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

Class PosTrack

      object --+    
               |    
GeomAnalyzerBase --+
                   |
                  PosTrack

Class for tracking positions of selected atoms in a trajectory. Pseudo atoms are included.

Since periodic boundary condition is assumed in the MD simulation, the atom positions are wrapped back into the simulation box when they move out of the box. The PosTrack class unwraps the atom positions with respect to their positions in the previous frame. It can be used when atom positions need to be tracked over time, such as diffusion.

Instance Methods

[hide private]

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

_precalc(self, calc)

_postcalc(self, calc, pbc, *_)
Result is a new frame with selected atoms unwrapped with respect to previous frame, if previous frame exists.

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__.

Overrides: object.__init__

_precalc(self, calc)

Overrides: GeomAnalyzerBase._precalc: (inherited documentation)

_postcalc(self, calc, pbc, *_)

Result is a new frame with selected atoms unwrapped with respect to previous frame, if previous frame exists. Otherwise it is a copy of the input frame.

Overrides: GeomAnalyzerBase._postcalc

Class PosTrack

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

_precalc(self, calc)

_postcalc(self, calc, pbc, *_)

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