Merge pull request #180 from martimunicoy/alchemistry_fix

Alchemistry fix
martimunicoy · Nov 16, 2023 · 0b8872a · 0b8872a
2 parents c0ae464 + 572d206
commit 0b8872a
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/peleffy/topology/alchemistry.py b/peleffy/topology/alchemistry.py
@@ -283,12 +283,12 @@ def topology_from_lambda_set(self, lambda_set):
 
         for bond_idx, bond in enumerate(alchemical_topology.bonds):
             if bond_idx in self._exclusive_bonds:
-                bond.apply_lambda(["spring_constant", "eq_dist"],
+                bond.apply_lambda(["spring_constant", ],
                                   lambda_set.get_lambda_for_bonded(),
                                   reverse=False)
 
             if bond_idx in self._non_native_bonds:
-                bond.apply_lambda(["spring_constant", "eq_dist"],
+                bond.apply_lambda(["spring_constant", ],
                                   lambda_set.get_lambda_for_bonded(),
                                   reverse=True)
 
@@ -309,12 +309,12 @@ def topology_from_lambda_set(self, lambda_set):
 
         for angle_idx, angle in enumerate(alchemical_topology.angles):
             if angle_idx in self._exclusive_angles:
-                angle.apply_lambda(["spring_constant", "eq_angle"],
+                angle.apply_lambda(["spring_constant", ],
                                    lambda_set.get_lambda_for_bonded(),
                                    reverse=False)
 
             if angle_idx in self._non_native_angles:
-                angle.apply_lambda(["spring_constant", "eq_angle"],
+                angle.apply_lambda(["spring_constant", ],
                                    lambda_set.get_lambda_for_bonded(),
                                    reverse=True)
 

diff --git a/peleffy/utils/utils.py b/peleffy/utils/utils.py
@@ -500,7 +500,7 @@ def set_level(self, level):
             CRITICAL]
         """
         import logging
-        logging.basicConfig()
+        #logging.basicConfig()
 
         if level.upper() == 'DEBUG':
             logging_level = logging.DEBUG