getWithin_kdTree

getWithin_kdTree.getWithin_kdTree(allAtoms, refSel, outSel, keepIdx, cellDims, distance)

This method uses the periodicCKDTree class to find all atoms within given distance from user selection.

The periodic KDTree class was written by Patrick Varilly. See https://github.com/patvarilly/periodic_kdtree

Parameters:

• allAtoms – atom coordinates for all seleted frames (3D numpy array)
• usrSel – atom indices that will be used in query_ball_point method
• keepIdx – array of shape (# atoms, # frames) to store ones where atoms should be kept within given distance and selection
• cellDims – cell dimensions for all selected frames
• distance – distance in angstrom for query_ball_point method

Returns:

the keepIdx array with ones where atoms are within given distance and 0 otherwise.