Morph

Interpolate matching atoms to a protein or coordinate array.

View source Guide and examplesInherits Animation

from proteinmotion import Morph

Constructor

Morph(protein, target, *, align=True, atom_map=None, **kwargs)

Parameters

Parameter	Default	Description
`protein`	Required	Protein object to read or animate.
`target`	Required	Destination Protein or coordinates with the same shape as the source.
`align`keyword only	`True`	Align the destination to the source before interpolation.
`atom_map`keyword only	`None`	One unique target atom index per source atom; used with a Protein destination.
`**kwargs`	—	Additional keyword options described below or in the linked constructor.

Additional keyword arguments

Parameter	Default	Description
`rate_func`keyword only	`smooth`	Callable that maps progress in [0, 1] to a finite value in [0, 1].

Notes

Protein inputs match atoms by chain, residue number, insertion code, residue name, and atom name. atom_map can supply an explicit one-to-one mapping. Raw arrays use their given atom order. Alignment uses matching Cα atoms when at least three exist.

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 = ubiquitin()
frame(self, p, margin=1.05)
rest = p.positions.copy()

def stretch(xyz):
    center = xyz.mean(axis=0)
    return center + (xyz - center) * [1.4, 1, 1]

self.play(Deform(p, stretch), run_time=2)
self.wait(0.5)
self.play(Morph(p, rest, align=False), run_time=2)
self.wait(0.5)

Output Preview · 5.0 s · 60 fps

Deformation and morph

A synthetic stretch followed by a return to the original coordinates.

Full source: Deformation Download MP4

Methods and properties

Name	Description
bind()method	Capture starting values when the scene schedules the animation.
apply()method	Evaluate the animation at eased progress alpha. Called by the timeline.
targetsproperty · inherited from Animation	Objects whose state this animation changes.