To broaden the topic a bit, what I'm wanting is a way to read structures without needing to know the format, leaving it up to CDK to work it out. Something like:
IAtomContainer readMolecule(String s); Iterator<IAtomContainer> readMolecules(InputStream is); From what I've found so far there is no easy way to do this. Smiles, V2000, V3000 and InChi all have to be handled in their own ways. FormatFactory helps a bit, but not much as the IChemFormat you get back still has to be treated separately depending on the format (e.g. the Molfile example). Tim On 20/01/2016 10:02, Egon Willighagen wrote: > On Wed, Jan 20, 2016 at 10:44 AM, John M <john.wilkinson...@gmail.com> wrote: >> Ultimately it's silly that V2000 and V3000 are considered different but >> haven't had time to put them in a single 'MolfileReader' yet. > The formats *are* different, but that does not mean the readers must be too! > > The MDL formats for reaction lists, etc, also used the V2000 reader. > No problem with that, but the formats are just different, though > interdependent. That we do have different readers, is mostly > historical; sometimes it's just easier to write a reader from scratch, > or not to try to make a reader too flexible to support multiple thing, > which makes code complexer. That's mostly the reasons why we have > different readers for the MDL molfiles versions. Nothing more. > > Egon > ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
