Package schrodinger :: Package trajectory :: Module analysis :: Class VolumeMapper

Class VolumeMapper

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           VolumeMapper

A tool to map atomic volume onto a grid. Each frame is superimposed onto a reference using fit_asl and ref_fit_pos. Next, the atoms selected by map_asl are mapped onto the grid.

Instance Methods

[hide private]

__init__(self, map_asl, fit_asl, grid, ref_fit_pos=None, *args, **kwargs)
@type map_asl: AtomSelection instance @param map_asl: The atom selection from which to indetify atom indices to be mapped.

doFrameInit(self, frame)
Initialize data that requires a frame instance for reference.

processFrame(self, frame)
Collect data for the provided frame.

getLabel(self)

Inherited from analysistool.AnalysisTool: getDataLabels, getFrameResults, getResults, plot, plot2D, postProcess, setSlice, shouldProcessFrame

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

grid

Inherited from object: __class__

Method Details

[hide private]

init(self, map_asl, fit_asl, grid, ref_fit_pos=None, *args, **kwargs)
(Constructor)


@type map_asl: AtomSelection instance
@param map_asl:
    The atom selection from which to indetify atom indices to be mapped.

@type fit_asl: AtomSelection instance
@param fit_asl:
    The atom selection from which to indetify atom indices to be
    transformed.

@type grid: a Grid3D instance
@param grid:
    a Grid 3D instance fully configured.  Atoms selected by map_asl
    are mapped onto it for each frame.

@type ref_fit_pos: numpy array with shape (n,3)
@param ref_fit_pos
    position array of reference conformer structure that will be used
    for the superposition.  Of not supplied, the first frame of the
    trajectory will be used.

Overrides: object.__init__

doFrameInit(self, frame)

Initialize data that requires a frame instance for reference.

This method will be called once, with the first frame that is processed.

Overrides: analysistool.AnalysisTool.doFrameInit: (inherited documentation)

processFrame(self, frame)

Collect data for the provided frame.

Overrides: analysistool.AnalysisTool.processFrame: (inherited documentation)

getLabel(self)

Overrides: analysistool.AnalysisTool.getLabel

Property Details

[hide private]

grid

Get Method:: unreachable.grid(self)

Class VolumeMapper

__init__(self, map_asl, fit_asl, grid, ref_fit_pos=None, *args, **kwargs) (Constructor)

doFrameInit(self, frame)

processFrame(self, frame)

getLabel(self)

grid

init(self, map_asl, fit_asl, grid, ref_fit_pos=None, *args, **kwargs)
(Constructor)