schrodinger.trajectory.desmondsimulation module

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

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.trajectory.desmondsimulation.ChorusSimulation

alias of DesmondSimulation

class schrodinger.trajectory.desmondsimulation.DesmondSimulation(cmsfile, trjfile)

analyze(analysis_tools)

charge

Charges of individual atoms in the structure.

frame_iter

getFrame(n)

Return N-th frame

getFrameStructure(n)

Return a schrodinger.structure.Structure object with coordinate, velocity and box properties for frame n.

getFrameTime(n)

return chemical time of frame n.

getTimes()

return all chemical times that associate with this trajectory.

mass

Mass of individual atoms in the structure.

total_frame

Total number of frames.

total_mass

Total mass of all atoms in the structure.

writeCms(cmsfilename, n)

Write a cms file with coordinate and velocity from the specified frame.

class schrodinger.trajectory.desmondsimulation.FepSimulation(cmsfile, trjfile, fep_idx_map, fep_atom_map)

Bases: schrodinger.trajectory.desmondsimulation.DesmondSimulation

A class for handling Fep Simulation

schrodinger.trajectory.desmondsimulation.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:

Return a desmond of fep simulation object

Return type:

trajectory.desmondsimulation or trajectory.fepsimulation

schrodinger.trajectory.desmondsimulation.get_fep_ct_indices(cmsfile)

return fep ct indices in pair

schrodinger.trajectory.desmondsimulation.get_fep_idx_map(cmsfile)