Package schrodinger :: Package trajectory :: Module analysis :: Class Dihedral

Class Dihedral

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           Dihedral

A tool to calculate dihedral angles from selected atom sets.

Instance Methods

[hide private]

__init__(self, atomsel1, atomsel2, atomsel3, atomsel4, *args, **kwargs)
Initialize frame slicing information.

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)

_getAtoms(self, frame, index)
Return four StructureAtom objects for dihedral 'index' of this Dihedral analysis in the Structure of 'frame'.

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

Inherited from analysistool.AnalysisTool: doFrameInit, 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, atomsel1, atomsel2, atomsel3, atomsel4, *args, **kwargs)
(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.

Overrides: object.__init__: (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

_getAtoms(self, frame, index)

Return four StructureAtom objects for dihedral 'index' of this Dihedral analysis in the Structure of 'frame'. The 'index' parameter is indexed from zero.

This method is marked as private because it is considered experimental. It may be modified or dropped in the future.

Parameters:

index (int)
frame (_DesmondFrame)

plot(self, *args, **kwargs)

A generic matplotlib 2D plot implementation.

Overrides: analysistool.AnalysisTool.plot

Class Dihedral

__init__(self, atomsel1, atomsel2, atomsel3, atomsel4, *args, **kwargs) (Constructor)

processFrame(self, frame)

getFrameResults(self)

getLabel(self)

_getAtoms(self, frame, index)

plot(self, *args, **kwargs)

init(self, atomsel1, atomsel2, atomsel3, atomsel4, *args, **kwargs)
(Constructor)