Package schrodinger :: Package trajectory :: Module lipid_analysis :: Class PhospholipidBilayerThickness

Class PhospholipidBilayerThickness

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           PhospholipidBilayerThickness

This method will center the system in around the Z-axis == 0, and will calculate Phosphorus-Phosphorus distance from two bilayer leaflets.

Instance Methods

[hide private]

__init__(self, atomsel, n_iter=5, origin=array([ 0., 0., 0.]), is_small_box=False, *args, **kwargs)
Initialize frame slicing information.

_updatePositions(self, frame)

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

_calc_Zcenter(self)
Figure out how much to displace the system along the Z-axis

_wrap(self)
After the system has been displaced, we need to wrap particles back into the central box

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, atomsel, n_iter=5, origin=array([ 0., 0., 0.]), is_small_box=False, *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)

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 PhospholipidBilayerThickness

__init__(self, atomsel, n_iter=5, origin=array([ 0., 0., 0.]), is_small_box=False, *args, **kwargs) (Constructor)

doFrameInit(self, frame)

processFrame(self, frame)

getFrameResults(self)

getLabel(self)

plot(self, *args, **kwargs)

init(self, atomsel, n_iter=5, origin=array([ 0., 0., 0.]), is_small_box=False, *args, **kwargs)
(Constructor)