Thread

Thread the actual cartoon or atoms and bonds into view with eased travel over the full clip.

View source Guide and examplesInherits Animation

from proteinmotion import Thread

Constructor

Thread(
    protein,
    camera=None,
    *,
    mode='geometry',
    aspect=None,
    radius=0.45,
    settle=None,
    swirl=1.0,
    head=None,
    glow=12.0,
    glow_color=None,
    glow_brightness=1.0,
    easing=None,
    stagger=0.0,
    resolution=None,
    seed=0,
    rate_func=None,
    delay_seconds=None,
    stagger_fraction=None,
    wire_options=None,
)

Parameters

Parameter	Default	Description
`protein`	Required	Protein with at least one traced chain. Cartoon, ribbon and ball-and-stick are supported; surface raises ValueError.
`camera`	`None`	Scene camera for off-screen entry; None uses a starting distance based on the molecule size.
`mode`keyword only	`'geometry'`	geometry transports the current representation; wire retains the original wire-and-crossfade effect.
`aspect`keyword only	`None`	Scene width divided by height for entry positioning; defaults to 16/9.
`radius`keyword only	`0.45`	3D line cylinder radius in ångströms.
`settle`keyword only	`None`	Final fraction of the clip for the wire-to-protein crossfade. Applies only to wire mode.
`swirl`keyword only	`1.0`	Strength of the corkscrew around each flight path; 0 gives smooth arcs.
`head`keyword only	`None`	Radius of the wire's tip, as a multiple of the wire radius.
`glow`keyword only	`12.0`	Halo radius around each leading terminus, as a multiple of radius; 0 turns the glow off.
`glow_color`keyword only	`None`	Halo color; None blends each chain's color with warm white.
`glow_brightness`keyword only	`1.0`	Halo intensity multiplier.
`easing`keyword only	`None`	Travel easing returning a value in [0, 1]. None selects quintic smooth for geometry or ease_in_out_sine for wire mode.
`stagger`keyword only	`0.0`	Delay between chains, as a fraction of the threading time, in chain order.
`resolution`keyword only	`None`	Spacing in Å between wire points.
`seed`keyword only	`0`	Integer that varies the flight paths.
`rate_func`keyword only	`None`	Callable that maps progress in [0, 1] to a finite value in [0, 1].
`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).
`wire_options`keyword only	`None`	Legacy wire-only settings: settle, head, resolution. Requires mode=wire.

Notes

Geometry follows a route through the C terminus toward the N terminus. Residues and ligands move as rigid groups; inter-residue bonds may stretch. Final coordinates restore exactly. Flight paths illustrate an entrance, not physical folding. Do not combine with concurrent coordinate or representation animations. Mode wire preserves the original crossfade effect.

Example and output

Run this command from a repository checkout.

Code Render command

proteinmotion render examples/thread_hemoglobin.py ThreadHemoglobin \
  --fps 60 -o hemoglobin.mp4

Output Preview · 23.1 s · 60 fps

Hemoglobin, one chain at a time

Four wires fly in from four sides and thread the α and β subunits of human deoxyhemoglobin from their C termini, one after another. The cartoon and the four hemes then fade in, and the wires pull back out.

Full source: ThreadHemoglobin Download MP4

Methods and properties

Name	Description
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.