Re: [Cdk-user] inconsistency in ready molfiles

2016-01-20 Thread Tim Dudgeon
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 readMolecules(InputStream is); From what I've found so far there is no easy way to

Re: [Cdk-user] inconsistency in ready molfiles

2016-01-20 Thread John M
Hi Tim, V3000 reader doesn't accept ChemFiles, if you want to be squeaky clean try ' reader.accepts(IChemFile.class)': https://github.com/cdk/cdk/blob/39e87cafae1f044c16dd101e7a8bd7e1ccb00fa3/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java#L130-L139 Although it could read

Re: [Cdk-user] inconsistency in ready molfiles

2016-01-20 Thread Egon Willighagen
On Wed, Jan 20, 2016 at 10:44 AM, John M 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