Author: tlinnet
Date: Mon Oct 6 02:39:46 2014
New Revision: 26152
URL: http://svn.gna.org/viewcvs/relax?rev=26152&view=rev
Log:
Made initial preparation to loop over clustered spins and ids for
minimise.calculate() call.
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=26152&r1=26151&r2=26152&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/api.py (original)
+++ trunk/specific_analyses/relax_disp/api.py Mon Oct 6 02:39:46 2014
@@ -37,6 +37,7 @@
from lib.arg_check import is_list, is_str_list
from lib.dispersion.variables import EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, MODEL_LIST_MMQ, MODEL_R2EFF, PARAMS_R20
from lib.errors import RelaxError, RelaxImplementError
+from lib.selection import Selection, tokenise
from lib.text.sectioning import subsection
from multi import Processor_box
from pipe_control import pipes, relax_data, sequence
@@ -260,6 +261,71 @@
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)
+
+ # 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):
+ 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)
+
# Special exponential curve-fitting for the R2eff model.
if cdp.model_type == MODEL_R2EFF:
calculate_r2eff()
@@ -270,7 +336,7 @@
proton_mmq_flag = has_proton_mmq_cpmg()
# Loop over all spins.
- for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ for spin, cur_spin_id in spin_loop(selection=spin_id,
return_id=True, skip_desel=True):
# Skip protons for MMQ data.
if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
continue
@@ -278,13 +344,13 @@
# Get the attached proton.
proton = None
if proton_mmq_flag:
- proton = return_attached_protons(spin_id)[0]
+ proton = return_attached_protons(cur_spin_id)[0]
# The back calculated values.
- back_calc = back_calc_r2eff(spin=spin, spin_id=spin_id,
store_chi2=True)
+ back_calc = back_calc_r2eff(spin=spin, spin_id=cur_spin_id,
store_chi2=True)
# Pack the data.
- pack_back_calc_r2eff(spin=spin, spin_id=spin_id, si=0,
back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
+ pack_back_calc_r2eff(spin=spin, spin_id=cur_spin_id, si=0,
back_calc=back_calc, proton_mmq_flag=proton_mmq_flag)
def constraint_algorithm(self):
r26152 - /trunk/specific_analyses/relax_disp/api.py