Author: bugman
Date: Wed Jan 2 16:13:02 2008
New Revision: 4254
URL: http://svn.gna.org/viewcvs/relax?rev=4254&view=rev
Log:
Merged revisions 4241-4253 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r4241 | bugman | 2008-01-02 11:53:55 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix in the generic_fns.value.set() function.
The diff_params variable is now called tensor_params.
........
r4242 | bugman | 2008-01-02 11:56:41 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix in the generic_fns.value.set() function.
The self.relax.generic data structure no longer exists.
........
r4243 | bugman | 2008-01-02 12:22:57 +0100 (Wed, 02 Jan 2008) | 7 lines
Implemented the generic_fns.minimise.reset_min_stats() function using the
new relax design.
This was copied from the old reset_min_stats() class method but has had a
few significant changes
made to it. Now both the sequence specific and global min stats are reset
all together by one call
to the function.
........
r4244 | bugman | 2008-01-02 12:36:52 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix for the value.set() user function.
Empty lists are now caught.
........
r4245 | bugman | 2008-01-02 14:51:28 +0100 (Wed, 02 Jan 2008) | 5 lines
Updated the val arg unit test of the value.set() user function.
The unit test now properly checks the arg when a list is passed into it.
........
r4246 | bugman | 2008-01-02 14:59:35 +0100 (Wed, 02 Jan 2008) | 6 lines
Updated the value.set() user function.
More comments were added to the code, and empty lists passed in as the
param argument are now
checked for.
........
r4247 | bugman | 2008-01-02 15:01:17 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix for the val arg unit test of the value.set() user function.
An elif loop was incorrect.
........
r4248 | bugman | 2008-01-02 15:09:46 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix for the param arg unit test of the value.set() user function.
Lists are now properly checked.
........
r4249 | bugman | 2008-01-02 15:14:37 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix for the generic_fns.value.set() function.
The diff_values variable is now called tensor_values.
........
r4250 | bugman | 2008-01-02 15:20:44 +0100 (Wed, 02 Jan 2008) | 3 lines
Fixes to the docstring of the generic_fns.diffusion_tensor.set() function.
........
r4251 | bugman | 2008-01-02 15:25:43 +0100 (Wed, 02 Jan 2008) | 6 lines
Bug fix for the generic_fns.diffusion_tensor.set() function.
If no diffusion tensor exists, then a RelaxError is thrown when trying to
set the parameters. It's
not possible to create a tensor from scratch as the tensor type is unknown.
........
r4252 | bugman | 2008-01-02 15:27:23 +0100 (Wed, 02 Jan 2008) | 5 lines
Fixes to the docstring of the generic_fns.diffusion_tensor.set() function.
The fact that the function cannot be used to initialise a tensor is now
stated.
........
r4253 | bugman | 2008-01-02 16:11:16 +0100 (Wed, 02 Jan 2008) | 5 lines
Bug fix for the param arg unit test of the value.set() user function.
Lists of params with a single value are allowed!
........
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/diffusion_tensor.py
branches/N_state_model/generic_fns/minimise.py
branches/N_state_model/generic_fns/value.py
branches/N_state_model/prompt/value.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py
Propchange: branches/N_state_model/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jan 2 16:13:02 2008
@@ -1,1 +1,1 @@
-/1.3:1-3692,3695,3697-3713,3715-3719,3721-3728,3730-3731,3733-3755,3757-3807,3809-3833,3836-3838,3840-3869,3872-3905,3907-3986,4004,4014-4015,4018-4021,4027-4031,4061-4102,4104-4114,4137-4175,4223
+/1.3:1-3692,3695,3697-3713,3715-3719,3721-3728,3730-3731,3733-3755,3757-3807,3809-3833,3836-3838,3840-3869,3872-3905,3907-3986,4004,4014-4015,4018-4021,4027-4031,4061-4102,4104-4114,4137-4175,4223,4241-4253
Modified: branches/N_state_model/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/diffusion_tensor.py?rev=4254&r1=4253&r2=4254&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/diffusion_tensor.py (original)
+++ branches/N_state_model/generic_fns/diffusion_tensor.py Wed Jan 2
16:13:02 2008
@@ -871,16 +871,15 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If the diffusion tensor has not been setup, use the more powerful
function
- 'diffusion_tensor.init' to initialise the tensor parameters.
