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Fixing an off by one indexing error when slicing trajectories. #87

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Merged
harryswift01 merged 5 commits into from
May 9, 2025
Merged

Fixing an off by one indexing error when slicing trajectories. #87

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fc807d6
Fixing an off by one indexing error when slicing trajectories.
skfegan May 6, 2025
62b4bb7
Improving long line
skfegan May 6, 2025
142ad0c
improving linting
skfegan May 7, 2025
92e52de
improving linting
skfegan May 7, 2025
bdb09c7
improving linting
skfegan May 7, 2025
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7 changes: 6 additions & 1 deletion CodeEntropy/config/arg_config_manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,12 @@
},
"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 the last frame."
),
"default": -1,
},
"step": {
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8 changes: 6 additions & 2 deletions CodeEntropy/main_mcc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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