Package schrodinger :: Package trajectory :: Module desmondsimulation

Module desmondsimulation

A module to provide access to a Desmond simulation.

The DesmondSimulation class interacts with AnalysisTool subclasses to complete analyses of the simulation. AnalysisTool subclasses are passed in to the DesmondSimulation.analyze method and they implement an API that is required by DesmondSimulation. The API that the DesmondSimulation.analyze method requires is demonstrated by the following pseudo-code:

   def analyze(analyses):
       for frame in desmond_frames:
           for analysis in analyses:
               if analysis.shouldProcessFrame(frame):
                   if analysis not initialized:
                       analysis.doFrameInit(frame)
                   analysis.processFrame(frame)

       for analysis in analyses:
           analysis.postProcess()

The shouldProcessFrame method is implemented in the AnalysisTool superclass.

Methods that must be implemented in the AnalysisTool subclass are:

processFrame
getFrameResults

Methods that are optional but that will be used by DesmondSimulation if present are:

doFrameInit
postProcess

Classes

[hide private]

_DesmondFrame
_DesmondFrame contains simulation data at a particular time.

_ChorusFrame
_DesmondFrame contains simulation data at a particular time.

DesmondSimulation

ChorusSimulation

_FepTrajectory

FepSimulation
A class for handling Fep Simulation

Functions

[hide private]

_create_simulation(cmsfile, trjfile)

get_fep_ct_indices(cmsfile)
return fep ct indices in pair

get_fep_idx_map(cmsfile)

trajectory.desmondsimulation or trajectory.fepsimulation

create_simulation(cmsfile, trjfile=None)
Return a Desmond or FEP trajectory object.

Variables

[hide private]

_INVALID_FRAME_ID = -1

_structure_cache = {}

__package__ = 'schrodinger.trajectory'

Function Details

[hide private]

create_simulation(cmsfile, trjfile=None)

Return a Desmond or FEP trajectory object.

Parameters:

cmsfile (str) - Desmond CMS file
trjfile (str, None) - Optional trajectory file location. If not specified, will be derived from the cmsfile.

Returns: trajectory.desmondsimulation or trajectory.fepsimulation

Return a desmond of fep simulation object