Author: bugman
Date: Wed Sep 4 18:49:06 2013
New Revision: 20816
URL: http://svn.gna.org/viewcvs/relax?rev=20816&view=rev
Log:
Fixes for the changes to the dispersion experiment type variables throughout
the dispersion code.
Modified:
branches/relax_disp/auto_analyses/relax_disp.py
branches/relax_disp/gui/analyses/auto_relax_disp.py
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
branches/relax_disp/specific_analyses/relax_disp/parameters.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=20816&r1=20815&r2=20816&view=diff
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (original)
+++ branches/relax_disp/auto_analyses/relax_disp.py Wed Sep 4 18:49:06 2013
@@ -36,7 +36,7 @@
from pipe_control.pipes import has_pipe
from prompt.interpreter import Interpreter
from specific_analyses.relax_disp.disp_data import loop_frq
-from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG,
MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02,
R1RHO_EXP
+from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG,
EXP_TYPE_LIST_FIXED_TIME, EXP_TYPE_LIST_R1RHO, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02
from status import Status; status = Status()
@@ -312,7 +312,7 @@
self.interpreter.value.copy(pipe_from=MODEL_R2EFF,
pipe_to=model, param='r2eff')
# Calculate the R2eff values for the fixed relaxation time
period data types.
- if model == MODEL_R2EFF and cdp.exp_type in FIXED_TIME_EXP:
+ if model == MODEL_R2EFF and cdp.exp_type in
EXP_TYPE_LIST_FIXED_TIME:
self.interpreter.calc()
# Optimise the model.
@@ -354,7 +354,7 @@
"""
# Exponential curves.
- if model == 'R2eff' and cdp.exp_type not in FIXED_TIME_EXP:
+ if model == 'R2eff' and cdp.exp_type not in EXP_TYPE_LIST_FIXED_TIME:
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).
@@ -367,24 +367,24 @@
self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2eff', file='r2eff.agr', dir=path, force=True)
# The I0 parameter.
- if model == 'R2eff' and cdp.exp_type not in FIXED_TIME_EXP:
+ if model == 'R2eff' and cdp.exp_type not in EXP_TYPE_LIST_FIXED_TIME:
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 R20 parameter.
- #if cdp.exp_type in CPMG_EXP and model in [None, MODEL_LM63,
MODEL_CR72, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_EXPANDED]:
+ #if cdp.exp_type in EXP_TYPE_LIST_CPMG and model in [None,
MODEL_LM63, MODEL_CR72, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_EXPANDED]:
# self.interpreter.value.write(param='r2', file='r20.out',
dir=path, force=True)
# self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2', file='r20.agr', dir=path, force=True)
## The R20A and R20B parameters.
- #if cdp.exp_type in CPMG_EXP and model in [None, MODEL_CR72_FULL,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
+ #if cdp.exp_type in EXP_TYPE_LIST_CPMG and model in [None,
MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
# self.interpreter.value.write(param='r2a', file='r20a.out',
dir=path, force=True)
# self.interpreter.value.write(param='r2b', file='r20b.out',
dir=path, force=True)
# self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2a', file='r20a.agr', dir=path, force=True)
# self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2b', file='r20b.agr', dir=path, force=True)
## The R1rho parameter.
- #if cdp.exp_type in R1RHO_EXP and model in [None] + MODEL_LIST_R1RHO:
+ #if cdp.exp_type in EXP_TYPE_LIST_R1RHO and model in [None] +
MODEL_LIST_R1RHO:
# self.interpreter.value.write(param='r2', file='r1rho0.out',
dir=path, force=True)
# self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2', file='r1rho0.agr', dir=path, force=True)
@@ -432,7 +432,7 @@
self.interpreter.grace.write(x_data_type='res_num',
y_data_type='kC', file='kC.agr', dir=path, force=True)
# Minimisation statistics.
- if not (model == 'R2eff' and cdp.exp_type in FIXED_TIME_EXP):
+ if not (model == 'R2eff' and cdp.exp_type in
EXP_TYPE_LIST_FIXED_TIME):
self.interpreter.grace.write(y_data_type='chi2',
file='chi2.agr', dir=path, force=True)
# Finally save the results. This is last to allow the continuation
of an interrupted analysis while ensuring that all results files have been
created.
