On Thu, Jan 15, 2015 at 12:39 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > OK, will use IteratingSMILESReader, but the basic problem of format > detection remains. > FormatFactory.guessFormat() does not seem to recognise smiles, and > presumably wouldn't return IteratingSMILESReader (or IteratingSDFReader) > anyway.
Correct, this is the one format that is specifically excluded. The problem with .smi files is that it is too easily recognizes as other chemical formats... the format is ill-defined, and allows for comments and sorts, which gave problems. You should, though I didn't test it right now, be able to to "add" the SMILES format to the factory with: public void registerFormat(IChemFormatMatcher format)... So, please try: formatFactory.registerFormat(SMILESFormat.getInstance()) And then do the detection. Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
