Author: tlinnet
Date: Mon Oct 6 05:19:08 2014
New Revision: 26159
URL: http://svn.gna.org/viewcvs/relax?rev=26159&view=rev
Log:
Moved the looping over cluster spin ids into its own function in the API.
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=26159&r1=26158&r2=26159&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/api.py (original)
+++ trunk/specific_analyses/relax_disp/api.py Mon Oct 6 05:19:08 2014
@@ -261,82 +261,8 @@
check_mol_res_spin_data()
check_model_type()
- # Initialise cluster ids.
- cluster_ids = ['free spins']
-
- # Add the defined cluster IDs.
- if hasattr(cdp, 'clustering'):
- for key in list(cdp.clustering.keys()):
- if key not in cluster_ids:
- cluster_ids.append(key)
-
- # Now collect spins and spin_id per cluster ids.
- cluster_spin_list = []
- cluster_spin_id_list = []
- clust_contain_spin_id_list = []
-
- # Loop over the cluster ids
- if hasattr(cdp, 'clustering'):
- # Now loop over the cluster_ids in the list, and collect per id.
- for cluster_id in cluster_ids:
- cluster_id_spin_list = []
- cluster_id_spin_id_list = []
- # Now loop through spins in the clustered id, and collect
- col_sel_str = ''
- mol_token = None
- for clust_spin_id in cdp.clustering[cluster_id]:
- clust_spin = return_spin(clust_spin_id)
-
- # Skip de-selected
- if not clust_spin.select:
- continue
-
- # Skip protons for MMQ data.
- if clust_spin.model in MODEL_LIST_MMQ and
clust_spin.isotope == '1H':
- continue
-
- # Add to list.
- cluster_id_spin_list.append(clust_spin)
- cluster_id_spin_id_list.append(clust_spin_id)
-
- # Add id to string
- mol_token, res_token, spin_token =
tokenise(clust_spin_id)
- col_sel_str += '%s,' % (res_token)
-
- # Make selection for molecule.
- if mol_token == None:
- col_sel_str = ':' + col_sel_str
- else:
- col_sel_str = '#%s:' % mol_token + col_sel_str
-
- # Make a selection object, based on the cluster id.
- select_obj = Selection(col_sel_str)
- # Does the current cluster id contain the spin of interest.
- clust_contain_spin_id = select_obj.contains_spin_id(spin_id)
- # If the spin_id is set to None, then we calculate for all:
- if spin_id == None:
- clust_contain_spin_id = True
-
- cluster_spin_list.append(cluster_id_spin_list)
- cluster_spin_id_list.append(cluster_id_spin_id_list)
- clust_contain_spin_id_list.append(clust_contain_spin_id)
-
- # If clustering has not been specified, then collect for free spins,
according to selection.
- else:
- # Now loop over selected spins.
- free_spin_list = []
- free_spin_id_list = []
- for cur_spin, cur_spin_id in spin_loop(selection=spin_id,
return_id=True, skip_desel=True):
- # Skip protons for MMQ data.
- if cur_spin.model in MODEL_LIST_MMQ and cur_spin.isotope ==
'1H':
- continue
-
- free_spin_list.append(cur_spin)
- free_spin_id_list.append(cur_spin_id)
-
- cluster_spin_list.append(free_spin_list)
- cluster_spin_id_list.append(free_spin_id_list)
- clust_contain_spin_id_list.append(True)
+ # Get the looping list over cluster ids.
+ cluster_ids, cluster_spin_list, cluster_spin_id_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:
@@ -706,6 +632,96 @@
# Minimisation.
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity,
sim_index=sim_index)
+
+
+ def loop_cluster_ids(self, spin_id=None):
+ """Create list of cluster ids, and its associated list of spin
containers and spin_ids.
+
+ @param spin_id: The spin identification string.
+ @type spin_id: None
+ @return: The list of cluster ids, the nested list of spin
container instances, the nested list of spin ids and list of boolean if
spin_id is contained in cluster_id.
+ @rtype: list of str, list of list of spin container,
list of list of spin ids, list of bool
+ """
+
+ # Initialise cluster ids.
+ cluster_ids = ['free spins']
+
+ # Add the defined cluster IDs.
+ if hasattr(cdp, 'clustering'):
+ for key in list(cdp.clustering.keys()):
+ if key not in cluster_ids:
+ cluster_ids.append(key)
+
+ # Now collect spins and spin_id per cluster ids.
+ cluster_spin_list = []
+ cluster_spin_id_list = []
+ clust_contain_spin_id_list = []
+
+ # Loop over the cluster ids
+ if hasattr(cdp, 'clustering'):
+ # Now loop over the cluster_ids in the list, and collect per id.
+ for cluster_id in cluster_ids:
+ cluster_id_spin_list = []
+ cluster_id_spin_id_list = []
+ # Now loop through spins in the clustered id, and collect
+ col_sel_str = ''
+ mol_token = None
+ for clust_spin_id in cdp.clustering[cluster_id]:
+ clust_spin = return_spin(clust_spin_id)
+
+ # Skip de-selected
+ if not clust_spin.select:
+ continue
+
+ # Skip protons for MMQ data.
+ if clust_spin.model in MODEL_LIST_MMQ and
clust_spin.isotope == '1H':
+ continue
+
+ # Add to list.
+ cluster_id_spin_list.append(clust_spin)
+ cluster_id_spin_id_list.append(clust_spin_id)
+
+ # Add id to string
+ mol_token, res_token, spin_token =
tokenise(clust_spin_id)
+ col_sel_str += '%s,' % (res_token)
+
+ # Make selection for molecule.
+ if mol_token == None:
+ col_sel_str = ':' + col_sel_str
+ else:
+ col_sel_str = '#%s:' % mol_token + col_sel_str
+
+ # Make a selection object, based on the cluster id.
+ select_obj = Selection(col_sel_str)
+ # Does the current cluster id contain the spin of interest.
+ clust_contain_spin_id = select_obj.contains_spin_id(spin_id)
+ # If the spin_id is set to None, then we calculate for all:
+ if spin_id == None:
+ clust_contain_spin_id = True
+
+ cluster_spin_list.append(cluster_id_spin_list)
+ cluster_spin_id_list.append(cluster_id_spin_id_list)
+ clust_contain_spin_id_list.append(clust_contain_spin_id)
+
+ # If clustering has not been specified, then collect for free spins,
according to selection.
+ else:
+ # Now loop over selected spins.
+ free_spin_list = []
+ free_spin_id_list = []
+ for cur_spin, cur_spin_id in spin_loop(selection=spin_id,
return_id=True, skip_desel=True):
+ # Skip protons for MMQ data.
+ if cur_spin.model in MODEL_LIST_MMQ and cur_spin.isotope ==
'1H':
+ continue
+
+ free_spin_list.append(cur_spin)
+ free_spin_id_list.append(cur_spin_id)
+
+ cluster_spin_list.append(free_spin_list)
+ cluster_spin_id_list.append(free_spin_id_list)
+ clust_contain_spin_id_list.append(True)
+
+
+ return cluster_ids, cluster_spin_list, cluster_spin_id_list,
clust_contain_spin_id_list
def map_bounds(self, param, spin_id=None):
r26159 - /trunk/specific_analyses/relax_disp/api.py