Author: tlinnet
Date: Mon Oct 6 17:07:49 2014
New Revision: 26167
URL: http://svn.gna.org/viewcvs/relax?rev=26167&view=rev
Log:
In the dispersion API calculate(), used the API function model_loop() to loop
over the clusters instead.
Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate()
does not calculate chi2 value for clustered residues.
Modified:
trunk/specific_analyses/relax_disp/api.py
Modified: trunk/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=26167&r1=26166&r2=26167&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/api.py (original)
+++ trunk/specific_analyses/relax_disp/api.py Mon Oct 6 17:07:49 2014
@@ -261,9 +261,6 @@
check_mol_res_spin_data()
check_model_type()
- # Get the looping list over cluster ids.
- cluster_ids, cluster_spin_list, cluster_spin_id_list,
cluster_spin_sel_list, clust_contain_spin_id_list =
self.loop_cluster_ids(spin_id=spin_id)
-
# Special exponential curve-fitting for the R2eff model.
if cdp.model_type == MODEL_R2EFF:
calculate_r2eff()
@@ -273,48 +270,35 @@
# 1H MMQ flag.
proton_mmq_flag = has_proton_mmq_cpmg()
- # Loop over the cluster ids.
- for i, cluster_id in enumerate(cluster_ids):
- # Get the spins, ids and if the cluster contains the spin of
interest.
- cluster_spins = cluster_spin_list[i]
- cluster_spin_ids = cluster_spin_id_list[i]
- spin_of_interest = clust_contain_spin_id_list[i]
-
- # If spin of interest is present:
- if spin_of_interest:
- # If it is a free free spin, then calculate per spin.
- if cluster_id == 'free spins':
- for si, spin in enumerate(cluster_spins):
- cur_spin_id = cluster_spin_ids[si]
-
- # Skip protons for MMQ data.
- if spin.model in MODEL_LIST_MMQ and spin.isotope
== '1H':
- continue
-
- # Get the attached proton.
- proton = None
- if proton_mmq_flag:
- proton =
return_attached_protons(cur_spin_id)[0]
-
- # The back calculated values.
- back_calc = back_calc_r2eff(spins=[spin],
spin_ids=[cur_spin_id], store_chi2=True)
-
- # Pack the data.
- pack_back_calc_r2eff(spin=spin,
spin_id=cur_spin_id, si=0, back_calc=back_calc,
proton_mmq_flag=proton_mmq_flag)
-
- else:
- # The back calculated values.
- back_calc = back_calc_r2eff(spins=cluster_spins,
spin_ids=cluster_spin_ids, store_chi2=True)
-
- # Pack the data.
- for si, spin in enumerate(cluster_spins):
- cur_spin_id = cluster_spin_ids[si]
-
- # Skip protons for MMQ data.
- if spin.model in MODEL_LIST_MMQ and spin.isotope
== '1H':
- continue
-
- pack_back_calc_r2eff(spin=spin,
spin_id=cur_spin_id, si=si, back_calc=back_calc,
proton_mmq_flag=proton_mmq_flag)
+ # Loop over the spin blocks.
+ model_index = -1
+ for spin_ids in self.model_loop():
+ # Increment the model index.
+ model_index += 1
+
+ # The spin containers.
+ spins = spin_ids_to_containers(spin_ids)
+
+ # Skip deselected clusters.
+ skip = True
+ for spin in spins:
+ if spin.select:
+ skip = False
+ if skip:
+ continue
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_ids)[0]
+
+ # The back calculated values.
+ back_calc = back_calc_r2eff(spins=spins, spin_ids=spin_ids,
store_chi2=True)
+
+ # Pack the data.
+ for i, spin in enumerate(spins):
+ spin_id = spin_ids[i]
+ pack_back_calc_r2eff(spin=spin, spin_id=spin_id, si=i,
back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
def constraint_algorithm(self):
r26167 - /trunk/specific_analyses/relax_disp/api.py