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bjornwallner / DockQ

DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
MIT License
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Bug in aligning model to native (cython branch) #21

Closed alirezaomidi closed 7 months ago

alirezaomidi commented 9 months ago

In cython branch, an instance of Align.PairwiseAligner is created, configured, but not used: https://github.com/bjornwallner/DockQ/blob/01f97033ffee5a3e335e8f9bc1032676056a8288/src/DockQ/DockQ.py#L305-L310

Also, extracting the alignment is not accurate here: https://github.com/bjornwallner/DockQ/blob/01f97033ffee5a3e335e8f9bc1032676056a8288/src/DockQ/DockQ.py#L311-L312 and should be:

alignment['seqA'] = aln[0, :]
alignment['seqB'] = aln[1, :]
clami66 commented 7 months ago

Hi alireza,

Thanks for pointing the issue with the aligner! About the formatting issue, that was the correct way of doing it in older biopython versions (<1.79, I think). When the next version is released we will update the biopython requirements and fix this issue.