Fixing an off by one indexing error when slicing trajectories.#87
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harryswift01 merged 5 commits intomainfrom May 9, 2025
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This is a great fix for the slicing bug - it now correctly captures the full range of specified frames. The only small thing to tidy up is the length of the help string. Splitting it across multiple lines would keep it consistent with the rest of the code. Other than that, everything looks great!
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This all looks good to go now, thank you for this fix.
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Summary
This is to fix errors when the slicing of trajectories occurs (MDAnalysis uses the end variable and then goes to frame end-1).
Changes
Adapting the end parameter to account for the whole trajectory as the default, but to give the expected frames and frame count when end is set to a positive integer.
Impact
This should give the correct results. In particular, it will avoid the problem of the dihedral angle appearing as 0 when there was a mismatch between the frames MDAnalysis included in the timesteps loop and the expected number of frames reducing the number of incorrect peaks in the histograms for the conformational entropy.