schrodinger.trajectory.analysistool.AnalysisTool

Class AnalysisTool

AnalysisTool is a base class for creating analyses of schrodinger.trajectory.desmondsimulation.DesmondSimulation objects. See the analysis package for specific implementations.

Instance Methods

[hide private]

__init__(self, start=0, stop=-1, step=1)
Initialize frame slicing information.

setSlice(self, start=0, stop=-1, step=1)
Set the range and step info for the analysis.

shouldProcessFrame(self, n)
Return true if frame n should be processed.

getLabel(self)

getDataLabels(self)

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

plot2D(self, *args, **kwargs)
A generic matplotlib 2D plot implementation.

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

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

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

plot(self)

postProcess(self)
Complete a post-processing step.

init(self, start=0, stop=-1, step=1)
(Constructor)

Initialize frame slicing information.

The behavior of 'start', 'stop', 'step' is the same as the python built-in range function. That is, 'start' is included in the values to be processed, but 'stop' is not. Only the largest value satisfying 'start' and 'step' that is less than 'stop' will be processed.

getResults(self)

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

So, if r = analysis.getResults(), and the analysis instance calculates three values for each frame, then r[0] will be the first value across all frames.

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.

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.

postProcess(self)

Complete a post-processing step.

Defaults to doing nothing.