Actelion / openchemlib

Open source Java-based chemistry library
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Incorrect order (?) of ring closure digits when writing SMILES #28

Closed baoilleach closed 2 years ago

baoilleach commented 6 years ago

Given the Kekule SMILES:

    C1=NC2=C(N1)CCC3=NON=C23 11048

...OpenChemLib (2018.5) writes out the following aromatic SMILES:

C(Cc1nonc-11)c2c1nc[nH]2

I think that you probably meant:

C(Cc1nonc1-1)c2c1nc[nH]2

That is, I think you wanted an implicit aromatic bond to close the ring, and an explicit single bond to join the two aromatic rings.

thsa commented 6 years ago

thanks, are right. Here was a bug related to using the same closure number two times at the same atom. This is fixed and will be pushed with the next regular update (supposedly early next week).

On Fri, Jun 22, 2018 at 3:42 PM, baoilleach notifications@github.com wrote:

Given the Kekule SMILES:

C1=NC2=C(N1)CCC3=NON=C23 11048

...OpenChemLib (2018.5) writes out the following aromatic SMILES:

C(Cc1nonc-11)c2c1nc[nH]2

I think that you probably meant:

C(Cc1nonc1-1)c2c1nc[nH]2

That is, I think you wanted an implicit aromatic bond to close the ring, and an explicit single bond to join the two aromatic rings.

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