Author: bugman
Date: Fri Jun 7 16:31:35 2013
New Revision: 19951
URL: http://svn.gna.org/viewcvs/relax?rev=19951&view=rev
Log:
Removed cdp.model as this makes no sense - a different model can be used per
spin cluster.
Now the variable cdp.model_type is used to identify the 'R2eff' model. For
all other dispersion
models this variable is set to 'Disp'.
Modified:
branches/relax_disp/auto_analyses/relax_disp.py
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
branches/relax_disp/specific_analyses/relax_disp/nessy.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
Modified: branches/relax_disp/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/relax_disp.py?rev=19951&r1=19950&r2=19951&view=diff
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (original)
+++ branches/relax_disp/auto_analyses/relax_disp.py Fri Jun 7 16:31:35 2013
@@ -192,7 +192,7 @@
self.optimise()
# Write out the results.
- self.write_results(path=self.results_dir+sep+model)
+ self.write_results(path=self.results_dir+sep+model, model=model)
# Perform model selection, writing out the final results.
if len(model_pipes) >= 2:
@@ -204,7 +204,7 @@
warn(RelaxWarning("Model selection in the dispersion
auto-analysis has been skipped as only %s models have been optimised." %
len(model_pipes)))
- def write_results(self, path=None):
+ def write_results(self, path=None, model=None):
"""Create a set of results, text and Grace files for the current
data pipe.
@keyword path: The directory to place the files into.
@@ -215,7 +215,7 @@
self.interpreter.results.write(file='results', dir=path, force=True)
# Exponential curves.
- if cdp.model == MODEL_R2EFF and cdp.exp_type not in FIXED_TIME_EXP:
+ if cdp.model_type == 'R2eff' and cdp.exp_type not in FIXED_TIME_EXP:
self.interpreter.relax_disp.plot_exp_curves(file='intensities.agr', dir=path,
force=True) # Average peak intensities.
self.interpreter.relax_disp.plot_exp_curves(file='intensities_norm.agr',
dir=path, force=True, norm=True) # Average peak intensities (normalised).
@@ -223,20 +223,20 @@
self.interpreter.relax_disp.plot_disp_curves(dir=path, force=True)
# The R2eff parameter.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
self.interpreter.value.write(param='r2eff', file='r2eff.out',
dir=path, force=True)
self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2eff', file='r2eff.agr', dir=path, force=True)
# The I0 parameter.
- if cdp.model == MODEL_R2EFF and cdp.exp_type not in FIXED_TIME_EXP:
+ if cdp.model_type == 'R2eff' and cdp.exp_type not in FIXED_TIME_EXP:
self.interpreter.value.write(param='i0', file='i0.out',
dir=path, force=True)
self.interpreter.grace.write(x_data_type='res_num',
y_data_type='i0', file='i0.agr', dir=path, force=True)
# The Phi_ex parameter.
- if cdp.model in [MODEL_LM63]:
+ if model in [None, MODEL_LM63]:
self.interpreter.value.write(param='phi_ex', file='phi_ex.out',
dir=path, force=True)
self.interpreter.grace.write(x_data_type='res_num',
y_data_type='phi_ex', file='phi_ex.agr', dir=path, force=True)
# Minimisation statistics.
- if not (cdp.model == MODEL_R2EFF and cdp.exp_type in FIXED_TIME_EXP):
+ if not (cdp.model_type == 'R2eff' and cdp.exp_type in
FIXED_TIME_EXP):
self.interpreter.grace.write(y_data_type='chi2',
file='chi2.agr', dir=path, force=True)
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19951&r1=19950&r2=19951&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Fri Jun 7
16:31:35 2013
@@ -135,7 +135,7 @@
values, errors, missing, frqs = return_r2eff_arrays(spins=[spin],
spin_ids=[spin_id], fields=fields, field_count=field_count)
# Initialise the relaxation dispersion fit functions.
- model = Dispersion(model=cdp.model,
num_params=param_num(spins=[spin]), num_spins=1, num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=spin.model,
num_params=param_num(spins=[spin]), num_spins=1, num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
model.func(param_vector)
@@ -356,7 +356,7 @@
upper = []
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -588,15 +588,14 @@
@type params: list of str
"""
- # Set the model.
