Class ProteinRMSF

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

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

Instance Methods

[hide private]

__init__(self, msys_model, cms_model, aids, fit_aids=None, fit_ref_pos=None)
see PosAlign.__init__ for parameters

length N numpy.ndarray

reduce(self, pos_t, *_, **__)
@type pos_t: List of Nx3 C{numpy.ndarray} where N is the number of atoms.

Inherited from RMSF (private): _postcalc

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__

Static Methods

[hide private]

_getCommonName(res)

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, msys_model, cms_model, aids, fit_aids=None, fit_ref_pos=None)
(Constructor)

see PosAlign.__init__ for parameters

Parameters:

fit_ref_pos - positions of reference conformer structure for translation/rotation calculation

Overrides: object.__init__

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


@type pos_t: List of Nx3 C{numpy.ndarray} where N is the number of
             atoms. The length of the list is the number of frames.

@rtype : list[string], list[float]
@return: residue tags and RMSF for each residue

Returns: length N numpy.ndarray
Overrides: RMSF.reduce

Class ProteinRMSF

__init__(self, msys_model, cms_model, aids, fit_aids=None, fit_ref_pos=None) (Constructor)

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

init(self, msys_model, cms_model, aids, fit_aids=None, fit_ref_pos=None)
(Constructor)