Package schrodinger :: Package application :: Package desmond :: Module energygroup :: Class EnergyGroup

Class EnergyGroup

trajectory.analysistool.AnalysisTool --+
                                       |
                                      EnergyGroup

A tool to calculate group-group interaction.

Instance Methods

[hide private]

__init__(self, groups, trjfile, cfgfile, *args, **kwargs)
Parameters

doFrameInit(self, frame)
Setup groups and launch vrun

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

getFrameResults(self)
Return results as a numpy array for all values and frames with the first index being across frames.

getLabel(self)

plot(self, *args, **kwargs)
A generic matplotlib 2D plot implementation.

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

Method Details

[hide private]

init(self, groups, trjfile, cfgfile, *args, **kwargs)
(Constructor)


Parameters

groups
    group definition, a list of atomselection. an atom can only
    appear in one group.

trjfile
    desmond trajectory directory.

cfgfile
    original config file used to generate trajectory

Overrides: trajectory.analysistool.AnalysisTool.__init__

doFrameInit(self, frame)

Setup groups and launch vrun

Overrides: trajectory.analysistool.AnalysisTool.doFrameInit

processFrame(self, frame)

Collect data for the provided frame.

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

getFrameResults(self)

Return results as a numpy array for all values and frames with the first index being across frames.

So, if fr = analysis.getFrameResults(), and the analysis instance calculates three values for each frame, then fr[0] will be the three values for the first frame.

Overrides: trajectory.analysistool.AnalysisTool.getFrameResults: (inherited documentation)

getLabel(self)

Overrides: trajectory.analysistool.AnalysisTool.getLabel

plot(self, *args, **kwargs)

A generic matplotlib 2D plot implementation.

Overrides: trajectory.analysistool.AnalysisTool.plot

Class EnergyGroup

__init__(self, groups, trjfile, cfgfile, *args, **kwargs) (Constructor)

doFrameInit(self, frame)

processFrame(self, frame)

getFrameResults(self)

getLabel(self)

plot(self, *args, **kwargs)

init(self, groups, trjfile, cfgfile, *args, **kwargs)
(Constructor)