Hi Jack, you are indeed getting the expected outcome. The MF generator just generate gross formulae (just atoms, no bonds) and you need a constitutional isomer generator to generator all isomers of that structure (add the bonds).
If you only need one random isomer, I wrote a class many years ago called SingleStructureRandomGenerator.java in the package org.openscience.cdk.structgen. (http://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/structgen/SingleStructureRandomGenerator.html) It is now almost exactly 20 years old and has probably not been tested since then, so I cannot say (and have not time at the moment to test) if it is still working after so many refactoring of the CDK. Would be great if you could give it a try and report here :) The alternative (at the moment) is to use OMG (https://sourceforge.net/projects/openmg/) to generate just one isomer but that might take longer than with above solution. Kind regards, Chris PS: just to add: We are working on a proper isomer generator for the CDK but I cannot say when it is ready. — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 14. Jan 2021, at 00:19, Jack <jackcampanell...@gmail.com> wrote: > > 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 > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
