Author: tlinnet Date: Mon Oct 6 17:07:54 2014 New Revision: 26168 URL: http://svn.gna.org/viewcvs/relax?rev=26168&view=rev Log: Removed then function loop_cluster_ids() from dispersion API(). This should be implemented elsewhere. 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=26168&r1=26167&r2=26168&view=diff ============================================================================== --- trunk/specific_analyses/relax_disp/api.py (original) +++ trunk/specific_analyses/relax_disp/api.py Mon Oct 6 17:07:54 2014 @@ -625,90 +625,6 @@ # 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, its associated list of spin containers, its associated list of spin_ids, the selection string for the cluster id and bool to determine if spin of interest is in the cluster. - - @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, the selection string for the cluster 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 str, 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 = [] - cluster_spin_sel_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 - - # 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) - cluster_spin_sel_list.append(col_sel_str) - 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): - 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) - cluster_spin_sel_list.append(None) - clust_contain_spin_id_list.append(True) - - return cluster_ids, cluster_spin_list, cluster_spin_id_list, cluster_spin_sel_list, clust_contain_spin_id_list def map_bounds(self, param, spin_id=None):