Author: bugman
Date: Thu Nov 21 21:59:57 2013
New Revision: 21588
URL: http://svn.gna.org/viewcvs/relax?rev=21588&view=rev
Log:
Converted the 'MQ CR72' dispersion model to handle MMQ data.
This model can now handle proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG-type
data. Some debugging
might still be required.
Modified:
branches/relax_disp/specific_analyses/relax_disp/parameters.py
branches/relax_disp/specific_analyses/relax_disp/variables.py
branches/relax_disp/target_functions/relax_disp.py
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=21588&r1=21587&r2=21588&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Thu Nov 21
21:59:57 2013
@@ -34,7 +34,7 @@
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 generate_r20_key,
has_exponential_exp_type, loop_cluster, loop_exp_frq,
return_value_from_frq_index
-from specific_analyses.relax_disp.variables import MODEL_M61B,
MODEL_MMQ_2SITE
+from specific_analyses.relax_disp.variables import MODEL_LIST_MMQ, MODEL_M61B
def assemble_param_vector(spins=None, key=None, sim_index=None):
@@ -554,7 +554,7 @@
# Chemical exchange difference (dw >= 0).
elif param_name in ['dw', 'dwH']:
- if not spins[0].model in [MODEL_MMQ_2SITE]:
+ if not spins[0].model in MODEL_LIST_MMQ:
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
b.append(0.0)
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=21588&r1=21587&r2=21588&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/variables.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/variables.py Thu Nov 21
21:59:57 2013
@@ -150,7 +150,7 @@
MODEL_LIST_MQ_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_MQ_CR72,
MODEL_MMQ_2SITE]
"""The list of the R2eff model together with all dispersion models
specifically for MQ CPMG-type experiments."""
-MODEL_LIST_MMQ = [MODEL_MMQ_2SITE]
+MODEL_LIST_MMQ = [MODEL_MQ_CR72, MODEL_MMQ_2SITE]
"""The list of all dispersion models specifically for MMQ CPMG-type
experiments."""
MODEL_LIST_ANALYTIC = [MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72,
MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01,MODEL_M61, MODEL_M61B,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_MQ_CR72]
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=21588&r1=21587&r2=21588&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Thu Nov 21 21:59:57
2013
@@ -1009,29 +1009,48 @@
k_AB = pB * kex
# Initialise.
- chi2_sum = 0.0
-
- # Loop over the spins.
- for spin_index in range(self.num_spins):
- # Loop over the spectrometer frequencies.
- for frq_index in range(self.num_frq):
- # The R20 index.
- r20_index = frq_index + spin_index*self.num_frq
-
- # Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
- dwH_frq = dwH[spin_index] *
self.frqs_H[0][spin_index][frq_index]
-
- # Back calculate the R2eff values.
- r2eff_mq_cr72(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq,
dwH=dwH_frq, kex=kex, k_AB=k_AB, k_BA=k_BA,
cpmg_frqs=self.cpmg_frqs[0][frq_index], tcp=self.tau_cpmg[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index], power=self.power[0][frq_index])
-
- # For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
- for point_index in range(self.num_disp_points[0][frq_index]):
- if self.missing[spin_index][frq_index][point_index]:
- self.back_calc[spin_index][frq_index][point_index] =
self.values[spin_index][frq_index][point_index]
-
- # Calculate and return the chi-squared value.
- chi2_sum += chi2(self.values[spin_index][frq_index],
self.back_calc[spin_index][frq_index], self.errors[spin_index][frq_index])
+ aliased_dwH = 0.0
+ chi2_sum = 0.0
+
+ # Loop over the experiment types.
+ for exp_index in range(self.num_exp):
+ # Loop over the spins.
+ for spin_index in range(self.num_spins):
+ # Loop over the spectrometer frequencies.
+ for frq_index in range(self.num_frq):
+ # The R20 index.
+ r20_index = frq_index + spin_index*self.num_frq
+
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw[spin_index] *
self.frqs[exp_index][spin_index][frq_index]
+ dwH_frq = dwH[spin_index] *
self.frqs_H[exp_index][spin_index][frq_index]
+
+ # Alias the dw frequency combinations.
+ if self.exp_types[exp_index] == EXP_TYPE_CPMG_SQ:
+ aliased_dw = dw_frq
+ elif self.exp_types[exp_index] ==
EXP_TYPE_CPMG_PROTON_SQ:
+ aliased_dw = dwH_frq
+ elif self.exp_types[exp_index] == EXP_TYPE_CPMG_DQ:
+ aliased_dw = dwH_frq + dw_frq
+ elif self.exp_types[exp_index] == EXP_TYPE_CPMG_ZQ:
+ aliased_dw = dwH_frq - dw_frq
+ elif self.exp_types[exp_index] == EXP_TYPE_CPMG_MQ:
+ aliased_dw = dw_frq
+ aliased_dwH = dwH_frq
+ elif self.exp_types[exp_index] ==
EXP_TYPE_CPMG_PROTON_MQ:
+ aliased_dw = dwH_frq
+ aliased_dwH = dw_frq
+
+ # Back calculate the R2eff values.
+ r2eff_mq_cr72(r20=R20[r20_index], pA=pA, pB=pB,
dw=aliased_dw, dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA,
cpmg_frqs=self.cpmg_frqs[exp_index][frq_index],
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
+
+ # For all missing data points, set the back-calculated
value to the measured values so that it has no effect on the chi-squared
value.
+ for point_index in
range(self.num_disp_points[exp_index][frq_index]):
+ if
self.missing[exp_index][spin_index][frq_index][point_index]:
+
self.back_calc[exp_index][spin_index][frq_index][point_index] =
self.values[spin_index][frq_index][point_index]
+
+ # Calculate and return the chi-squared value.
+ chi2_sum +=
chi2(self.values[exp_index][spin_index][frq_index],
self.back_calc[exp_index][spin_index][frq_index],
self.errors[exp_index][spin_index][frq_index])
# Return the total chi-squared value.
return chi2_sum
r21588 - in /branches/relax_disp: specific_analyses/relax_disp/ target_functions/