Author: bugman
Date: Thu Nov 21 14:17:45 2013
New Revision: 21574
URL: http://svn.gna.org/viewcvs/relax?rev=21574&view=rev
Log:
Some bug fixes for the previous commit (r21573).
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
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=21574&r1=21573&r2=21574&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Thu Nov 21
14:17:45 2013
@@ -48,7 +48,7 @@
from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, get_curve_type, has_exponential_exp_type,
has_proton_mmq_cpmg, loop_cluster, loop_exp_frq_point,
loop_exp_frq_point_time, loop_frq, loop_time, pack_back_calc_r2eff,
return_cpmg_frqs, return_index_from_disp_point, return_index_from_exp_type,
return_index_from_frq, return_offset_data, return_param_key_from_data,
return_r1_data, return_r2eff_arrays, return_spin_lock_nu1,
spin_ids_to_containers
from specific_analyses.relax_disp.optimisation import Disp_memo,
Disp_minimise_command, grid_search_setup
from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, get_param_names,
linear_constraints, param_index_to_param_info, param_num
-from specific_analyses.relax_disp.variables import MODEL_LIST_FULL,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94,
MODEL_IT99, MODEL_LIST_MMQ, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE,
MODEL_MP05, MODEL_MQ_CR72, 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_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_MMQ,
MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72,
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_TAP03, 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
@@ -748,7 +748,7 @@
back_calc = self._back_calc_r2eff(spin=spin, spin_id=spin_id)
# Pack the data.
- pack_back_calc_r2eff(spin=spin, spin_index=0,
back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
+ pack_back_calc_r2eff(spin=spin, spin_id=spin_id,
spin_index=0, back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
def constraint_algorithm(self):
@@ -781,20 +781,35 @@
# All other models (with R2eff/R1rho base data).
else:
+ # MMQ flags.
+ proton_mmq_flag = has_proton_mmq_cpmg()
+
# Unpack the data.
spin, spin_id = data_id
# Back calculate the R2eff/R1rho data.
back_calc = self._back_calc_r2eff(spin=spin, spin_id=spin_id)
+
+ # Get the attached proton data.
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+ proton_back_calc = self._back_calc_r2eff(spin=proton,
spin_id=spin_id)
# Convert to a dictionary matching the R2eff data structure.
values = {}
for exp_type, frq, point, exp_type_index, frq_index, point_index
in loop_exp_frq_point(return_indices=True):
+ # Alias the correct data.
+ current_bc = back_calc
+ current_spin = spin
+ if exp_type in [EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_PROTON_MQ]:
+ current_spin = proton
+ current_bc = proton_back_calc
+
# The parameter key.
param_key = return_param_key_from_data(exp_type=exp_type,
frq=frq, point=point)
# Skip missing data.
- if param_key not in spin.r2eff.keys():
+ if not hasattr(current_spin, 'r2eff') or param_key not in
current_spin.r2eff.keys():
continue
# Store the result.
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=21574&r1=21573&r2=21574&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
14:17:45 2013
@@ -1051,11 +1051,13 @@
return count
-def pack_back_calc_r2eff(spin=None, spin_index=None, back_calc=None,
proton_mmq_flag=False):
+def pack_back_calc_r2eff(spin=None, spin_id=None, spin_index=None,
back_calc=None, proton_mmq_flag=False):
"""Store the back calculated R2eff data for the given spin.
@keyword spin: The spin data container to store the data in.
@type spin: SpinContainer instance
+ @keyword spin_id: The spin ID string.
+ @type spin_id: str
@keyword spin_index: The index of the given spin in the cluster.
@type spin_index: int
@keyword back_calc: The back calculated data. The first index
corresponds to the experiment type, the second is the spin of the cluster,
the third is the magnetic field strength, and the fourth is the dispersion
point.
@@ -1067,7 +1069,7 @@
# Get the attached proton.
proton = None
if proton_mmq_flag:
- proton = return_attached_protons(memo.spin_ids[spin_index])[0]
+ proton = return_attached_protons(spin_id)[0]
# Loop over the R2eff data.
for exp_type, frq, point, exp_type_index, frq_index, point_index in
loop_exp_frq_point(return_indices=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=21574&r1=21573&r2=21574&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/relax_disp/specific_analyses/relax_disp/optimisation.py Thu Nov
21 14:17:45 2013
@@ -488,4 +488,4 @@
# Loop over each spin, packing the data.
for spin_index in range(len(memo.spins)):
- pack_back_calc_r2eff(spin=memo.spins[spin_index],
spin_index=spin_index, back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
+ pack_back_calc_r2eff(spin=memo.spins[spin_index],
spin_id=memo.spin_ids[spin_index], spin_index=spin_index,
back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
r21574 - in /branches/relax_disp/specific_analyses/relax_disp: api.py disp_data.py optimisation.py