-
- The diffusion tensor parameters can only be set when the run corresponds
to model-free
- analysis. The units of the parameters are:
+ 'diffusion_tensor.init' to initialise the tensor parameters. This
function cannot be used to
+ initialise a diffusion tensor.
+
+ The units of the parameters are:
Inverse seconds for tm.
Seconds for Diso, Da, Dx, Dy, Dz, Dpar, Dper.
Unitless for Dratio and Dr.
Radians for all angles (alpha, beta, gamma, theta, phi).
-
When setting a diffusion tensor parameter, the residue number has no
effect. As the
internal parameters of spherical diffusion are {tm}, spheroidal
diffusion are {tm, Da,
@@ -911,6 +910,10 @@
# Alias the current data pipe.
cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Set up the diffusion tensor data if it doesn't exist.
+ if not diff_data_exists():
+ raise RelaxNoTensorError, 'diffusion'
# Initialise.
geo_params = []
Modified: branches/N_state_model/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/minimise.py?rev=4254&r1=4253&r2=4254&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/minimise.py (original)
+++ branches/N_state_model/generic_fns/minimise.py Wed Jan 2 16:13:02 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2005, 2007 Edward d'Auvergne
#
+# Copyright (C) 2003-2005, 2007-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -25,12 +25,80 @@
from re import search
# relax module imports.
-from data import Data as elax_data_store
+from data import Data as relax_data_store
+from selection import spin_loop
#from processes import RelaxPopen3
from relax_errors import RelaxError, RelaxNoPipeError
from thread_classes import RelaxParentThread, RelaxThread
+def reset_min_stats(data_pipe=None, index=None):
+ """Function for resetting the minimisation statistics."""
+
+ # The data pipe.
+ if data_pipe == None:
+ data_pipe = relax_data_store.current_pipe
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[data_pipe]
+
+
+ # Global minimisation statistics.
+ #################################
+
+ # Chi-squared.
+ if hasattr(cdp, 'chi2'):
+ cdp.chi2 = None
+
+ # Iteration count.
+ if hasattr(cdp, 'iter'):
+ cdp.iter = None
+
+ # Function count.
+ if hasattr(cdp, 'f_count'):
+ cdp.f_count = None
+
+ # Gradient count.
+ if hasattr(cdp, 'g_count'):
+ cdp.g_count = None
+
+ # Hessian count.
+ if hasattr(cdp, 'h_count'):
+ cdp.h_count = None
+
+ # Warning.
+ if hasattr(cdp, 'warning'):
+ cdp.warning = None
+
+
+ # Sequence specific minimisation statistics.
+ ############################################
+
+ # Loop over all spins.
+ for spin in spin_loop():
+ # Chi-squared.
+ if hasattr(spin, 'chi2'):
+ spin.chi2 = None
+
+ # Iteration count.
+ if hasattr(spin, 'iter'):
+ spin.iter = None
+
+ # Function count.
+ if hasattr(spin, 'f_count'):
+ spin.f_count = None
+
+ # Gradient count.
+ if hasattr(spin, 'g_count'):
+ spin.g_count = None
+
+ # Hessian count.
+ if hasattr(spin, 'h_count'):
+ spin.h_count = None
+
+ # Warning.
+ if hasattr(spin, 'warning'):
+ spin.warning = None
@@ -143,65 +211,6 @@
# Standard minimisation.
else:
minimise(run=run, min_algor=min_algor, min_options=min_options,
func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations,
constraints=constraints, scaling=scaling, print_flag=print_flag)
-
-
- def reset_min_stats(self, run, index=None):
- """Function for resetting the minimisation statistics."""
