Class Ramachandran

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.

Parameters:

• interactive_plot (bool) - If True, clicking on a point in the plot will print information about the residue and values of the point chosen. If False, the plot will not be interactive, but a reference to a simulation frame will not be held and so memory use should be somewhat lower.
• phi_psi_atoms (list) - A list of six-element tuple that represent the indices of C0, N0, CA, C1 and N1. Note that, the index begins with 1. If phi_psi_atoms is not specified, we will fall back to previous implementation.

Overrides: analysistool.AnalysisTool.__init__

Collect the atom indices from the first frame and set up the phi and psi Dihedral analyses.

Parameters:

• frame - A _DesmondFrame instance.

Overrides: analysistool.AnalysisTool.doFrameInit

Collect data for the provided frame.

Overrides: analysistool.AnalysisTool.processFrame

(inherited documentation)

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: analysistool.AnalysisTool.getFrameResults

(inherited documentation)

Draw a Ramachandran plot.

Parameters:

• frames (sequence of ints) - The frame indices to plot. Default is all available frames.
• colormap (matplotlib.colors.Colormap) - A colormap to indicate the simulation frame that a datapoint belongs to. Default is 'pylab.cm.copper'.

Overrides: analysistool.AnalysisTool.plot