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

Class PosAlign

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

Known Subclasses:

RMSD
, RMSF

This analyzer first aligns the geometric center of the solute atoms to that of cms_model, then calculates the rotation/translation transformation for converting the structure (fit_aids) of a centered trajectory frame to a given geometry (fit_ref_pos) and finally applies the transformation to a position array of only the selected atoms (aids).

If the alignment is not specified (aka. fit_aids is None), only the geometric centering is performed.

Instance Methods

[hide private]

__init__(self, msys_model, cms_model, aids, fit_aids=None, fit_ref_pos=None)
x.__init__(...) initializes x; see help(type(x)) for signature

_postcalc(self, calc, *_)

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

[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)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

fit_ref_pos (Mx3 numpy.ndarray or None
Both msys_model and cms_model must be previously obtained through the read_cms function.
) - positions of reference conformer structure for translation/rotation calculation
msys_model (msys.System)
cms_model (schrodinger.structure.Structure)
fit_aids (list of ints, or None)
aids (list of ints)

Overrides: object.__init__

_postcalc(self, calc, *_)

Overrides: GeomAnalyzerBase._postcalc: (inherited documentation)

Class PosAlign

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

_postcalc(self, calc, *_)

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