fixing indexing issue for start and end parameters affecting timesteps

Author: skfegan

CodeEntropy/calculations/ConformationFunctions.py

@@ -38,13 +38,14 @@ def assign_conformation(
     # get the values of the angle for the dihedral
     # dihedral angle values have a range from -180 to 180
     for timestep in data_container.trajectory[start:end:step]:
+        timestep_index = timestep.frame - start
         value = dihedral.value()
         # we want postive values in range 0 to 360 to make the peak assignment work
         # using the fact that dihedrals have circular symetry
         # (i.e. -15 degrees = +345 degrees)
         if value < 0:
             value += 360
-        phi[timestep.frame] = value
+        phi[timestep_index] = value
 
     # create a histogram using numpy
     number_bins = int(360 / bin_width)

CodeEntropy/calculations/LevelFunctions.py

@@ -94,10 +94,11 @@ def get_matrices(
             trans_axes, rot_axes = GF.get_axes(data_container, level, bead_index)
 
             # Sort out coordinates, forces, and torques for each atom in the bead
-            weighted_forces[bead_index][timestep.frame] = GF.get_weighted_forces(
+            timestep_index = timestep.frame - start
+            weighted_forces[bead_index][timestep_index] = GF.get_weighted_forces(
                 data_container, list_of_beads[bead_index], trans_axes, highest_level
             )
-            weighted_torques[bead_index][timestep.frame] = GF.get_weighted_torques(
+            weighted_torques[bead_index][timestep_index] = GF.get_weighted_torques(
                 data_container, list_of_beads[bead_index], rot_axes
             )