of True.
+ return True
def num_instances(self):
Modified: branches/consistency_tests_1.3/specific_fns/model_free/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/model_free/model_free.py?rev=4897&r1=4896&r2=4897&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/model_free/model_free.py
(original)
+++ branches/consistency_tests_1.3/specific_fns/model_free/model_free.py Mon
Jan 28 17:56:39 2008
@@ -1074,6 +1074,27 @@
# Return the parameter names.
return self.param_vector
+
+
+ def is_spin_param(self, name):
+ """Determine whether the given parameter is spin specific.
+
+ Unless a diffusion parameter is encountered, this method will return
true.
+
+ @param name: The name of the parameter.
+ @type name: str
+ @return: If the parameter is a diffusion parameter, False I
returned. Otherwise True
+ is returned.
+ @rtype: bool
+ """
+
+ # Catch a diffusion parameter.
+ if diffusion_tensor.return_data_name(name):
+ return False
+
+ # All the rest:
+ else:
+ return True
def linear_constraints(self, index=None):
Modified:
branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py?rev=4897&r1=4896&r2=4897&view=diff
==============================================================================
---
branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py
(original)
+++
branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py
Mon Jan 28 17:56:39 2008
@@ -48,7 +48,7 @@
val = [0.8]
# Partition.
- spin_params, spin_values, other_params, other_values, model_values =
value.partition_params(val, param)
+ spin_params, spin_values, other_params, other_values =
value.partition_params(val, param)
# Tests.
self.assertEqual(spin_params, ['S2'])
@@ -68,7 +68,7 @@
val = [1e7]
# Partition.
- spin_params, spin_values, other_params, other_values, model_values =
value.partition_params(val, param)
+ spin_params, spin_values, other_params, other_values =
value.partition_params(val, param)
# Tests.
self.assertEqual(spin_params, [])
@@ -88,7 +88,7 @@
val = [1e7, 0.8]
# Partition.
- spin_params, spin_values, other_params, other_values, model_values =
value.partition_params(val, param)
+ spin_params, spin_values, other_params, other_values =
value.partition_params(val, param)
# Tests.
self.assertEqual(spin_params, ['S2'])
@@ -108,7 +108,7 @@
val = [1e7, 0.8, -160e-6]
# Partition.
- spin_params, spin_values, other_params, other_values, model_values =
value.partition_params(val, param)
+ spin_params, spin_values, other_params, other_values =
value.partition_params(val, param)
# Tests.
self.assertEqual(spin_params, ['S2', 'CSA'])
@@ -128,7 +128,7 @@
val = [1e7, 0.8, 2e7, -160e-6, 0.13]
# Partition.
- spin_params, spin_values, other_params, other_values, model_values =
value.partition_params(val, param)
+ spin_params, spin_values, other_params, other_values =
value.partition_params(val, param)
# Tests.
self.assertEqual(spin_params, ['S2', 'CSA'])
@@ -148,7 +148,7 @@
val = []
# Partition.
- spin_params, spin_values, other_params, other_values, model_values =
value.partition_params(val, param)
+ spin_params, spin_values, other_params, other_values =
value.partition_params(val, param)
# Tests.
self.assertEqual(spin_params, [])
r4897 - in /branches/consistency_tests_1.3: ./ generic_fns/ specific_fns/ specific_fns/model_free/ test_suite/unit_tests/_ge...