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wrong depiction #188

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biotech7 opened this issue May 21, 2024 · 1 comment
Open

wrong depiction #188

biotech7 opened this issue May 21, 2024 · 1 comment

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@biotech7
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it generated wrong depiction as to this SMILES:
O(C(c1cccc2c1cccc2)c3cccc4ccccc34)C(C(C)Sc5ccc(cc5)Br)=O
1716268358826
right depiction should be:
1716268453276

@xavierholt
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Those rings aren't bonded - they're just drawn far too close to each other. So this looks to be a problem with the "overlap resolution" step of the layout algorithm. When I dump the per-vertex overlap scores, I see 4 vertices with scores of ~1 while the rest have ~0. So the overlap is detected, but the algorithm isn't able to fix it.

Ideally you could set the overlapResolutionIterations option to something higher (the default is 1), but that doesn't seem to help in this case.

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