HydrogenBonds

Detect hydrogen bonds from donor–acceptor distance and hydrogen geometry.

from proteinmotion import HydrogenBonds

Constructor

HydrogenBonds(
    protein,
    *,
    donors=None,
    acceptors=None,
    max_distance=3.5,
    min_angle=150,
    hydrogens='auto',
    donor_h_cutoff=1.3,
)

Parameters

Parameter	Default	Description
`protein`	Required	Protein object to read or animate.
`donors`keyword only	`None`	Donor Region or atom indices; None uses standard amino-acid templates.
`acceptors`keyword only	`None`	Acceptor Region or atom indices; None uses standard amino-acid templates.
`max_distance`keyword only	`3.5`	Maximum donor–acceptor distance in ångströms.
`min_angle`keyword only	`150`	Minimum donor–hydrogen–acceptor angle in degrees.
`hydrogens`keyword only	`'auto'`	"explicit", "auto", or "backbone"; controls the use of loaded or inferred hydrogens.
`donor_h_cutoff`keyword only	`1.3`	Maximum donor–hydrogen assignment distance in ångströms.

Notes

Pairs pass when 1.5 Å < D–A ≤ max_distance and D–H–A ≥ min_angle. Default templates cover standard amino acids. auto uses loaded hydrogens first and can infer backbone amide hydrogens. Use include_hydrogens=True when loading explicit H. For protonation-dependent or nonstandard groups, supply prepared coordinates and donor/acceptor selections.

Example and output

This excerpt runs inside a scene’s construct() method. The full example file includes imports, structure loading, and camera setup. Run it from a repository checkout.

Code Scene excerpt

p = helix_view(self)
hb = HydrogenBonds(
    p,
    donors=p.select(residues=(23, 34), atoms="N"),
    max_distance=3.5,
    min_angle=150,
    hydrogens="backbone",
)
lines = hb.highlight(
    mode="3d",
    color="#f2ba67",
    radius=0.07,
    dash_count=5,
    show_distances=False,
)
self.play(Write(lines), run_time=2)
self.play(self.camera.animate.orbit(0.6), run_time=3)
self.wait(1)

Output Preview · 6.0 s · 60 fps

Hydrogen bonds

Geometry-based N···O contacts with inferred backbone H.

Full source: HydrogenBondLines Download MP4

Methods and properties

Name	Description
hydrogen_position()method	Return the explicit or inferred hydrogen position for a detected pair.
pairsproperty · inherited from _Analysis	Tuple of Interaction records recomputed when coordinates or analysis settings change.
highlight()method · inherited from _Analysis	Create styled hydrogen-bond lines. Options go to InteractionHighlight.