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

Class RMSF

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

Known Subclasses:

ProteinRMSF

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

Instance Methods

[hide private]

__init__(self, msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)
@type msys_model: C{msys.System} @type cms_model: C{schrodinger.structure.Structure} @type aids: C{list} of C{int}s @type fit_aids: C{list} of C{int}s @param fit_ref_pos: positions of reference conformer structure for translation/rotation calculation @type fit_ref_pos: Mx3 C{numpy.ndarray} @param in_place: if C{True}, calculate RMSF without applying alignment transformations

_precalc(self, calc)
Reusable intermediate data saved in calc: We use the _center function, and create one copy of the trajectory frame and one copy of the full-system CT.

_postcalc(self, calc, _, fr)

length N numpy.ndarray

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

Inherited from _MaestroAnalysis (private): _getCentered

Inherited from GeomAnalyzerBase: __call__

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

Static Methods

[hide private]

Inherited from GeomAnalyzerBase (private): _get_sites, _sites2gids

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)
(Constructor)


@type   msys_model: C{msys.System}
@type    cms_model: C{schrodinger.structure.Structure}
@type         aids: C{list} of C{int}s
@type     fit_aids: C{list} of C{int}s
@param fit_ref_pos: positions of reference conformer structure for
                    translation/rotation calculation
@type  fit_ref_pos: Mx3 C{numpy.ndarray}
@param    in_place: if C{True}, calculate RMSF without applying
                    alignment transformations

Both C{msys_model} and C{cms_model} must be previously obtained through
the C{read_cms} function.

Parameters:

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

Overrides: object.__init__

_precalc(self, calc)

Reusable intermediate data saved in calc: We use the _center function, and create one copy of the trajectory frame and one copy of the full-system CT. In both, the solute atoms are centered.

Overrides: GeomAnalyzerBase._precalc: (inherited documentation)

_postcalc(self, calc, _, fr)

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

Class RMSF

__init__(self, msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False) (Constructor)

_precalc(self, calc)

_postcalc(self, calc, _, fr)

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

init(self, msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)
(Constructor)