Greetings CDK devs/support team, I'm currently using MolecularFormulaGenerator to generate a list of formulas and then piping those formulas to SmilesGenerator in order to retrieve a list of smile strings.
However, these resulting smile strings don't have any notion of bonds, rings, etc. For example, if MolecularFormulaGenerator returns say 'C6H6' then the corresponding smile string looks like: '[H].[H].[H].[H].[H].[H].[C].[C].[C].[C].[C].[C]'. I'm wondering if there is some sort of intermediate step I might have to take in order to generate structural isomers for each molecular formula before generating smiles. I've scoured the CDK's api documentation and the wiki but I can't find any classes or set of classes that would accomplish this. Admittedly, this could definitely be because of my 'barely passing Chem 101' knowledge of fundamental Chemistry. If someone could offer some insight into where I should look, which classes I should use, or if I'm just simply missing something I would be forever grateful. Thanks a million! - Jack Campanella
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