Hydrogen Bonding Tools

A set of tools for analyzing hydrogen bonding, found in Packages/HydrogenBonds/ directory:

hbonds

Finds putative h-bonds based on angle and distance

hmatrix

Writes out a binary matrix indicating which atoms have possible h-bonds at each time-point in a trajectory.

hcorrelation

Computes the time-correlation function for h-bonds.

native-hbs.py

Track hydrogen bonds from a reference across a trajectory