Custom bonds

strainjedi.jedi.get_hbonds(mol, covf=1.3, vdwf=0.9)

Get all hbonds in a structure. Hbonds are defined as the HY bond inside X-H···Y where X and Y can be O, N, F and the angle XHY is larger than 90° and the distance between HY is shorter than 0.9 times the sum of the vdw radii of H and Y.

mol: class

Structure of which the hbonds should be determined.

Returns

2D array of indices.