Author: bugman
Date: Tue Nov 19 17:42:30 2013
New Revision: 21529
URL: http://svn.gna.org/viewcvs/relax?rev=21529&view=rev
Log:
Many more fixes for the MMQ-type dispersion models for the proton spin data.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.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=21529&r1=21528&r2=21529&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Tue Nov 19
17:42:30 2013
@@ -36,7 +36,7 @@
# relax module imports.
from dep_check import C_module_exp_fn
from lib.dispersion.two_point import calc_two_point_r2eff,
calc_two_point_r2eff_err
-from lib.errors import RelaxError
+from lib.errors import RelaxError, RelaxImplementError
from lib.text.sectioning import subsection
from multi import Processor_box
from pipe_control import pipes, sequence
@@ -116,6 +116,10 @@
@rtype: numpy rank-1 float array
"""
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
+ return
+
# Create the initial parameter vector.
param_vector = assemble_param_vector(spins=[spin])
@@ -695,14 +699,28 @@
# All other models (the base data is the R2eff/R1rho values).
else:
+ # MMQ flags.
+ proton_sq_flag = has_proton_sq_cpmg()
+ proton_mq_flag = has_proton_mq_cpmg()
+ proton_mmq_flag = proton_sq_flag or proton_mq_flag
+
# Loop over the sequence.
for spin, spin_id in spin_loop(return_id=True):
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
+ continue
+
# Skip deselected spins.
if not spin.select:
continue
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
# Skip spins with no R2eff/R1rho values.
- if not hasattr(spin, 'r2eff'):
+ if not hasattr(spin, 'r2eff') and not hasattr(proton,
'r2eff'):
continue
# Yield the spin container and ID.
@@ -1115,11 +1133,17 @@
@rtype: list of float
"""
- # Get the spin container.
- spin = return_spin(spin_id)
-
- # Return the data.
- return spin.intensities
+ # The R2eff model.
+ if cdp.model_type == 'R2eff':
+ # Unpack the data.
+ spin, exp_type, frq, point = data_id
+
+ # Return the data.
+ return spin.intensities
+
+ # All other models.
+ else:
+ raise RelaxImplementError
return_data_name_doc = Desc_container("Relaxation dispersion curve
fitting data type string matching patterns")
@@ -1167,8 +1191,23 @@
# Unpack the data.
spin, spin_id = data_id
+ # MMQ flags.
+ proton_sq_flag = has_proton_sq_cpmg()
+ proton_mq_flag = has_proton_mq_cpmg()
+ proton_mmq_flag = proton_sq_flag or proton_mq_flag
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
# The errors.
- return spin.r2eff_err
+ r2eff_err = {}
+ if hasattr(spin, 'r2eff_err'):
+ r2eff_err.update(spin.r2eff_err)
+ if hasattr(proton, 'r2eff_err'):
+ r2eff_err.update(proton.r2eff_err)
+ return r2eff_err
# Return the error list.
return errors
@@ -1297,10 +1336,14 @@
# Set the Monte Carlo parameter values.
#######################################
- # Loop over the residues.
+ # Loop over the spins.
for spin in spin_loop():
- # Skip deselected residues.
+ # Skip deselected spins.
if not spin.select:
+ continue
+
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
continue
# Loop over all the data names.
@@ -1391,8 +1434,20 @@
# Unpack the data.
spin, spin_id = data_id
+ # MMQ flags.
+ proton_sq_flag = has_proton_sq_cpmg()
+ proton_mq_flag = has_proton_mq_cpmg()
+ proton_mmq_flag = proton_sq_flag or proton_mq_flag
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
# Pack the data.
spin.r2eff_sim = sim_data
+ if proton != None:
+ proton.r2eff_sim = sim_data
def sim_return_param(self, model_info, index):
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=21529&r1=21528&r2=21529&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Tue Nov 19
17:42:30 2013
@@ -1049,6 +1049,25 @@
for exp_type, exp_type_index in loop_exp(return_indices=True):
# Loop over each spin.
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
+ continue
+
+ # MMQ flags.
