pydseamslib.cyoda.populateHbonds

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pydseamslib.cyoda.populateHbonds#

pydseamslib.cyoda.populateHbonds(filename: str, yCloud: pydseamslib.cyoda.PointCloudDouble, nList: List[List[int]], targetFrame: int, Htype: int) → List[List[int]]#

Create a vector of vectors containing the hydrogen bond connectivity information. Decides the existence of the hydrogen bond depending on the O–O and O–H vectors from the neighbour list already constructed

Parameters:

  • filename (Filename of the trajectory, with the hydrogen and oxygen coordinates)

  • yCloud (The input molSys::PointCloud for the oxygen atoms only)

  • nList (Row-ordered neighbour list by atom ID)

  • targetFrame (The target or current frame number (starts from 1) and is not the timestep value)

  • Htype (The type ID of the hydrogen atoms)

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