- cdp.model = model
+ # The model group.
+ if model == MODEL_R2EFF:
+ cdp.model_type = 'R2eff'
+ else:
+ cdp.model_type = 'disp'
# Loop over the sequence.
- for spin in spin_loop():
- # Skip deselected spins.
- if not spin.select:
- continue
-
+ for spin in spin_loop(skip_desel=True):
# The model and parameter names.
spin.model = model
spin.params = params
@@ -930,7 +929,7 @@
"""
# The R2eff model data (the base data is peak intensities).
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Loop over the sequence.
for spin in spin_loop():
# Skip deselected spins.
@@ -984,7 +983,7 @@
raise RelaxError("The relaxation dispersion experiment type has
not been specified.")
# Test if the model has been set.
- if not hasattr(cdp, 'model'):
+ if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
# Test if the curve count exists.
@@ -1070,7 +1069,7 @@
"""
# The R2eff model (with peak intensity base data).
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Unpack the data.
spin, frq, point = data_id
@@ -1115,7 +1114,11 @@
# Duplicate all non-sequence specific data.
for data_name in dir(dp_from):
# Skip the container objects.
- if data_name in ['mol', 'interatomic', 'structure', 'exp_info']:
+ if data_name in ['mol', 'interatomic', 'structure', 'exp_info',
'result_files']:
+ continue
+
+ # Skip dispersion specific parameters.
+ if data_name in ['model']:
continue
# Skip special objects.
@@ -1230,7 +1233,7 @@
raise RelaxError("The relaxation dispersion experiment type has
not been specified.")
# Test if the model has been set.
- if not hasattr(cdp, 'model'):
+ if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
# Test if the curve count exists.
@@ -1240,10 +1243,6 @@
elif cdp.exp_type == 'r1rho':
raise RelaxError("The spin-lock field strengths have not
been set up.")
- # Test if the spectrometer frequencies have been set.
- if cdp.model in [MODEL_LM63, MODEL_CR72, MODEL_M61] and not
hasattr(cdp, 'spectrometer_frq'):
- raise RelaxError("The spectrometer frequency information has not
been specified.")
-
# Initialise some empty data pipe structures so that the target
function set up does not fail.
if not hasattr(cdp, 'cpmg_frqs_list'):
cdp.cpmg_frqs_list = []
@@ -1251,7 +1250,7 @@
cdp.spin_lock_nu1_list = []
# Special exponential curve-fitting for the 'R2eff' model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Sanity checks.
if cdp.exp_type in FIXED_TIME_EXP:
raise RelaxError("The R2eff model with the fixed time period
CPMG experiment cannot be optimised.")
@@ -1278,6 +1277,10 @@
for spin_ids in self.model_loop():
# The spin containers.
spins = spin_ids_to_containers(spin_ids)
+
+ # Test if the spectrometer frequencies have been set.
+ if spins[0].model in [MODEL_LM63, MODEL_CR72, MODEL_M61] and not
hasattr(cdp, 'spectrometer_frq'):
+ raise RelaxError("The spectrometer frequency information has
not been specified.")
# The R2eff/R1rho data.
values, errors, missing, frqs = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=fields, field_count=field_count)
@@ -1313,7 +1316,7 @@
print("Unconstrained grid search size: %s (constraints
may decrease this size).\n" % grid_size)
# Initialise the function to minimise.
- model = Dispersion(model=cdp.model,
num_params=param_num(spins=spins), num_spins=len(spins), num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=spins[0].model,
num_params=param_num(spins=spins), num_spins=len(spins), num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
# Grid search.
if search('^[Gg]rid', min_algor):
@@ -1543,7 +1546,7 @@
"""
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Unpack the data.
spin, frq, point = data_id
@@ -1632,7 +1635,7 @@
"""
# The R2eff model (with peak intensity base data).
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Unpack the data.
spin, frq, point = data_id
Modified: branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py?rev=19951&r1=19950&r2=19951&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py Fri Jun 7
16:31:35 2013
@@ -67,20 +67,18 @@
raise RelaxError("The relaxation dispersion experiment type has not
been specified.")
