Author: bugman
Date: Thu Nov 21 11:42:43 2013
New Revision: 21572
URL: http://svn.gna.org/viewcvs/relax?rev=21572&view=rev
Log:
Bug fix for the multiple quantum relaxation dispersion models.
These require both the heteronuclear and proton chemical shift differences.
But the proton
difference was being scaled by the heteronuclear Larmor frequency and not the
proton frequency.
Modified:
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/optimisation.py
branches/relax_disp/target_functions/relax_disp.py
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=21572&r1=21571&r2=21572&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Thu Nov 21
11:42:43 2013
@@ -134,7 +134,7 @@
field_count = cdp.spectrometer_frq_count
# Initialise the data structures for the target function.
- values, errors, missing, frqs, exp_types, relax_times =
return_r2eff_arrays(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
+ values, errors, missing, frqs, frqs_H, exp_types, relax_times =
return_r2eff_arrays(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
# The offset and R1 data for R1rho off-resonance models.
chemical_shifts, offsets, tilt_angles, r1 = None, None, None, None
@@ -147,7 +147,7 @@
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Initialise the relaxation dispersion fit functions.
- model = Dispersion(model=spin.model,
num_params=param_num(spins=[spin]), num_spins=1, num_frq=field_count,
exp_types=exp_types, values=values, errors=errors, missing=missing,
frqs=frqs, cpmg_frqs=cpmg_frqs, spin_lock_nu1=spin_lock_nu1,
chemical_shifts=chemical_shifts, spin_lock_offsets=offsets,
tilt_angles=tilt_angles, r1=r1, relax_times=relax_times,
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=spin.model,
num_params=param_num(spins=[spin]), num_spins=1, num_frq=field_count,
exp_types=exp_types, values=values, errors=errors, missing=missing,
frqs=frqs, frqs_H=frqs_H, cpmg_frqs=cpmg_frqs, spin_lock_nu1=spin_lock_nu1,
chemical_shifts=chemical_shifts, spin_lock_offsets=offsets,
tilt_angles=tilt_angles, r1=r1, relax_times=relax_times,
scaling_matrix=scaling_matrix)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
chi2 = model.func(param_vector)
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=21572&r1=21571&r2=21572&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Thu Nov 21
11:42:43 2013
@@ -528,7 +528,7 @@
# Get all the data.
try:
- values, errors, missing, frqs, exp_types, relax_times =
return_r2eff_arrays(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
+ values, errors, missing, frqs, frqs_H, exp_types, relax_times =
return_r2eff_arrays(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
# No R2eff data, so skip the rest.
except RelaxError:
@@ -2084,23 +2084,27 @@
errors = []
missing = []
frqs = []
+ frqs_H = []
relax_times = []
for exp_i in range(exp_num):
values.append([])
errors.append([])
missing.append([])
frqs.append([])
+ frqs_H.append([])
relax_times.append([])
for spin_i in range(spin_num):
values[-1].append([])
errors[-1].append([])
missing[-1].append([])
frqs[-1].append([])
+ frqs_H[-1].append([])
for field_i in range(field_count):
values[-1][-1].append([])
errors[-1][-1].append([])
missing[-1][-1].append([])
frqs[-1][-1].append(None)
+ frqs_H[-1][-1].append(None)
for field_i in range(field_count):
relax_times[-1].append(None)
@@ -2151,9 +2155,10 @@
# The key.
key = return_param_key_from_data(exp_type=exp_type, frq=frq,
point=point)
- # The Larmor frequency for this spin and field strength (in
MHz*2pi to speed up the ppm to rad/s conversion).
+ # The Larmor frequency for this spin (and that of an attached
proton for the MMQ models) and field strength (in MHz*2pi to speed up the ppm
to rad/s conversion).
if frq != None:
- frqs[exp_type_index][spin_index][frq_index] = 2.0 * pi * frq
/ g1H * return_gyromagnetic_ratio(current_spin.isotope) * 1e-6
+ frqs[exp_type_index][spin_index][frq_index] = 2.0 * pi * frq
/ g1H * return_gyromagnetic_ratio(spin.isotope) * 1e-6
+ frqs_H[exp_type_index][spin_index][frq_index] = 2.0 * pi *
frq * 1e-6
# Missing data.
if key not in current_spin.r2eff.keys():
@@ -2214,7 +2219,7 @@
missing[exp_type_index][spin_index][frq_index] =
array(missing[exp_type_index][spin_index][frq_index], int32)
# Return the structures.
- return values, errors, missing, frqs, exp_types, relax_times
+ return values, errors, missing, frqs, frqs_H, exp_types, relax_times
def return_spin_lock_nu1(ref_flag=True):
Modified: branches/relax_disp/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/optimisation.py?rev=21572&r1=21571&r2=21572&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/relax_disp/specific_analyses/relax_disp/optimisation.py Thu Nov
21 11:42:43 2013
@@ -297,7 +297,7 @@
raise RelaxError("The spectrometer frequency information has not
been specified.")
