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Add generic aromatic bond#738

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padix-key merged 1 commit intobiotite-dev:mainfrom
padix-key:aromatic-bond
Jan 20, 2025
Merged

Add generic aromatic bond#738
padix-key merged 1 commit intobiotite-dev:mainfrom
padix-key:aromatic-bond

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@padix-key
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The kekulized form of aromatic bonds (i.e. their representations as single, double or triple bonds) is a visualization artifact: Chemically aromatic bonds have no bond order, but the pi-elections are delocalized in the entire pi-system.

For this reason I think it makes sense to lift the restriction to assign a bond to either of AROMATIC_SINGLE, AROMATIC_DOUBLE or AROMATIC_TRIPLE, but to allow a generic AROMATIC as well. Although, this might lead to some limitations in visualization, there are some advantages

  • Models predicting aromatic bonds do not necessarily need to know the kekulized form.
  • Some software does not internally represent aromatic bonds in kekulized form (e.g. RDKit).
  • SDF and PDBx support generic aromatic bonds as well.

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codspeed-hq bot commented Jan 17, 2025

CodSpeed Performance Report

Merging #738 will not alter performance

Comparing padix-key:aromatic-bond (2b0f6d9) with main (8138e0e)

Summary

✅ 59 untouched benchmarks

@padix-key padix-key merged commit b5c9df7 into biotite-dev:main Jan 20, 2025
@padix-key padix-key deleted the aromatic-bond branch January 24, 2025 11:02
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