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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

 

Refer to the docstring of Com.__init__.

Parameters:
  • asl - ASL expression to specify the atom selection
  • gids - GIDs of atoms

    Both msys_model and cms_model must be previously obtained through the read_cms function. They both should have the same atom coordinates and the same simulation box matrix. cms_model is used to obtain atom GIDs from ASL selection. msys_model is used to retrieve atom attribute from GIDs.

    Either asl or gids must be specified, but not both.

Overrides: object.__init__