vmd.atomsel.hbonds

atomsel.hbonds()

Get hydrogen bonds present in current frame of selection using simple geometric criteria.

Parameters:

• cutoff (float) – Distance cutoff between donor and acceptor atoms
• maxangle (float) – Angle cutoff between donor, hydrogen, and acceptor. Angle must be less than this value from 180 degrees.
• acceptor (atomsel) – If given, atomselection for selector atoms, and this selection is assumed to have donor atoms. Both selections must be in the same molecule. If there is overlap between donor and acceptor selection, the output may be inaccurate. Optional.

Returns:

(list of 3 lists) –

Donor atom indices, acceptor atom indices, and

proton atom indices of identified hydrogen bonds