I have a method writeToOutputStream(Structure structure, OutputStream outputStream) that does the mmtf writing. I have flexibility in what type of OutputStream to use. The byte[] is accessible using a ByteArrayOutputStream. If it makes more sense to pass an input stream, I guess this should be possible too using PipedInputStream.
Is this the most efficient way to communicate with Jmol given that it's embedded in the same process? For instance, could I just populate some data structure directly? (I might still go with MMTF, since it's fully implemented already) -Spencer On Fri, Aug 26, 2016 at 5:02 PM, Robert Hanson <hans...@stolaf.edu> wrote: > 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 > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > >
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