Author: bugman
Date: Fri May 3 18:10:56 2013
New Revision: 19646
URL: http://svn.gna.org/viewcvs/relax?rev=19646&view=rev
Log:
Shifted all of the constant relaxation dispersion variables into the specific
module.
All of the dispersion code now uses the variables of
specific_analyses.relax_disp.variables.
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
branches/relax_disp/specific_analyses/relax_disp/variables.py
branches/relax_disp/user_functions/relax_disp.py
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=19646&r1=19645&r2=19646&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Fri May 3
18:10:56 2013
@@ -57,7 +57,7 @@
from specific_analyses.api_common import API_common
from specific_analyses.relax_disp.disp_data import exp_curve_index_from_key,
exp_curve_key_from_index, intensity_key, loop_all_data,
loop_dispersion_point, loop_exp_curve, loop_spectrometer, relax_time,
return_key
from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
param_index_to_param_info, param_num
-from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
R1RHO_EXP, VAR_TIME_EXP
+from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
MODEL_R2EFF, MODEL_LM63, MODEL_CR72, R1RHO_EXP, VAR_TIME_EXP
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
@@ -65,13 +65,6 @@
# C modules.
if C_module_exp_fn:
from target_functions.relax_fit import setup, func, dfunc, d2func,
back_calc_I
-
-
-# Some module variables.
-FIXED_TIME_EXP = ['cpmg fixed']
-VAR_TIME_EXP = ['cpmg', 'r1rho']
-CPMG_EXP = ['cpmg', 'cpmg fixed']
-R1RHO_EXP = ['r1rho']
class Relax_disp(API_base, API_common):
@@ -121,7 +114,7 @@
"""
# The R2eff model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_R2EFF:
# Check.
if cdp.exp_type in FIXED_TIME_EXP:
raise RelaxError("Back-calculation is not allowed for the
fixed time experiment types.")
@@ -689,10 +682,10 @@
add_result_file(type='grace', label='Grace', file=file_path)
- def _select_model(self, model='R2eff'):
+ def _select_model(self, model=MODEL_R2EFF):
"""Set up the model for the relaxation dispersion analysis.
- @keyword model: The relaxation dispersion analysis type. This can
be one of 'R2eff', 'fast 2-site', 'slow 2-site'.
+ @keyword model: The relaxation dispersion analysis type. This can
be one of 'R2eff', 'LM63', 'CR72'.
@type model: str
"""
@@ -713,21 +706,21 @@
raise RelaxError("The relaxation dispersion experiment type has
not been set.")
# Test for the C-modules.
- if 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 VAR_TIME_EXP and not
C_module_exp_fn:
raise RelaxError("The exponential curve-fitting C module cannot
be found.")
# R2eff/R1rho model.
- if model == 'R2eff':
+ if model == MODEL_R2EFF:
print("R2eff/R1rho value and error determination.")
params = ['r2eff', 'i0']
# LM63 model.
- elif model == 'LM63':
+ elif model == MODEL_LM63:
print("The Luz and Meiboom (1963) 2-site fast exchange model.")
params = ['r2', 'rex', 'kex']
# CR72 model.
- elif model == 'CR72':
+ elif model == MODEL_CR72:
print("The Carver and Richards (1972) 2-site model for all time
scales.")
params = ['r2', 'r2a', 'ka', 'dw']
@@ -953,7 +946,7 @@
cdp.spin_lock_nu1_list = []
# Special exponential curve-fitting for the 'R2eff' model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_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.")
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=19646&r1=19645&r2=19646&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri May 3
18:10:56 2013
@@ -31,7 +31,7 @@
from lib.errors import RelaxError
from lib.mathematics import round_to_next_order
from specific_analyses.relax_disp.disp_data import loop_exp_curve
-from specific_analyses.relax_disp.variables import VAR_TIME_EXP
+from specific_analyses.relax_disp.variables import MODEL_R2EFF, VAR_TIME_EXP
def assemble_param_vector(spins=None, key=None, sim_index=None):
@@ -51,7 +51,7 @@
param_vector = []
# The R2eff model parameters.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_R2EFF:
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -188,7 +188,7 @@
return scaling_matrix
# The R2eff model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_R2EFF:
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -267,7 +267,7 @@
param_index = 0
# The R2eff model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_R2EFF:
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -422,7 +422,7 @@
j = 0
# The R2eff model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_R2EFF:
for spin_index in range(len(spins)):
# Alias the spin.
spin = spins[spin_index]
@@ -505,7 +505,7 @@
spin_index = 0
# The R2eff model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_R2EFF:
# The number of spin specific parameters (R2eff and I0 per spin).
num = len(spins) * 2
@@ -538,7 +538,7 @@
"""
# The R2eff model.
- if cdp.model == 'R2eff':
+ if cdp.model == MODEL_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/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/variables.py?rev=19646&r1=19645&r2=19646&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/variables.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/variables.py Fri May 3
18:10:56 2013
@@ -23,8 +23,26 @@
# Module docstring.
"""Variables for the relaxation dispersion specific analysis."""
-# Some variables for relaxation dispersion.
+# The experiment type lists.
FIXED_TIME_EXP = ['cpmg fixed']
+"""The list of fixed relaxation time period experiments."""
+
VAR_TIME_EXP = ['cpmg', 'r1rho']
+"""The list of variable relaxation time period experiments."""
+
CPMG_EXP = ['cpmg', 'cpmg fixed']
+"""The list of CPMG-type experiments."""
+
R1RHO_EXP = ['r1rho']
+"""The list of R1rho-type experiments."""
+
+
+# The model names.
+MODEL_R2EFF = 'R2eff'
+"""The model for determining the R2eff/R1rho values from peak intensities."""
+
+MODEL_LM63 = 'LM63'
+"""The Luz and Meiboom (1963) 2-site fast exchange model."""
+
+MODEL_CR72 = 'CR72'
+"""The Carver and Richards (1972) 2-site model for all time scales."""
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=19646&r1=19645&r2=19646&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Fri May 3 18:10:56 2013
@@ -36,14 +36,10 @@
from pipe_control.mol_res_spin import get_spin_ids
from graphics import ANALYSIS_IMAGE_PATH, WIZARD_IMAGE_PATH
from specific_analyses.relax_disp.disp_data import cpmg_frq, relax_time,
spin_lock_field
+from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_LM63,
MODEL_R2EFF
from specific_analyses.setup import relax_disp_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
-
-# The model names.
-MODEL_R2EFF = 'R2eff'
-MODEL_LM63 = 'LM63'
-MODEL_CR72 = 'CR72'
# The user function class.
r19646 - in /branches/relax_disp: specific_analyses/relax_disp/ user_functions/