It would be totally inconvenient to treat the byte[] mmtf data as String data. You can cache the binary data as a byte array and then pass a cache:// protocol. Way better would be to pass the data as a buffered stream, but I don't think that is set up in Jmol.
You have the data in what form? Full byte array? BufferedInputStream? The MMTF reader needs a javajs.api.GenericBinaryDocument. This it gets from jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollectionFromReader. I think I can tweak viewer.loadModelFromFile to allow you to feed it a BufferedInputStream. Right now it is only set up for a java.io.Reader. Will that work for you? Bob On Fri, Aug 26, 2016 at 7:46 AM, Spencer Bliven <spencer.bli...@gmail.com> wrote: > I'm trying to update the way BioJava interacts with Jmol. We're currently > loading structures into Jmol by converting them to PDB format and passing > that string to JmolViewer.openStringInline(). Now that Jmol 14.6 is > available in maven, we need to move away from PDB. > > My first choice would be to use MMTF as the exchange format. Is there a > way to pass MMTF to Jmol? Resolver.determineAtomSetCollectionReader > failed (probably correctly) to recognize an MMTF binary stream when > converted to a string using the default encoding, so openStringInline() > doesn't work. > > Possibly related, the mmtf demo at http://chemapps.stolaf.edu/ > jmol/jsmol/mmtf.htm gives an unrecognized file format error for me. > > -Spencer > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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