Indigo
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SMILES output does not retain stereochemistry information
Steps to reproduce:
- Convert SMILES
O=C(O)[C@@]([H])(N)C
string to Mol by executing convert or layout endpoint - Convert resulted Mol string to SMILES (convert endpoint)
Actual result:
- Resulted SMILES is
O=C(C(C)(N)[H])O
instead ofO=C(O)[C@@]([H])(N)C
- convert & layout endpoints returns different results
Expected result:
- Resulted and original SMILEs are equal
- Layout & Convert returns the same Mol files
the molfile is generated correctly into S-isomer. So the issue is related to Ketcher Daylight SMILES saving
After converting resulted mol file to Extended SMILES the result is O=C(C@(N)[H])O instead of O=C(O)C@@(N)C