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Convert wedge bonds into tetrahedral chirality?

Asked by [ Admin ]

Brecher has written a long recommendation on how and how not to represent tetrahedral chirality with wedge bonds in 2D diagrams. The paper shows many examples on how to incorrectly do that. Now, that makes recovering the correct stereochemistry non-trivial.

Is anyone aware of software that can recover tetrahedral chirality from bond wedge information from 2D diagrams? Preferable Open Source, but I am interested in free (as in free beer) and non-free solutions too. Additionally, please describe if the utility is compatible with the Brecher recommendations, and what test suite is available to test that compatibility.

NN comments
tim.vandermeersch
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The Brecher paper seems like a great resource. Thanks for the link. I’m interested in implementing this for OB, but we can share test sets, code?, etc…

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3 answers

1

baoilleach [ Admin ]

OpenBabel (devel) and RDKit both recover chirality from bond wedge information. Not sure how conformant they are with the recommendations.

NN comments
chem-bla-ics
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Has this functionality undergone some validation?

baoilleach
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I can only comment on what I’ve done, which is to take Pubchem 2D, 3D, SMILES and InChIs for the same compound and see whether OpenBabel can work out that they are the same. At the point where I started identifying errors in PubChem I stopped worrying about our code.

tim.vandermeersch
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The OpenBabel code works as long as you use the same convention. This is documented in the code but by no means a standard. There are various techniques to improve the code but I haven’t had the time yet. AFAIK, there are no open source projects which are great in this. For example, 2 wedges and 2 hash bonds are sometimes used (e.g. Daylight SMILES depict) for a tetrahedral center. This is currently not accepted in OB. Fisher projections and complex 3D molecules (i.e. projected on the paper plane) could also be handled… “3D molecules” in 2D are probably the hardest to do.

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