Package schrodinger :: Package trajectory :: Module analysis :: Class LigandRMSD

Class LigandRMSD

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           LigandRMSD

A tool to calculate Root Mean Square Deviation from reference positions of a small molecule. Taking symmetry into account.

Instance Methods

[hide private]

__init__(self, rmsd_asl, ref_rmsd_pos, 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.

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

_remove_polar_h(self, st, mapping_list)

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: getDataLabels, getResults, plot2D, postProcess, setSlice, shouldProcessFrame

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, rmsd_asl, ref_rmsd_pos, 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 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: 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)

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)

getLabel(self)

Overrides: analysistool.AnalysisTool.getLabel

plot(self, *args, **kwargs)

A generic matplotlib 2D plot implementation.

Overrides: analysistool.AnalysisTool.plot

Class LigandRMSD

__init__(self, rmsd_asl, ref_rmsd_pos, fit_asl=None, ref_fit_pos=None, *args, **kwargs) (Constructor)

doFrameInit(self, frame)

processFrame(self, frame)

getFrameResults(self)

getLabel(self)

plot(self, *args, **kwargs)

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