schrodinger.trajectory.hydrophobiccontactfinder 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.

class schrodinger.trajectory.hydrophobiccontactfinder.HydrophobicContactFinder(atomsel1, atomsel2, tol=0.01, *args, **kwargs)

Bases: schrodinger.trajectory.analysistool.AnalysisTool

A tool to find hydrogen bonds present between two sets of molecules.

doFrameInit(frame)

flatten(lst)

getAllBonds()

Return a set of all hydrogen bonds found by the analysis. Results are in the same form as getFrameResults() - a pair of (acceptor, donor) integers.

getClosestDistance(atoms1, atoms2, pbc)

getFrameResults()

For each frame, return a list of (acceptor, donor) integer tuples, each value being a 1-based atom index into the overall simulation structure.

Note that the returned value here is not a numpy array as each frame may have a different number of hydrogen bonds.

getHydrophobicResidueIndex(st)

getResults()

isOrthogonal(box, tol)

labelProtAtm(atm_idx)

labelProtRes(atm_idx)

processFrame(frame)

processHydrophobicFrame(frame)

processPiCationFrame(frame)

processPiPiFrame(frame)

updatePositions(st, frame)

schrodinger.trajectory.hydrophobiccontactfinder.find_centroid(atomlist)

Computes the centroid of a group of atoms

Parameters:atomlist (list) – list of atom objects Return type:Centroid Returns:Centroid object for the atoms