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I tested a script developed with MDAnalysis 2.5 with version 2.9 and noticed it was reporting fewer hydrogen bonds than previously. After a series of tests to narrow down the issue, I found the difference started in version 2.8 and is related to how the donors and acceptors are set.
and therefore detect the same number and type of H-bonds.
Actual behavior
From version 2.8, only the second method works to set the donor and acceptor selections. The first method wasn't working and wasn't reporting any errors. Instead it just reverted to default behaviour. In my case this resulted in some acceptors being ignored. I used one of the test systems to reproduce the problem below. In this case, it fails to exclude N atoms from the analysis.
I tested a script developed with MDAnalysis 2.5 with version 2.9 and noticed it was reporting fewer hydrogen bonds than previously. After a series of tests to narrow down the issue, I found the difference started in version 2.8 and is related to how the donors and acceptors are set.
Expected behavior
should set the donor and acceptor selections in the same way as:
and therefore detect the same number and type of H-bonds.
Actual behavior
From version 2.8, only the second method works to set the donor and acceptor selections. The first method wasn't working and wasn't reporting any errors. Instead it just reverted to default behaviour. In my case this resulted in some acceptors being ignored. I used one of the test systems to reproduce the problem below. In this case, it fails to exclude N atoms from the analysis.
Code to reproduce the behavior
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