schrodinger.trajectory.analysis.RMSD

Class RMSD

A tool to calculate Root Mean Square Deviation from reference positions.

Instance Methods

__init__(self, rmsd_asl, ref_rmsd_pos, in_place=False, fit_asl=None, ref_fit_pos=None, *args, **kwargs)
@type rmsd_asl: AtomSelection instance @param rmsd_asl: The atom selection from which to indetify atom indices to be compared.

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 analysistool.AnalysisTool: doFrameInit, getDataLabels, getResults, plot2D, postProcess, setSlice, shouldProcessFrame

init(self, rmsd_asl, ref_rmsd_pos, in_place=False, fit_asl=None, ref_fit_pos=None, *args, **kwargs)
(Constructor)


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

@type ref_rmsd_pos: numpy array with shape (n,3)
@param ref_rmsd_pos
    position array of reference conformer structure that will be used
    for RMSD calculation.

@type in_place: bool
@param in_place:
    Boolean to control whether the position should be
    transformed onto the reference position before calculation.
    The position is transformed by default.

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

@type ref_fit_pos: numpy array with shape (n,3)
@param ref_fit_pos
    fitting position array of reference conformer structure.

Overrides: analysistool.AnalysisTool.__init__

processFrame(self, frame)

Collect data for the provided frame.

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

plot(self, *args, **kwargs)

A generic matplotlib 2D plot implementation.

Overrides: analysistool.AnalysisTool.plot