Package schrodinger :: Package trajectory :: Module analysis :: Class SecondaryStructure

Class SecondaryStructure

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           SecondaryStructure

A tool to track secondary protein structure.

Secondary structure status corresponds to the values of class variables NONE (-1), LOOP (0), HELIX (1), STRAND (2), or TURN (3).

Instance Methods

[hide private]

__init__(self, selection=None, *args, **kwargs)
Initialize frame slicing information.

_updateSecondaryStructure(self)

_updatePositions(self, frame)

doFrameInit(self, frame)
Initialize protein structure and then just update the coordinates

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)

getDataLabels(self)
Return the data labels for the residues being tracked.

plot(self, *args, **kwargs)
Plot the secondary structure results with specific integer values for each structure type.

Inherited from analysistool.AnalysisTool: getResults, plot2D, postProcess, setSlice, shouldProcessFrame

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

Class Variables

[hide private]

NONE = -1

LOOP = 0
hash(x)

HELIX = 1

STRAND = 2

TURN = 3
hash(x)

__doc__ = ...

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, selection=None, *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.

Parameters:

selection (any FrameSelection object) - If provided, the secondary structure will be limited to the atoms in the selection.

Overrides: object.__init__

doFrameInit(self, frame)

Initialize protein structure and then just update the coordinates

Overrides: analysistool.AnalysisTool.doFrameInit

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

getDataLabels(self)

Return the data labels for the residues being tracked.

Overrides: analysistool.AnalysisTool.getDataLabels

plot(self, *args, **kwargs)

Plot the secondary structure results with specific integer values for each structure type. Values used are as noted in the class docstring. Small offsets are added to each residue so the lines are distinguishable on the plot.

Overrides: analysistool.AnalysisTool.plot

Class Variable Details

[hide private]

doc

Value:

"""
    A tool to track secondary protein structure.

    Secondary structure status corresponds to the values of class vari
ables
    NONE (%d), LOOP (%d), HELIX (%d), STRAND (%d), or TURN (%d).

    """ %(NONE, LOOP, HELIX, STRAND, TURN)

Class SecondaryStructure

__init__(self, selection=None, *args, **kwargs) (Constructor)

doFrameInit(self, frame)

processFrame(self, frame)

getFrameResults(self)

getLabel(self)

getDataLabels(self)

plot(self, *args, **kwargs)

__doc__

init(self, selection=None, *args, **kwargs)
(Constructor)

doc