-
- # Arguments.
- self.run = run
-
- # Global minimisation statistics.
- if index == None:
- # Chi-squared.
- if hasattr(relax_data_store, 'chi2') and
relax_data_store.chi2.has_key(self.run):
- relax_data_store.chi2[self.run] = None
-
- # Iteration count.
- if hasattr(relax_data_store, 'iter') and
relax_data_store.iter.has_key(self.run):
- relax_data_store.iter[self.run] = None
-
- # Function count.
- if hasattr(relax_data_store, 'f_count') and
relax_data_store.f_count.has_key(self.run):
- relax_data_store.f_count[self.run] = None
-
- # Gradient count.
- if hasattr(relax_data_store, 'g_count') and
relax_data_store.g_count.has_key(self.run):
- relax_data_store.g_count[self.run] = None
-
- # Hessian count.
- if hasattr(relax_data_store, 'h_count') and
relax_data_store.h_count.has_key(self.run):
- relax_data_store.h_count[self.run] = None
-
- # Warning.
- if hasattr(relax_data_store, 'warning') and
relax_data_store.warning.has_key(self.run):
- relax_data_store.warning[self.run] = None
-
- # Sequence specific minimisation statistics.
- else:
- # Chi-squared.
- if hasattr(relax_data_store.res[self.run][index], 'chi2'):
- relax_data_store.res[self.run][index].chi2 = None
-
- # Iteration count.
- if hasattr(relax_data_store.res[self.run][index], 'iter'):
- relax_data_store.res[self.run][index].iter = None
-
- # Function count.
- if hasattr(relax_data_store.res[self.run][index], 'f_count'):
- relax_data_store.res[self.run][index].f_count = None
-
- # Gradient count.
- if hasattr(relax_data_store.res[self.run][index], 'g_count'):
- relax_data_store.res[self.run][index].g_count = None
-
- # Hessian count.
- if hasattr(relax_data_store.res[self.run][index], 'h_count'):
- relax_data_store.res[self.run][index].h_count = None
-
- # Warning.
- if hasattr(relax_data_store.res[self.run][index], 'warning'):
- relax_data_store.res[self.run][index].warning = None
def return_conversion_factor(self, stat_type):
Modified: branches/N_state_model/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/value.py?rev=4254&r1=4253&r2=4254&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/value.py (original)
+++ branches/N_state_model/generic_fns/value.py Wed Jan 2 16:13:02 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2007 Edward d'Auvergne
#
+# Copyright (C) 2003-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -28,6 +28,7 @@
# relax module imports.
from data import Data as relax_data_store
from generic_fns import diffusion_tensor
+from generic_fns.minimise import reset_min_stats
from relax_errors import RelaxError, RelaxFileEmptyError, RelaxNoResError,
RelaxNoPipeError, RelaxNoSequenceError, RelaxRegExpError,
RelaxUnknownParamError, RelaxValueError
from specific_fns import get_specific_fn
@@ -211,9 +212,9 @@
# Diffusion tensor parameters.
##############################
- if diff_params:
+ if tensor_params:
# Set the diffusion parameters.
- diffusion_tensor.set(value=diff_values, param=diff_params)
+ diffusion_tensor.set(value=tensor_values, param=tensor_params)
# Residue specific parameters.
@@ -287,18 +288,8 @@
set(run=run, value=spin_values[j], error=None,
param=spin_params[j], index=i)
- # Reset the minimisation statistics.
- ####################################
-
- # Reset the global minimisation statistics.
- relax.generic.minimise.reset_min_stats(run)
-
- # Reset the sequence specific minimisation statistics.
- if relax_data_store.res.has_key(run):
- for i in xrange(len(relax_data_store.res[run])):
- relax.generic.minimise.reset_min_stats(run, i)
-
-
+ # Reset all minimisation statistics.
