schrodinger.trajectory.saltbridgefinder 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.saltbridgefinder.SaltBridgeFinder(atomsel1, atomsel2, tol=0.01, cutoff=3.2, *args, **kwargs)

Bases: schrodinger.trajectory.analysistool.AnalysisTool

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

doFrameInit(frame)

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.

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.

getResults()

getSBpartners(st)

getSBtype(atom_idx)

isOrthogonal(box, tol)

labelProtAtm(atm_idx)

processFrame(frame)

updatePositions(st, frame)

schrodinger.trajectory.saltbridgefinder.unique_list(seq)