# The R2eff/R1rho data.
- self.values, self.errors, self.missing, self.frqs, self.exp_types,
self.relax_times = return_r2eff_arrays(spins=spins, spin_ids=spin_ids,
fields=fields, field_count=len(fields), sim_index=sim_index)
+ self.values, self.errors, self.missing, self.frqs, self.frqs_H,
self.exp_types, self.relax_times = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=fields, field_count=len(fields),
sim_index=sim_index)
# The offset and R1 data for R1rho off-resonance models.
self.chemical_shifts, self.offsets, self.tilt_angles, self.r1 =
None, None, None, None
@@ -330,7 +330,7 @@
print("Unconstrained grid search size: %s (constraints may
decrease this size).\n" % self.grid_size)
# Initialise the function to minimise.
- model = Dispersion(model=self.spins[0].model,
num_params=self.param_num, num_spins=len(self.spins),
num_frq=len(self.fields), exp_types=self.exp_types, values=self.values,
errors=self.errors, missing=self.missing, frqs=self.frqs,
cpmg_frqs=self.cpmg_frqs, spin_lock_nu1=self.spin_lock_nu1,
chemical_shifts=self.chemical_shifts, spin_lock_offsets=self.offsets,
tilt_angles=self.tilt_angles, r1=self.r1, relax_times=self.relax_times,
scaling_matrix=self.scaling_matrix)
+ model = Dispersion(model=self.spins[0].model,
num_params=self.param_num, num_spins=len(self.spins),
num_frq=len(self.fields), exp_types=self.exp_types, values=self.values,
errors=self.errors, missing=self.missing, frqs=self.frqs, frqs_H=self.frqs_H,
cpmg_frqs=self.cpmg_frqs, spin_lock_nu1=self.spin_lock_nu1,
chemical_shifts=self.chemical_shifts, spin_lock_offsets=self.offsets,
tilt_angles=self.tilt_angles, r1=self.r1, relax_times=self.relax_times,
scaling_matrix=self.scaling_matrix)
# Grid search.
if search('^[Gg]rid', self.min_algor):
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=21572&r1=21571&r2=21572&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Thu Nov 21 11:42:43
2013
@@ -53,7 +53,7 @@
class Dispersion:
- def __init__(self, model=None, num_params=None, num_spins=None,
num_frq=None, exp_types=None, values=None, errors=None, missing=None,
frqs=None, cpmg_frqs=None, spin_lock_nu1=None, chemical_shifts=None,
spin_lock_offsets=None, tilt_angles=None, r1=None, relax_times=None,
scaling_matrix=None):
+ def __init__(self, model=None, num_params=None, num_spins=None,
num_frq=None, exp_types=None, values=None, errors=None, missing=None,
frqs=None, frqs_H=None, cpmg_frqs=None, spin_lock_nu1=None,
chemical_shifts=None, spin_lock_offsets=None, tilt_angles=None, r1=None,
relax_times=None, scaling_matrix=None):
"""Relaxation dispersion target functions for optimisation.
Models
@@ -103,6 +103,8 @@
@type missing: list of lists of lists of numpy rank-1
int arrays
@keyword frqs: The spin Larmor frequencies (in MHz*2pi
to speed up the ppm to rad/s conversion). The dimensions correspond to the
first three of the value, error and missing structures.
@type frqs: list of lists of numpy rank-1 float
arrays
+ @keyword frqs_H: The proton spin Larmor frequencies for
the MMQ-type models (in MHz*2pi to speed up the ppm to rad/s conversion).
The dimensions correspond to the first three of the value, error and missing
structures.
+ @type frqs_H: list of lists of numpy rank-1 float
arrays
@keyword cpmg_frqs: The CPMG frequencies in Hertz for each
separate dispersion point. This will be ignored for R1rho experiments.
@type cpmg_frqs: list of lists of lists of floats
@keyword spin_lock_nu1: The spin-lock field strengths in Hertz
for each separate dispersion point. This will be ignored for CPMG
experiments.
@@ -146,6 +148,7 @@
self.errors = errors
self.missing = missing
self.frqs = frqs
+ self.frqs_H = frqs_H
self.cpmg_frqs = cpmg_frqs
self.spin_lock_nu1 = spin_lock_nu1
self.chemical_shifts = chemical_shifts
@@ -947,7 +950,7 @@
# 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[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:
@@ -1017,7 +1020,7 @@
# 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[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])
r21572 - in /branches/relax_disp: specific_analyses/relax_disp/ target_functions/