Package schrodinger :: Package application :: Package desmond :: Package packages :: Module analysis :: Class RMSF

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Class RMSF

      object --+            
               |            
GeomAnalyzerBase --+        
                   |        
    _MaestroAnalysis --+    
                       |    
                PosAlign --+
                           |
                          RMSF

Known Subclasses:

ProteinRMSF

Root Mean Square Fluctation from reference positions (averaged position over the trajectory) for each atom, with optional alignment fitting.

Instance Methods

_postcalc(self, calc, *_)

length N numpy.ndarray

reduce(self, pos_t, *_, **__)
Temporal average of the RMSF over the trajectory

Inherited from PosAlign: __init__

Inherited from _MaestroAnalysis (private): _getCentered, _precalc

Inherited from GeomAnalyzerBase: __call__

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

Properties

Inherited from object: __class__

Method Details

_postcalc(self, calc, *_)

Overrides: GeomAnalyzerBase._postcalc: (inherited documentation)

reduce(self, pos_t, *_, **__)

Temporal average of the RMSF over the trajectory

Parameters:

pos_t (List of Nx3 numpy.ndarray where N is the number of atoms. The length of the list is the number of frames.)

Returns: length N numpy.ndarray