+ reset_min_stats()
Modified: branches/N_state_model/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/value.py?rev=4254&r1=4253&r2=4254&view=diff
==============================================================================
--- branches/N_state_model/prompt/value.py (original)
+++ branches/N_state_model/prompt/value.py Wed Jan 2 16:13:02 2008
@@ -380,6 +380,11 @@
if val != None and type(val) != float and type(val) != int and
type(val) != list:
raise RelaxNoneFloatListError, ('value', val)
if type(val) == list:
+ # Empty list.
+ if val == []:
+ raise RelaxListFloatError, ('value', val)
+
+ # Check for values.
for i in xrange(len(val)):
if type(val[i]) != float and type(val[i]) != int:
raise RelaxListFloatError, ('value', val)
@@ -388,6 +393,11 @@
if param != None and type(param) != str and type(param) != list:
raise RelaxNoneStrListError, ('parameter', param)
if type(param) == list:
+ # Empty list.
+ if param == []:
+ raise RelaxListStrError, ('parameter', param)
+
+ # Check for strings.
for i in xrange(len(param)):
if type(param[i]) != str:
raise RelaxListStrError, ('parameter', param)
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py?rev=4254&r1=4253&r2=4254&view=diff
==============================================================================
--- branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py
(original)
+++ branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py Wed
Jan 2 16:13:02 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007 Edward d'Auvergne
#
+# Copyright (C) 2007-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -26,7 +26,7 @@
# relax module imports.
from data import Data as relax_data_store
from prompt.value import Value
-from relax_errors import RelaxListFloatError, RelaxNoneFloatListError,
RelaxNoneStrError, RelaxNoneStrListError
+from relax_errors import RelaxError, RelaxListFloatError, RelaxListStrError,
RelaxNoneFloatListError, RelaxNoneStrError, RelaxNoneStrListError
from test_suite.unit_tests.value_testing_base import Value_base_class
# Unit test imports.
@@ -50,11 +50,17 @@
if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin' or
data[0] == 'float':
continue
- # Catch the list arguments.
- if data[0] == 'list':
+ # Catch all number lists.
+ if data[0] == 'int list' or data[0] == 'float list' or data[0]
== 'number list':
+ self.assertRaises(RelaxError, self.value_fns.set,
val=data[1], param='CSA')
+ if len(data[1]) != 1:
+ self.assertRaises(RelaxError, self.value_fns.set,
val=data[1], param=['CSA'])
+
+ # Catch all other list arguments.
+ elif type(data[1]) == list:
self.assertRaises(RelaxListFloatError, self.value_fns.set,
val=data[1], param=None)
- # The argument test.
+ # All other arguments.
else:
self.assertRaises(RelaxNoneFloatListError,
self.value_fns.set, val=data[1], param='CSA')
@@ -68,11 +74,18 @@
if data[0] == 'None' or data[0] == 'str':
continue
- # Catch the list arguments.
- if data[0] == 'list':
- self.assertRaises(RelaxListFloatError, self.value_fns.set,
param=data[1], val=None)
+ # Catch the string list arguments.
+ if data[0] == 'str list':
+ if len(data[1]) != 1:
+ self.assertRaises(RelaxError, self.value_fns.set,
param=data[1], val=[1.0])
+ else:
+ self.assertRaises(RelaxError, self.value_fns.set,
param=data[1], val=[1.0, 2.0])
- # The argument test.
+ # Catch all other list arguments.
+ elif type(data[1]) == list:
+ self.assertRaises(RelaxListStrError, self.value_fns.set,
param=data[1], val=None)
+
+ # All other arguments.
else:
self.assertRaises(RelaxNoneStrListError, self.value_fns.set,
param=data[1], val=None)
r4254 - in /branches/N_state_model: ./ generic_fns/ prompt/ test_suite/unit_tests/_prompt/