Modified: branches/relax_disp/gui/analyses/auto_relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/auto_relax_disp.py?rev=20816&r1=20815&r2=20816&view=diff
==============================================================================
--- branches/relax_disp/gui/analyses/auto_relax_disp.py (original)
+++ branches/relax_disp/gui/analyses/auto_relax_disp.py Wed Sep 4 18:49:06
2013
@@ -47,7 +47,7 @@
from gui.wizards.peak_intensity import Peak_intensity_wizard
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
from pipe_control.pipes import has_bundle, has_pipe
-from specific_analyses.relax_disp.variables import CPMG_EXP, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG_FULL,
MODEL_LIST_R1RHO_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02,
VAR_TIME_EXP
+from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG,
EXP_TYPE_LIST_VAR_TIME, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99,
MODEL_LIST_CPMG_FULL, MODEL_LIST_R1RHO_FULL, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02
from status import Status; status = Status()
@@ -124,7 +124,7 @@
ds.relax_gui.analyses[data_index].save_dir = self.gui.launch_dir
# Set the default dispersion models based on the experiment type.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
ds.relax_gui.analyses[data_index].disp_models = [
MODEL_R2EFF,
MODEL_NOREX,
@@ -156,10 +156,10 @@
# Set up some flags based on the experiment type.
self.relax_times_flag = False
- if cdp.exp_type in VAR_TIME_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_VAR_TIME:
self.relax_times_flag = True
self.relax_disp_cpmg = False
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
self.relax_disp_cpmg = True
# Execute the base class method to build the panel.
@@ -340,7 +340,7 @@
box.AddSpacer(10)
# Add the dispersion models GUI element, with spacing.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
self.model_field = Disp_model_list_cpmg(self, box)
else:
self.model_field = Disp_model_list_r1rho(self, box)
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20816&r1=20815&r2=20816&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Wed Sep 4
18:49:06 2013
@@ -48,7 +48,7 @@
from specific_analyses.api_common import API_common
from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, loop_cluster, loop_frq, loop_frq_point,
loop_frq_point_key, loop_frq_point_time, loop_point, loop_time, relax_time,
return_cpmg_frqs, return_index_from_disp_point, return_index_from_frq,
return_key_from_disp_point_index, return_offset_data,
return_param_key_from_data, return_r1_data, return_r2eff_arrays,
return_spin_lock_nu1, return_value_from_frq_index, spin_ids_to_containers
from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
loop_parameters, param_conversion, param_index_to_param_info, param_num
-from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_M61, MODEL_M61B, MODEL_NOREX,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02,
MODEL_TSMFK01, R1RHO_EXP, VAR_TIME_EXP
+from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_FIXED_TIME,
EXP_TYPE_LIST_VAR_TIME, MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_M61, MODEL_M61B,
MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02,
MODEL_TSMFK01
from target_functions.relax_disp import Dispersion
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
@@ -176,7 +176,7 @@
"""
# Check.
- if cdp.exp_type in FIXED_TIME_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_FIXED_TIME:
raise RelaxError("Back-calculation is not allowed for the fixed
time experiment types.")
# The key.
@@ -303,7 +303,7 @@
raise RelaxError("The relaxation dispersion experiment '%s' is
invalid." % exp_type)
# Sanity check.
- if exp_type not in FIXED_TIME_EXP and exp_type not in VAR_TIME_EXP:
+ if exp_type not in EXP_TYPE_LIST_FIXED_TIME and exp_type not in
EXP_TYPE_LIST_VAR_TIME:
raise RelaxError("The experiment type '%s' is neither a fixed
relaxation time period or variable relaxation time period experiment." %
exp_type)
# Store the value.
@@ -644,7 +644,7 @@
raise RelaxError("The relaxation dispersion experiment type has
not been set.")
# Test for the C-modules.
- if model == MODEL_R2EFF and cdp.exp_type in VAR_TIME_EXP and not
C_module_exp_fn:
+ if model == MODEL_R2EFF and cdp.exp_type in EXP_TYPE_LIST_VAR_TIME
and not C_module_exp_fn:
raise RelaxError("The exponential curve-fitting C module cannot
be found.")
# R2eff/R1rho model.
@@ -877,7 +877,7 @@
raise RelaxError("The spin-lock field strengths have not
been set up.")
# Only allow the fixed relaxation time period data types.
- if cdp.exp_type not in FIXED_TIME_EXP:
+ if cdp.exp_type not in EXP_TYPE_LIST_FIXED_TIME:
raise RelaxError("The experiment '%s' is not of the fixed
relaxation time period data type, the R2eff/R1rho values cannot be directly
calculated." % cdp.exp_type)
# Printouts.
@@ -1135,7 +1135,7 @@
# Special exponential curve-fitting for the 'R2eff' model.
if cdp.model_type == 'R2eff':
# Sanity checks.
- if cdp.exp_type in FIXED_TIME_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_FIXED_TIME:
raise RelaxError("The R2eff model with the fixed time period
CPMG experiment cannot be optimised.")
