Commit 0fe842e1 authored by Fabrice Allain's avatar Fabrice Allain
Browse files

Added exponent parameter

parent bdb256a9
......@@ -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]
......
......@@ -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"/>
......
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