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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
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Correct the judgment of hydrogen bonds #370

Open Linsastar opened 7 months ago

Linsastar commented 7 months ago

Errors of adding the essential hydrogen bond interaction have been corrected. In particular, OE was divided into OE1 and OE2. Besides, OE1, OE2, OD1, OD2 and O were defined as the hydrogen acceptors and the rest hydrogen donors.

a-r-j commented 7 months ago

Thanks for the PR @Linsastar!

Could you clarify why the atoms are different to those specified in the existing Hbond acceptors and donors

Linsastar commented 7 months ago

Thanks for the PR @Linsastar!

Could you clarify why the atoms are different to those specified in the existing Hbond acceptors and donors Hi, Arian, My name is Chenyang Gong and I'm an undergraduate student of Dr. Yandong Huang. Comparing the protocols by you and us, there are mainly three differences. First, backbone O (acceptor) and N (donor) atoms are ignored by you. In addition, S atoms on Met, Ser or Thr are not considered by you. But we think these S are likely donors. Finally, we take HSE as the default state of a neutral His where imidazole N-epsilon is protonated and N-delta is deprotonated. Thus, N-epsilon can be a donor and N-delta an acceptor.

a-r-j commented 6 months ago

Hi Chenyang, thanks for clarifying, that all makes sense to me. Appreciate it!

To cover your points:

  1. Backbone atoms are a clear omission by us here. I think it would be useful however from a code POV to allow users to choose between sc-sc, bb-sc, bb-bb H bonds. What do you think?
  2. Re S atoms, my understanding is that the MET thiother group does not exhibit strong electronegativity. This also seems to be reflected in the current reference for the selection (and some cursory reading). We'll need some concrete references to back up this change,
  3. This change makes sense to me.
Linsastar commented 6 months ago

Hi Arian, Thanks for your feedback! (1) It makes sense to me that users have three hbond options, sc-sc, bb-sc, bb-bb, according to the locations of donors and acceptors. (2) Indeed, Sulfur involved hydrogen bonds are typically weak when compared with others and thus can be discarded.

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