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

Class Coc

      object --+            
               |            
GeomAnalyzerBase --+        
                   |        
            CenterOf --+    
                       |    
                     Com --+
                           |
                          Coc

Class for computing center of charge under periodic boundary condition. Pseudo atoms are included.

For each frame, the results will be the unwrapped-center-of-charge. If return_unwrapped_atompos is True, the results will be a 2-tuple: (unwrapped-center-of-charge, [unwrapped-positions-of-involved-atoms]).

Instance Methods

[hide private]

__init__(self, msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)
Refer to the docstring of Com.__init__.

Inherited from CenterOf (private): _calcCircMean, _postcalc, _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]

Inherited from GeomAnalyzerBase (private): _get_sites, _sites2gids

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)
(Constructor)

Refer to the docstring of Com.__init__.

Parameters:

return_unwrapped_atompos - if False, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.

Overrides: object.__init__

Class Coc

__init__(self, msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False) (Constructor)

init(self, msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)
(Constructor)