Thank you for the prompt response, Chris! I gave SingleStructureRandomGenerator a try and it works great! Must be some pretty robust infrastructure you have there!
My goal is to eventually have a list of N physically possible isomers for any given molecular formula so I'm going to mess around with your structure generator as well as OMG. I'd be happy to try out the CDK's new isomer generator whenever it's released as well! Seriously, thank you for all of your help and all the work you and your team have done on the CDK. - Jack On Thu, Jan 14, 2021 at 2:16 AM Christoph Steinbeck < christoph.steinb...@uni-jena.de> wrote: > 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 > >
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