Added exponent parameter

ariaec/conf/aria_ec.ini

@@ -116,6 +116,7 @@ md_parameters_steps_cool2:                  4000
 iteration_n_structures:                     100
 iteration_n_best_structures:                15
 iteration_n_kept_structures:                0
+exponent:                                   20
 max_contribution:                           1000
 merging_method:                             standard
 violation_analysis_violation_threshold:     0.5
@@ -124,9 +125,13 @@ water_refinement_n_structures:              10
 water_refinement_enabled:                   no
 water_refinement_write_solvent_molecules:   no
 procheck_executable:
+procheck_enabled:                           yes
 prosa_executable:
+prosa_enabled:                              yes
 whatif_executable:
+whatif_enabled:                             yes
 clashlist_executable:
+clahlist_enabled:                           no
 pickle_output:                              no
 
 [contactmap]

ariaec/templates/aria_project.xml

@@ -46,7 +46,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="1000.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="1.0" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="1.0" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="1" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -54,7 +54,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="5.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.9999" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.9999" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="2" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -62,7 +62,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="3.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.999" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.999" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="3" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -70,7 +70,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="1.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.99" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.99" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="4" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -78,7 +78,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="1.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.98" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.98" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="5" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -86,7 +86,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="1.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.96" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.96" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="6" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -94,7 +94,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="0.1" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.93" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.93" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="7" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -102,7 +102,7 @@
       <merging method="standard"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="0.1" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.9" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.9" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <iteration number="8" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
@@ -110,17 +110,17 @@
       <merging method="%(merging_method)s"/>
       <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
       <violation_analysis violation_tolerance="0.1" violation_threshold="%(violation_analysis_violation_threshold)s"/>
-      <partial_assignment weight_threshold="0.8" max_contributions="%(max_contribution)s"/>
+      <partial_assignment weight_threshold="0.8" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
       <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
     </iteration>
     <water_refinement solvent="%(water_refinement_solvent)s" n_structures="%(water_refinement_n_structures)s" enabled="%(water_refinement_enabled)s" write_solvent_molecules="%(water_refinement_write_solvent_molecules)s"/>
   </protocol>
   <analysis>
     <structures_analysis enabled="yes"/>
-    <procheck executable="%(procheck_executable)s" enabled="yes"/>
-    <prosa executable="%(prosa_executable)s" enabled="yes"/>
-    <whatif executable="%(whatif_executable)s" enabled="yes"/>
-    <clashlist executable="%(clashlist_executable)s" enabled="no"/>
+    <procheck executable="%(procheck_executable)s" enabled="%(procheck_enabled)s"/>
+    <prosa executable="%(prosa_executable)s" enabled="%(prosa_enabled)s"/>
+    <whatif executable="%(whatif_executable)s" enabled="%(whatif_enabled)s"/>
+    <clashlist executable="%(clashlist_executable)s" enabled="%(clahlist_enabled)s"/>
   </analysis>
   <report>
     <ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>