schrodinger.trajectory.proteininteractionsfinder module

A module of classes to analyze Desmond trajectories.

Please see the AnalysisTool documentation for a description of the API that handles interaction between AnalysisTool objects and schrodinger.trajectory.desmondsimulation.DesmondSimulation instances.

Copyright Schrodinger, LLC. All rights reserved.

Type of interactions: 1) hbond b-b 2) hbond b-s 3) hbond s-s 4) hbond s-b 5) salt-bridge 6) pi-pi 7) pi-cation

class schrodinger.trajectory.proteininteractionsfinder.ProteinProteinInteractionsFinder(atomsel1, atomsel2=None, *args, **kwargs)

Bases: schrodinger.trajectory.analysistool.AnalysisTool

A class which finds all protein-protein interactions.

doFrameInit(frame)

getLabel()

getSummaryResults()

processFrame(frame)

tag2ca

updatePositions(frame)

schrodinger.trajectory.proteininteractionsfinder.get_atom_residue_tags(st)

Returns:three structure-specific data structures: 1. atom2tag – a map which matches atom index to residue tag 2. ordered_residues – N-> C ordered residue tags 3. tag2ca – a map which matches residue tag to full-system CT ca index

schrodinger.trajectory.proteininteractionsfinder.res_str(r)

Return type:str Returns:string tag of a residue