fixing and adding additional test cases for the per-timestep switch over

Author: harryswift01

CodeEntropy/entropy.py

@@ -211,7 +211,6 @@ def _compute_entropies(
                     self._process_united_atom_entropy(
                         mol_id,
                         mol,
-                        res_id,
                         ve,
                         ce,
                         level,
@@ -329,7 +328,6 @@ def _process_united_atom_entropy(
         self,
         mol_id,
         mol_container,
-        res_id,
         ve,
         ce,
         level,

CodeEntropy/levels.py

@@ -377,7 +377,7 @@ def get_axes(self, data_container, level, index=0):
             trans_axes = data_container.atoms.principal_axes()
             rot_axes = data_container.atoms.principal_axes()
 
-        if level == "residue":
+        elif level == "residue":
             # Translation
             # for residues use principal axes of whole molecule for translation
             trans_axes = data_container.atoms.principal_axes()
@@ -409,7 +409,7 @@ def get_axes(self, data_container, level, index=0):
                 # use spherical coordinates function to get rotational axes
                 rot_axes = self.get_sphCoord_axes(vector)
 
-        if level == "united_atom":
+        elif level == "united_atom":
             # Translation
             # for united atoms use principal axes of residue for translation
             trans_axes = data_container.residues.principal_axes()