Thanks Bob, that works great. I didn't know that the filename could be null if the reader is supplied.
I doubt anyone cares about the details, but if so see https://github.com/biojava/biojava/pull/570 -Spencer On Mon, Aug 29, 2016 at 3:15 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > You can now just use > > viewer.openReader("filename", reader) > > where reader is one of byte[] or BufferedInputStream or Reader > > I'm not catching how Jmol is fitting in there in terms of loading an MMTF > file. How does that reading fit into BioJava's writing? > > > Bob > > > > On Sun, Aug 28, 2016 at 3:48 PM, Spencer Bliven <spencer.bli...@gmail.com> > wrote: > >> 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.SmarterJm >>> olAdapter.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 >>> >>> >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> 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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