Author: bugman
Date: Tue Feb 25 09:23:31 2014
New Revision: 22298
URL: http://svn.gna.org/viewcvs/relax?rev=22298&view=rev
Log:
Merged revisions 22295 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22295 | bugman | 2014-02-25 09:13:32 +0100 (Tue, 25 Feb 2014) | 6 lines
Complete support for deselected spins has been added to the relaxation
dispersion analysis.
This fixes bug #21715 (https://gna.org/bugs/?21715), the failure of the
relaxation dispersion
auto-analysis when running a clustered analysis due to an IndexError during
minimisation.
........
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/specific_analyses/relax_disp/disp_data.py
branches/double_rotor/specific_analyses/relax_disp/optimisation.py
branches/double_rotor/specific_analyses/relax_disp/parameters.py
Propchange: branches/double_rotor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Feb 25 09:23:31 2014
@@ -1,1 +1,1 @@
-/trunk:1-22294
+/trunk:1-22297
Modified: branches/double_rotor/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/disp_data.py?rev=22298&r1=22297&r2=22298&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/double_rotor/specific_analyses/relax_disp/disp_data.py Tue Feb
25 09:23:31 2014
@@ -214,6 +214,19 @@
# Return the count.
return count
+
+
+def count_spins(spins=None):
+ """Count the number of selected spins in the spin cluster."""
+
+ # Count the selected spins.
+ spin_num = 0
+ for spin in spins:
+ if spin.select:
+ spin_num += 1
+
+ # Return the count.
+ return spin_num
def cpmg_frq(spectrum_id=None, cpmg_frq=None):
@@ -2698,7 +2711,10 @@
# The counts.
exp_num = num_exp_types()
- spin_num = len(spins)
+ spin_num = 0
+ for spin in spins:
+ if spin.select:
+ spin_num += 1
# Initialise the data structures for the target function.
fields_orig = fields
@@ -2723,10 +2739,15 @@
# Assemble the data.
data_flag = False
- for si in range(spin_num):
+ si = 0
+ for spin_index in range(len(spins)):
+ # Skip deselected spins.
+ if not spins[spin_index].select:
+ continue
+
# Alias the spin.
- spin = spins[si]
- spin_id = spin_ids[si]
+ spin = spins[spin_index]
+ spin_id = spin_ids[spin_index]
# No data.
shift = 0.0
@@ -2809,6 +2830,9 @@
else:
theta[ei][si][mi][oi].append(atan(omega1 / Delta_omega))
+ # Increment the spin index.
+ si += 1
+
# No shift data for the spin cluster.
if not data_flag:
return None, None, None
@@ -2874,7 +2898,7 @@
"""
# The spin count.
- spin_num = len(spins)
+ spin_num = count_spins(spins)
# Initialise the data structure.
r1 = -ones((spin_num, field_count), float64)
@@ -2949,7 +2973,7 @@
# The counts.
exp_num = num_exp_types()
- spin_num = len(spins)
+ spin_num = count_spins(spins)
# 1H MMQ flag.
proton_mmq_flag = has_proton_mmq_cpmg()
@@ -2990,10 +3014,15 @@
# Pack the R2eff/R1rho data.
data_flag = False
- for si in range(spin_num):
+ si = 0
+ for spin_index in range(len(spins)):
+ # Skip deselected spins.
+ if not spins[spin_index].select:
+ continue
+
# Alias the spin.
- spin = spins[si]
- spin_id = spin_ids[si]
+ spin = spins[spin_index]
+ spin_id = spin_ids[spin_index]
# Get the attached proton.
proton = None
@@ -3089,6 +3118,9 @@
# Store the time.
relax_times[ei][mi] = relax_time
+
+ # Increment the spin index.
+ si += 1
# No R2eff/R1rho data for the spin cluster.
if not data_flag:
Modified: branches/double_rotor/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/optimisation.py?rev=22298&r1=22297&r2=22298&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/double_rotor/specific_analyses/relax_disp/optimisation.py Tue
Feb 25 09:23:31 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2013 Edward d'Auvergne
#
+# Copyright (C) 2013-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -35,7 +35,7 @@
from lib.errors import RelaxError
from lib.text.sectioning import subsection
from multi import Memo, Result_command, Slave_command
-from specific_analyses.relax_disp.disp_data import has_disp_data,
has_proton_mmq_cpmg, loop_exp, loop_exp_frq, loop_exp_frq_offset_point,
loop_frq, loop_offset, 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,
return_value_from_frq_index
+from specific_analyses.relax_disp.disp_data import count_spins,
has_disp_data, has_proton_mmq_cpmg, loop_exp, loop_exp_frq,
loop_exp_frq_offset_point, loop_frq, loop_offset, 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,
return_value_from_frq_index
from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
loop_parameters, param_conversion, param_num
from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_LIST_CPMG, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_LIST_MMQ, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05,
MODEL_NS_R1RHO_2SITE, MODEL_TAP03, MODEL_TP02
from target_functions.relax_disp import Dispersion
@@ -431,7 +431,7 @@
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, frqs_H=self.frqs_H,
cpmg_frqs=self.cpmg_frqs, spin_lock_nu1=self.spin_lock_nu1,
chemical_shifts=self.chemical_shifts, offset=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=count_spins(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, offset=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):
