Re: [Jmol-users] Loading MMTF programmatically

[Spencer Bliven]

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  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 
> 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 
>> 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

 
 --

 ___
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 Jmol-users@lists.sourceforge.net
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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
>>>
>>>
>>> 
>>> --
>>>
>>> ___
>>> 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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Re: [Jmol-users] Loading MMTF programmatically

[Robert Hanson]

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 
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  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 > > 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
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Re: [Jmol-users] Loading MMTF programmatically

[Spencer Bliven]

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  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 
> 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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Re: [Jmol-users] Loading MMTF programmatically

[Robert Hanson]

Spencer, I've simplified that in what I am releasing today. You can use a
byte[] or BufferedInputStream to introduce mmtf files.

  /**
   * Opens the file and creates the model set, given the reader.
   *
   * not used in Jmol
   *
   * @param fullPathName full path name or null
   * @param reader a Reader, byte[], or BufferedInputStream
   *
   * @return   null or error message
   */

  public String openReader(String fullPathName, Object reader)

​
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Re: [Jmol-users] Loading MMTF programmatically

[Robert Hanson]

The call you will need to make is to this, in org.jmol.viewer.Viewer:

  public String loadModelFromFile(String fullPathName, String fileName,
  String[] fileNames, Object reader,
  boolean isAppend,
  Map htParams, SB
loadScript,
  SB sOptions, int tokType, boolean
isConcat) {


fullPathName should be just that

fileName is the no-path name of the file from the fullPathName

fileNames must be null

isAppend = true is optional and allows you to append this model to the
current set of models

reader is your  BufferedInputStream

htPararms allows setting all sorts of options for file loading such as
custom unit cell, custom space group, lattice, packing, biomolecule, etc.

It's possible that loadScript should be non-null. (It's what is put in the
state if a state is ever created.)

sOptions will be ignored

tokType must be 0

isConcat should be false

​Bob
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Re: [Jmol-users] Loading MMTF programmatically

[Robert Hanson]

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 
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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