# Test if the model has been set.
- if not hasattr(cdp, 'model'):
+ if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
- # Translate the model.
- function = translate_model()
-
# The directory.
- if dir == None:
- dir = cdp.model.lower()
- if not access(dir, F_OK):
+ if dir != None and not access(dir, F_OK):
raise RelaxDirError('CPMGFit', dir)
# Loop over each spin.
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ # Translate the model.
+ function = translate_model(spin.model)
+
# The spin input file name.
file_in = dir + sep + spin_file_name(spin_id=spin_id)
if not access(file_in, F_OK):
@@ -144,16 +142,12 @@
raise RelaxError("The relaxation dispersion experiment type has not
been specified.")
# Test if the model has been set.
- if not hasattr(cdp, 'model'):
+ if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
- # Translate the model.
- function = translate_model()
-
# Directory creation.
- if dir == None:
- dir = cdp.model.lower()
- mkdir_nofail(dir, verbosity=0)
+ if dir != None:
+ mkdir_nofail(dir, verbosity=0)
# The 'run.sh' script.
batch = open_write_file('batch_run.sh', dir, force)
@@ -161,6 +155,9 @@
# Generate the input files for each spin.
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ # Translate the model.
+ function = translate_model(spin.model)
+
# Create the input file.
file_in = create_spin_input(function=function, spin=spin,
spin_id=spin_id, dir=dir)
@@ -279,7 +276,7 @@
return name
-def translate_model():
+def translate_model(model):
"""Translate the dispersion model from relax notation to CPMGFit
notation.
@return: The CPMGFit model name.
@@ -293,11 +290,11 @@
}
# No translation, so fail.
- if cdp.model not in translation:
- raise RelaxError("The conversion of the relax model '%s' to a
CPMGFit model is not supported." % cdp.model)
+ if model not in translation:
+ raise RelaxError("The conversion of the relax model '%s' to a
CPMGFit model is not supported." % model)
# Printout.
- print("Translating the relax '%s' model to the CPMGFit '%s' model." %
(cdp.model, translation[cdp.model]))
+ print("Translating the relax '%s' model to the CPMGFit '%s' model." %
(model, translation[model]))
# Return the translated name.
- return translation[cdp.model]
+ return translation[model]
Modified: branches/relax_disp/specific_analyses/relax_disp/nessy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/nessy.py?rev=19951&r1=19950&r2=19951&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/nessy.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/nessy.py Fri Jun 7
16:31:35 2013
@@ -60,7 +60,7 @@
raise RelaxError("The relaxation dispersion experiment type has not
been specified.")
# Test if the model has been set.
- if not hasattr(cdp, 'model'):
+ if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
# Directory creation.
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=19951&r1=19950&r2=19951&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri Jun 7
16:31:35 2013
@@ -51,7 +51,7 @@
param_vector = []
# The R2eff model parameters.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -197,7 +197,7 @@
return scaling_matrix
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -272,7 +272,7 @@
param_index = 0
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -454,7 +454,7 @@
j = 0
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Only use the parameters of the first spin of the cluster.
spin = spins[0]
for i in range(n):
@@ -549,7 +549,7 @@
spin_index = 0
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# The number of spin specific parameters (R2eff and I0 per spin).
num = len(spins) * 2
@@ -582,7 +582,7 @@
"""
# The R2eff model.
- if cdp.model == MODEL_R2EFF:
+ if cdp.model_type == 'R2eff':
# Exponential curves (with clustering).
if cdp.exp_type in VAR_TIME_EXP:
return 2 * len(spins)
Modified: branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/sherekhan.py?rev=19951&r1=19950&r2=19951&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/sherekhan.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/sherekhan.py Fri Jun 7
16:31:35 2013
@@ -64,7 +64,7 @@
raise RelaxError("The relaxation dispersion experiment type has not
been specified.")
# Test if the model has been set.
- if not hasattr(cdp, 'model'):
+ if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
# Test that this is a fixed time period experiment.
r19951 - in /branches/relax_disp: auto_analyses/ specific_analyses/relax_disp/