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
>>
>>
>
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> ------------------
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>
>
--
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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