Package schrodinger :: Package trajectory :: Module order_parameters :: Class OrderParameter

Class OrderParameter

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           OrderParameter


Given the Direcator (local or global), and the descriptor (local or global),
calculate the order parameter
  |S_k| = | 1/N sum( ((3 * M dot m)^2 -1) / 2) |
Where 'M' is the director vector and 'm' is the descriptor vectors

Instance Methods

[hide private]

__init__(self, director_type, descriptor_type, atomsel, *args, **kwargs)
Initialize frame slicing information.

_get_lipids_direction(self, st, tail_type)
Extract carbons attached to either sn1 or sn2 lipid tails

_get_SMARTS_direction(self, st, smarts_pattern)
Process smarts, if smarts are used, get the vectors that match it.

doFrameInit(self, frame)
Initialize analysis.

_updatePositions(self, frame)
Just update the positions of selected atoms, no need to reconstruct a new structure.

_updateDirector(self, frame)
If the director dynamic update it every frame, otherise just keep it same.

_updateDescriptor(self)
Update the descriptor every frame.

_calc_order_param(self)

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__

Class Variables

[hide private]

director_dict = {'X': [1.0, 0.0, 0.0], 'X-axis': [1.0, 0.0, 0....

smarts_dict = {'CH': '([CX3,CX4][#1])'}

Instance Variables

[hide private]

_st
self._mols_aid = [map(lambda x: x-1, mol.getAtomIndices())...

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, director_type, descriptor_type, atomsel, *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)

_get_SMARTS_direction(self, st, smarts_pattern)

Process smarts, if smarts are used, get the vectors that match it. Store the list of index pairs, so the smarts pattern is not called every frame.

doFrameInit(self, frame)

Initialize analysis. this only runs once.

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

plot(self, *args, **kwargs)

A generic matplotlib 2D plot implementation.

Overrides: analysistool.AnalysisTool.plot

Class Variable Details

[hide private]

director_dict

Value:

{'X': [1.0, 0.0, 0.0],
 'X-axis': [1.0, 0.0, 0.0],
 'Y': [0.0, 1.0, 0.0],
 'Y-axis': [0.0, 1.0, 0.0],
 'Z': [0.0, 0.0, 1.0],
 'Z-axis': [0.0, 0.0, 1.0],
 'dipole': <function get_dipole_direction at 0x7f59457aa758>,
 'moment_of_intertia': <function get_moment_direction at 0x7f59457aa7d
...

Instance Variable Details

[hide private]

_st


self._mols_aid = [map(lambda x: x-1, mol.getAtomIndices())
                  for mol in self._st.molecule]

Class OrderParameter

__init__(self, director_type, descriptor_type, atomsel, *args, **kwargs) (Constructor)

_get_SMARTS_direction(self, st, smarts_pattern)

doFrameInit(self, frame)

processFrame(self, frame)

getFrameResults(self)

getLabel(self)

plot(self, *args, **kwargs)

director_dict

_st

init(self, director_type, descriptor_type, atomsel, *args, **kwargs)
(Constructor)