@@ -539,6 +539,10 @@
# Monte Carlo minimisation statistics.
if memo.sim_index != None:
for spin in memo.spins:
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
# Chi-squared statistic.
spin.chi2_sim[memo.sim_index] = self.chi2
@@ -560,6 +564,10 @@
# Normal statistics.
else:
for spin in memo.spins:
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
# Chi-squared statistic.
spin.chi2 = self.chi2
@@ -584,5 +592,14 @@
proton_mmq_flag = has_proton_mmq_cpmg()
# Loop over each spin, packing the data.
- for si in range(len(memo.spins)):
- pack_back_calc_r2eff(spin=memo.spins[si],
spin_id=memo.spin_ids[si], si=si, back_calc=self.back_calc,
proton_mmq_flag=proton_mmq_flag)
+ si = 0
+ for spin_index in range(len(memo.spins)):
+ # Skip deselected spins.
+ if not memo.spins[spin_index].select:
+ continue
+
+ # Pack the data.
+ pack_back_calc_r2eff(spin=memo.spins[spin_index],
spin_id=memo.spin_ids[spin_index], si=si, back_calc=self.back_calc,
proton_mmq_flag=proton_mmq_flag)
+
+ # Increment the spin index.
+ si += 1
Modified: branches/double_rotor/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/parameters.py?rev=22298&r1=22297&r2=22298&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/relax_disp/parameters.py
(original)
+++ branches/double_rotor/specific_analyses/relax_disp/parameters.py Tue Feb
25 09:23:31 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2013 Edward d'Auvergne
#
+# Copyright (C) 2004-2014 Edward d'Auvergne
#
# Copyright (C) 2009 Sebastien Morin
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
@@ -33,7 +33,7 @@
from lib.text.sectioning import subsection
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.disp_data import count_spins,
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_LIST_MMQ,
MODEL_M61B, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR
@@ -342,6 +342,10 @@
# Initialise parameters if needed.
for spin in spins:
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
# The R2 parameter.
if 'r2' in spin.params:
if sim_index != None:
@@ -687,6 +691,10 @@
if cdp.model_type == 'R2eff':
# Loop over the spins.
for spin_index in range(len(spins)):
+ # Skip deselected spins.
+ if not spins[spin_index].select:
+ continue
+
# Yield the two parameters.
params = ['r2eff', 'i0']
for i in range(2):
@@ -700,6 +708,10 @@
else:
# First the R2 parameters (one per spin per field strength).
for spin_index in range(len(spins)):
+ # Skip deselected spins.
+ if not spins[spin_index].select:
+ continue
+
# The R2 parameter.
if 'r2' in spins[0].params:
for exp_type, frq in loop_exp_frq():
@@ -720,6 +732,10 @@
# Then the chemical shift difference parameters 'phi_ex',
'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per
spin).
for spin_index in range(len(spins)):
+ # Skip deselected spins.
+ if not spins[spin_index].select:
+ continue
+
# Yield the data.
if 'phi_ex' in spins[spin_index].params:
param_index += 1
@@ -748,6 +764,10 @@
# Then a separate block for the proton chemical shift difference
parameters for the MQ models (one per spin).
for spin_index in range(len(spins)):
+ # Skip deselected spins.
+ if not spins[spin_index].select:
+ continue
+
if 'dwH' in spins[spin_index].params:
param_index += 1
yield 'dwH', param_index, spin_index, None
@@ -857,12 +877,15 @@
# The R2eff model.
if cdp.model_type == 'R2eff':
+ # Count the selected spins.
+ spin_num = count_spins(spins)
+
# Exponential curves (with clustering).
if has_exponential_exp_type():
- return 2 * len(spins)
+ return 2 * spin_num
# Fixed time period experiments (with clustering).
- return 1 * len(spins)
+ return 1 * spin_num
# Check the spin cluster.
for spin in spins:
@@ -969,6 +992,10 @@
else:
# Set the same parameter value for all spins in the cluster.
for spin in spins:
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
# Set the simulation value.
if sim_index != None:
sim_obj = getattr(spin, param_name+'_sim')
r22298 - in /branches/double_rotor: ./ specific_analyses/relax_disp/