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# Interface for extracting data and generating images from Jmol readable files.

JmolData is a no GUI version of Jmol useful for extracting data from files Jmol reads and for generating image files.

AUTHORS:

- Jonathan Gutow (2012-06-14): complete doctest coverage
- Jonathan Gutow (2012-03-21): initial version

class `sage.interfaces.jmoldata.``JmolData`

  Bases: `sage.structure.sage_object.SageObject`

  Todo

  Create an animated image file (GIF) if spin is on and put data extracted from a file into a variable/string/structure to return

  `export_image`(targetfile, datafile, datafile_cmd='script', image_type='PNG', figsize=5, **kwds)

    This executes JmolData.jar to make an image file.

    INPUT:

    - targetfile – the full path to the file where the image should be written.
    - datafile – full path to the data file Jmol can read or text of a script telling Jmol what to read or load.
    - datafile_cmd – (default `'script'`) `'load'` or `'script'` should be `"load"` for a data file.
    - image_type – (default `"PNG"`) `'PNG'` `'JPG'` or `'GIF'`
    - figsize – number (default 5) equal to (pixels/side)/100

    OUTPUT:

    Image file, .png, .gif or .jpg (default .png)

    Note

    Examples will generate an error message if a functional Java Virtual Machine (JVM) is not installed on the machine the Sage instance is running on.

    Warning

    Programmers using this module should check that the JVM is available before making calls to avoid the user getting error messages. Check for the JVM using the function `is_jvm_available()`, which returns True if a JVM is available.

    EXAMPLES:

    Use Jmol to load a pdb file containing some DNA from a web data base and make an image of the DNA. If you execute this in the notebook, the image will appear in the output cell:

        sage: from sage.interfaces.jmoldata import JmolData
        sage: JData = JmolData()
        sage: script = "load =1lcd;display DNA;moveto 0.0 { -473 -713 -518 59.94} 100.0 0.0 0.0 {21.17 26.72 27.295} 27.544636 {0.0 0.0 0.0} -25.287832 64.8414 0.0;"
        sage: testfile = tmp_filename(ext="DNA.png")
        sage: JData.export_image(targetfile=testfile,datafile=script,image_type="PNG")  # optional -- java internet
        sage: print os.path.exists(testfile)  # optional -- java internet
        True

    Use Jmol to save an image of a 3-D object created in Sage. This method is used internally by plot3d to generate static images. This example doesn’t have correct scaling:

        sage: from sage.interfaces.jmoldata import JmolData
        sage: JData = JmolData()
        sage: D=dodecahedron()
        sage: from sage.misc.misc import SAGE_TMP
        sage: archive_name=os.path.join(SAGE_TMP, "archive.jmol.zip")
        sage: D.export_jmol(archive_name)  #not scaled properly...need some more steps.
        sage: testfile = os.path.join(SAGE_TMP, "testimage.png")
        sage: script = 'set defaultdirectory "%s"\n script SCRIPT\n'%archive_name
        sage: JData.export_image(targetfile =testfile,datafile = script, image_type="PNG") # optional -- java
        sage: print os.path.exists(testfile) # optional -- java
        True

  `is_jvm_available`()

    Returns True if the Java Virtual Machine is available and False if not.

    EXAMPLES:

    Check that it returns a boolean:

        sage: from sage.interfaces.jmoldata import JmolData
        sage: JData = JmolData()
        sage: type(JData.is_jvm_available())
        <type 'bool'>

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