Fixing an off by one indexing error when slicing trajectories.

Author: skfegan

CodeEntropy/config/arg_config_manager.py

@@ -25,7 +25,7 @@
     },
     "end": {
         "type": int,
-        "help": "Stop analysing the trajectory at this frame index",
+        "help": "Stop analysing the trajectory at this frame index. This is the frame index of the last frame to be included, so for example if start=0 and end=500 there would be 501 frames analysed. The default -1 will include everything up to the last frame.",
         "default": -1,
     },
     "step": {

CodeEntropy/main_mcc.py

@@ -127,13 +127,17 @@ def main():
     if step is None:
         step = 1
     # Count number of frames, easy if not slicing
+    # MDAnalysis trajectory slicing only includes up to end-1
+    # This works the way we want it to if the whole trajectory is being included
     if start == 0 and end == -1 and step == 1:
+        end = len(u.trajectory)
         number_frames = len(u.trajectory)
     elif end == -1:
         end = len(u.trajectory)
-        number_frames = math.floor((end - start) / step) + 1
+        number_frames = math.floor((end - start) / step) 
     else:
-        number_frames = math.floor((end - start) / step) + 1
+        end = end + 1
+        number_frames = math.floor((end - start) / step)
     logger.debug(f"Number of Frames: {number_frames}")
 
     # Create pandas data frame for results