BackboneMorph

Move matched backbone residues in order and fade unmatched residues.

View source Guide and examplesInherits Animation

from proteinmotion import BackboneMorph

Constructor

BackboneMorph(
    source,
    destination,
    *,
    match=None,
    residue_delay=0.008,
    fade_out=(0.0, 0.35),
    fade_in=(0.65, 1.0),
    align=True,
    motion_easing='smooth',
    easing=None,
    delay_seconds=None,
    stagger_fraction=None,
    **match_options,
)

Parameters

Parameter	Default	Description
`source`	Required	Source Protein.
`destination`	Required	Destination Protein.
`match`keyword only	`None`	ContactMatch correspondence; None computes one using match_options.
`residue_delay`keyword only	`0.008`	Delay in seconds between successive residue starts.
`fade_out`keyword only	`(0.0, 0.35)`	Normalized progress interval for fading unmatched source residues.
`fade_in`keyword only	`(0.65, 1.0)`	Normalized progress interval for fading unmatched destination residues.
`align`keyword only	`True`	Align the destination to the source before interpolation.
`motion_easing`keyword only	`'smooth'`	Per-residue motion: "smooth" or "linear".
`easing`keyword only	`None`	Named easing (smooth, linear, ease_in_out_sine, there_and_back) or callable mapping [0, 1] to [0, 1]. Per-item easing preserves stagger timing.
`delay_seconds`keyword only	`None`	Delay between successive residue, chain, or glyph starts, in seconds. Choose one delay option.
`stagger_fraction`keyword only	`None`	Total clip fraction reserved for staggered starts, in [0, 1).
`**match_options`	—	Options passed to match_backbones() when match is None.

Notes

Matched residues move with their Cα (protein) or C1′ (DNA/RNA) in deposited chain order. Each move lasts run_time − (matched count − 1) × residue_delay seconds. Whole residues retain their internal geometry as source and target representations crossfade. Unmatched source and destination residues use fade_out and fade_in intervals. Both objects’ geometry, transforms, and opacity belong to this animation. Each endpoint selects one chain. Explicit pairs require the correct anchor atom.

Example and output

Run this command from a repository checkout.

Code Render command

proteinmotion render examples/backbone_morph.py BackboneDemo \
  -o morph.mp4 --fps 60

Output Preview · 11.5 s · 30 fps

Calmodulin to troponin C morph

A contact-map match selects 114 Cα pairs. Matched residues move in sequence from N to C; unmatched residues fade out or in.

Full source: BackboneDemo Download MP4

Methods and properties

Name	Description
resultproperty	The destination object to select, label and animate after this morph.
targetsproperty	Objects whose state this animation changes.
bind()method	Capture starting values when the scene schedules the animation.
apply()method	Evaluate the animation at eased progress alpha. Called by the timeline.
during()method · inherited from Animation	Set this animation duration and start delay in seconds.

result

View source

BackboneMorph.result

The destination object to select, label and animate after this morph.

targets

View source

BackboneMorph.targets

Objects whose state this animation changes.

bind()

View source

BackboneMorph.bind()

Capture starting values when the scene schedules the animation.

Returns: None

Called by ProteinScene.play(). An animation instance can be bound once.

apply()

View source

BackboneMorph.apply(alpha)

Evaluate the animation at eased progress alpha. Called by the timeline.

Parameter	Default	Description
`alpha`	Required	Eased animation progress in [0, 1].

Returns: None

during()

View source

Inherited from animation.Animation.

BackboneMorph.during(seconds, *, delay=0)

Set this animation duration and start delay in seconds.

Parameter	Default	Description
`seconds`	Required	Positive animation duration in seconds.
`delay`keyword only	`0`	Nonnegative animation start delay in seconds.