# Optimisation.
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=20816&r1=20815&r2=20816&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Wed Sep 4
18:49:06 2013
@@ -46,7 +46,7 @@
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
from pipe_control.result_files import add_result_file
-from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
R1RHO_EXP
+from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG,
EXP_TYPE_LIST_FIXED_TIME, EXP_TYPE_LIST_R1RHO
from stat import S_IRWXU, S_IRGRP, S_IROTH
from os import chmod, path, sep
@@ -195,7 +195,7 @@
"""
# The dispersion data.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
disp_data = cdp.cpmg_frqs
else:
disp_data = cdp.spin_lock_nu1
@@ -349,9 +349,9 @@
"""
# CPMG type data.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
fields = cdp.cpmg_frqs_list
- elif cdp.exp_type in R1RHO_EXP:
+ elif cdp.exp_type in EXP_TYPE_LIST_R1RHO:
fields = cdp.spin_lock_nu1_list
else:
raise RelaxError("The experiment type '%s' is unknown." %
cdp.exp_type)
@@ -421,7 +421,7 @@
data.append([])
# Add a new label.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
label = "R\\s2eff\\N"
else:
label = "R\\s1\\xr\\B\\N"
@@ -452,7 +452,7 @@
data.append([])
# Add a new label.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
label = "Back-calculated R\\s2eff\\N"
else:
label = "Back-calculated R\\s1\\xr\\B\\N"
@@ -505,7 +505,7 @@
data[-1][-1].append(spin.r2eff_err[key])
# The axis labels.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
axis_labels = ['\\qCPMG pulse train frequency (Hz)\\Q',
'\\qR\\s2,eff\\N\\Q (rad.s\\S-1\\N)']
else:
axis_labels = ['\\qSpin-lock field strength (Hz)\\Q',
'\\qR\\s1\\xr\\B\\N\\Q (rad.s\\S-1\\N)']
@@ -728,15 +728,15 @@
index = 0
# CPMG-type experiments.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
index = cdp.cpmg_frqs_list.index(value)
# R1rho-type experiments.
- elif cdp.exp_type in R1RHO_EXP:
+ elif cdp.exp_type in EXP_TYPE_LIST_R1RHO:
index = cdp.spin_lock_nu1_list.index(value)
# Remove the reference point (always at index 0).
- if cdp.exp_type in FIXED_TIME_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_FIXED_TIME:
index -= 1
# Return the index.
@@ -770,11 +770,11 @@
"""
# CPMG-type experiments.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
return return_index_from_disp_point(cdp.cpmg_frqs[key])
# R1rho-type experiments.
- elif cdp.exp_type in R1RHO_EXP:
+ elif cdp.exp_type in EXP_TYPE_LIST_R1RHO:
return return_index_from_disp_point(cdp.spin_lock_nu1[key])
@@ -797,7 +797,7 @@
"""
# Checks.
- if ref and cdp.exp_type not in FIXED_TIME_EXP:
+ if ref and cdp.exp_type not in EXP_TYPE_LIST_FIXED_TIME:
raise RelaxError("The reference peak intensity does not exist for
the variable relaxation time period experiment types.")
# The key.
@@ -822,14 +822,14 @@
"""
# Insert the reference point (always at index 0).
- if cdp.exp_type in FIXED_TIME_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_FIXED_TIME:
disp_point_index += 1
# The frequency.
frq = return_value_from_frq_index(frq_index)
# CPMG data.
- if cdp.exp_type in CPMG_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_CPMG:
point = cdp.cpmg_frqs_list[disp_point_index]
points = cdp.cpmg_frqs
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=20816&r1=20815&r2=20816&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Wed Sep 4
18:49:06 2013
@@ -36,7 +36,7 @@
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin
from specific_analyses.relax_disp.disp_data import count_frq, loop_cluster,
loop_frq, loop_frq_point
-from specific_analyses.relax_disp.variables import MODEL_R2EFF, MODEL_M61B,
VAR_TIME_EXP
+from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_VAR_TIME,
MODEL_R2EFF, MODEL_M61B
def assemble_param_vector(spins=None, key=None, sim_index=None):
@@ -743,7 +743,7 @@
# The R2eff model.
if cdp.model_type == 'R2eff':
# Exponential curves (with clustering).
- if cdp.exp_type in VAR_TIME_EXP:
+ if cdp.exp_type in EXP_TYPE_LIST_VAR_TIME:
return 2 * len(spins)
# Fixed time period experiments (with clustering).
r20816 - in /branches/relax_disp: auto_analyses/ gui/analyses/ specific_analyses/relax_disp/