From cab261fce4ddc8a91fc9f99cefabed43f9862059 Mon Sep 17 00:00:00 2001
From: Fabrice Allain <fabrice.allain@pasteur.fr>
Date: Fri, 24 Jun 2016 18:00:48 +0200
Subject: [PATCH] Addign sigma mode parameter in aria project templates

---
 ariaec/commands.pyc                      | Bin 10938 -> 10629 bytes
 ariaec/conf/aria_ec.ini                  |   1 +
 ariaec/econverter.pyc                    | Bin 27988 -> 27963 bytes
 ariaec/protein.pyc                       | Bin 16147 -> 16122 bytes
 ariaec/templates/aria_project_v2.3.0.xml |   2 +-
 ariaec/templates/aria_project_v2.3.2.xml |   2 +-
 6 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index 7d69d747f07668206011e9deb6608742e0d4899c..a1d6a3e552a4c754b39af3e1823b2a7dcf6da480 100644
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diff --git a/ariaec/conf/aria_ec.ini b/ariaec/conf/aria_ec.ini
index 63363c5..a2f94a2 100644
--- a/ariaec/conf/aria_ec.ini
+++ b/ariaec/conf/aria_ec.ini
@@ -151,6 +151,7 @@ calib_estimator:                            ratio_of_averages
 calib_error_estimator:                      distance
 viol_violation_tolerance:                   1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1
 viol_violation_threshold:                   0.5
+viol_sigma_mode:                            fix
 partassign_weight_threshold:                1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8
 partassign_max_contributions:               1000
 partassign_exponent:                        6
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
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diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index f956164d2c46ab8fdb6ffeeb06a7e24790fdd89c..6dbaa81944f2a451217af8954f7d7a8d50136ff3 100644
GIT binary patch
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diff --git a/ariaec/templates/aria_project_v2.3.0.xml b/ariaec/templates/aria_project_v2.3.0.xml
index 8015ce7..40db98c 100644
--- a/ariaec/templates/aria_project_v2.3.0.xml
+++ b/ariaec/templates/aria_project_v2.3.0.xml
@@ -46,7 +46,7 @@
       <assignment/>
       <merging method="${merging_method}"/>
       <calibration relaxation_matrix="${calib_relaxation_matrix}" distance_cutoff="${calib_distance_cutoff}" estimator="${calib_estimator}" error_estimator="${calib_error_estimator}"/>
-      <violation_analysis violation_tolerance="${viol_violation_tolerance[iter]}" violation_threshold="${viol_violation_threshold}"/>
+      <violation_analysis violation_tolerance="${viol_violation_tolerance[iter]}" violation_threshold="${viol_violation_threshold}" sigma_mode="${viol_sigma_mode}"/>
       <partial_assignment  weight_threshold="${partassign_weight_threshold[iter]}" max_contributions="${partassign_max_contributions}"/>
       <network_anchoring high_residue_threshold="${netanch_high_residue_threshold}" enabled="${netanch_enabled}" min_residue_threshold="${netanch_min_residue_threshold}" min_atom_threshold="${netanch_min_atom_threshold}"/>
     </iteration>
diff --git a/ariaec/templates/aria_project_v2.3.2.xml b/ariaec/templates/aria_project_v2.3.2.xml
index ef7e461..1b60868 100644
--- a/ariaec/templates/aria_project_v2.3.2.xml
+++ b/ariaec/templates/aria_project_v2.3.2.xml
@@ -47,7 +47,7 @@
       <assignment/>
       <merging method="${merging_method}"/>
       <calibration relaxation_matrix="${calib_relaxation_matrix}" distance_cutoff="${calib_distance_cutoff}" estimator="${calib_estimator}" error_estimator="${calib_error_estimator}"/>
-      <violation_analysis violation_tolerance="${viol_violation_tolerance[iter]}" violation_threshold="${viol_violation_threshold}"/>
+      <violation_analysis violation_tolerance="${viol_violation_tolerance[iter]}" violation_threshold="${viol_violation_threshold}"  sigma_mode="${viol_sigma_mode}"/>
       <partial_assignment weight_threshold="${partassign_weight_threshold[iter]}" max_contributions="${partassign_max_contributions}" exponent="${partassign_exponent}"/>
       <network_anchoring high_residue_threshold="${netanch_high_residue_threshold}" enabled="${netanch_enabled}" min_residue_threshold="${netanch_min_residue_threshold}" min_atom_threshold="${netanch_min_atom_threshold}"/>
     </iteration>
-- 
GitLab