+ proton_sq_flag = has_proton_sq_cpmg()
+ proton_mq_flag = has_proton_mq_cpmg()
+ proton_mmq_flag = proton_sq_flag or proton_mq_flag
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
+ # Alias the correct spin.
+ current_spin = spin
+ if exp_type in [EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_PROTON_MQ]:
+ current_spin = proton
+
# The unique file name.
file_name = "disp%s.agr" % spin_id.replace('#',
'_').replace(':', '_').replace('@', '_')
if num_exp_types() > 1:
@@ -1086,16 +1105,16 @@
key = return_param_key_from_data(frq=frq, point=point)
# No data present.
- if key not in spin.r2eff:
+ if key not in current_spin.r2eff:
continue
# Add the data.
- data[-1].append([point, spin.r2eff[key]])
+ data[-1].append([point, current_spin.r2eff[key]])
# Add the error.
- if hasattr(spin, 'r2eff_err') and key in spin.r2eff_err:
+ if hasattr(current_spin, 'r2eff_err') and key in
current_spin.r2eff_err:
err = True
- data[-1][-1].append(spin.r2eff_err[key])
+ data[-1][-1].append(current_spin.r2eff_err[key])
# Add the back-calculated data.
for frq, frq_index in loop_frq(return_indices=True):
@@ -1117,11 +1136,11 @@
key = return_param_key_from_data(frq=frq, point=point)
# No data present.
- if not hasattr(spin, 'r2eff_bc') or key not in
spin.r2eff_bc:
+ if not hasattr(current_spin, 'r2eff_bc') or key not in
current_spin.r2eff_bc:
continue
# Add the data.
- data[-1].append([point, spin.r2eff_bc[key]])
+ data[-1].append([point, current_spin.r2eff_bc[key]])
# Handle the errors.
if err:
@@ -1144,16 +1163,16 @@
key = return_param_key_from_data(frq=frq, point=point)
# No data present.
- if key not in spin.r2eff or not hasattr(spin,
'r2eff_bc') or key not in spin.r2eff_bc:
+ if key not in current_spin.r2eff or not
hasattr(current_spin, 'r2eff_bc') or key not in current_spin.r2eff_bc:
continue
# Add the data.
- data[-1].append([point, spin.r2eff[key] -
spin.r2eff_bc[key]])
+ data[-1].append([point, current_spin.r2eff[key] -
current_spin.r2eff_bc[key]])
# Handle the errors.
if err:
err = True
- data[-1][-1].append(spin.r2eff_err[key])
+ data[-1][-1].append(current_spin.r2eff_err[key])
# The axis labels.
if exp_type in EXP_TYPE_LIST_CPMG:
@@ -1234,9 +1253,28 @@
# Loop over each spin.
for spin, id in spin_loop(return_id=True, skip_desel=True):
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
+ continue
+
# No data present.
if not hasattr(spin, 'intensities'):
continue
+
+ # MMQ flags.
+ proton_sq_flag = has_proton_sq_cpmg()
+ proton_mq_flag = has_proton_mq_cpmg()
+ proton_mmq_flag = proton_sq_flag or proton_mq_flag
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
+ # Alias the correct spin.
+ current_spin = spin
+ if exp_type in [EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_PROTON_MQ]:
+ current_spin = proton
# Append a new set structure and set the name to the spin ID.
data[graph_index].append([])
@@ -1251,15 +1289,15 @@
# Loop over each key.
for key in keys:
# No key present.
- if key not in spin.intensities:
+ if key not in current_spin.intensities:
continue
# Add the data.
- if hasattr(spin, 'intensity_err'):
- data[graph_index][-1].append([time,
spin.intensities[key], spin.intensity_err[key]])
+ if hasattr(current_spin, 'intensity_err'):
+ data[graph_index][-1].append([time,
current_spin.intensities[key], spin.intensity_err[key]])
err = True
else:
- data[graph_index][-1].append([time,
spin.intensities[key]])
+ data[graph_index][-1].append([time,
current_spin.intensities[key]])
# Increment the frq index.
graph_index += 1
r21529 - in /branches/relax_disp/specific_analyses/relax_disp: api.py disp_data.py