RotateTorsions

Turn torsions by amounts in degrees, for example a full side-chain rotation.

View source Guide and examplesInherits SetTorsions

from proteinmotion import RotateTorsions

Constructor

RotateTorsions(
    target,
    *,
    phi=None,
    psi=None,
    omega=None,
    chi1=None,
    chi2=None,
    chi3=None,
    chi4=None,
    chi5=None,
    conformation=None,
    anchor='center',
    secondary='auto',
    path='allowed',
    stagger=None,
    reverse=False,
    easing='smooth',
)

Parameters

Parameter	Default	Description
`target`	Required	Protein or Region whose amino acids change.
`phi`keyword only	`None`	φ, C(i−1)–N–Cα–C. Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`psi`keyword only	`None`	ψ, N–Cα–C–N(i+1). Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`omega`keyword only	`None`	ω, the peptide bond Cα–C–N(i+1)–Cα(i+1). Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`chi1`keyword only	`None`	χ1 side-chain torsion. Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`chi2`keyword only	`None`	χ2 side-chain torsion. Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`chi3`keyword only	`None`	χ3 side-chain torsion. Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`chi4`keyword only	`None`	χ4 side-chain torsion. Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`chi5`keyword only	`None`	χ5 side-chain torsion. Amount to turn in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged; 360 makes a full turn.
`conformation`keyword only	`None`	Sets φ and ψ together: helix, alpha, 310, pi, strand, beta, parallel, antiparallel, ppii, extended, or left.
`anchor`keyword only	`'center'`	Part that stays still: "center" keeps the middle of each chain in place, "n" or "c" a terminus; a Region is held in place as a whole.
`secondary`keyword only	`'auto'`	"auto" blends the cartoon toward the DSSP assignment of the final conformation; "keep" leaves it unchanged.
`path`keyword only	`'allowed'`	"allowed" turns φ and ψ the way that keeps each residue in favored and allowed Ramachandran regions; "shortest" takes the smaller turn.
`stagger`keyword only	`None`	Fraction of the clip, in [0, 1), used to start residues one after another from N to C.
`reverse`keyword only	`False`	Stagger from C to N.
`easing`keyword only	`'smooth'`	Easing of each torsion's change.

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 Full script

"""Turn one ψ angle, then wind a whole peptide into an α helix.

A 12-residue alanine peptide is built as an extended β strand. ψ of Ala6 turns to
−45° with its atoms shown over the cartoon; then every residue moves to φ = −57°,
ψ = −47°, starting at the N terminus. DSSP assigns the helix from the final
coordinates, and the cartoon blends from coil to helix as the angles change.
"""

from proteinmotion import (
    FadeIn,
    Protein,
    ProteinScene,
    RamachandranPlot,
    SetTorsions,
    Text,
    Unwrite,
    Write,
)


class TorsionBasics(ProteinScene):
    def construct(self):
        peptide = Protein.build("AAAAAAAAAAAA", "strand").cartoon()
        middle = peptide.select(residues=6)
        middle.show_atoms()
        self.add(peptide)
        self.camera.frame(peptide, margin=1.0, aspect=self.width / self.height, screen_position=(0.32, 0.55))
        self.camera.phi = 0.3
        plot = RamachandranPlot(peptide, highlight=middle, position=(0.62, 0.14), size=(0.35, 0.7))
        self.add(Text("Torsion angles", font_size=48, font="semibold", position=(0.05, 0.07)))
        marker = middle.torsion_marker("psi", radius=1.6)
        self.play(FadeIn(plot), Write(marker), run_time=1.5)
        self.play(SetTorsions(middle, psi=-45, anchor="n"), run_time=2.5)
        self.play(Unwrite(marker), run_time=0.6)
        self.play(SetTorsions(peptide, conformation="helix", stagger=0.5), run_time=5)
        self.play(self.camera.animate.orbit(0.8), run_time=2.5)

Output Preview · 12.1 s · 60 fps

Torsion angles

A 12-residue alanine peptide: ψ of Ala6 turns, then every residue moves to α-helix angles.

Full source: TorsionBasics Download MP4

Methods and properties

Name	Description
lockedproperty · inherited from SetTorsions	(residue index, torsion) pairs that could not rotate because they lie in rings.
bind()method · inherited from SetTorsions	Capture starting values when the scene schedules the animation.
apply()method · inherited from SetTorsions	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.
targetsproperty · inherited from Animation	Objects whose state this animation changes.

locked

View source

Inherited from torsions.SetTorsions.

RotateTorsions.locked

(residue index, torsion) pairs that could not rotate because they lie in rings.

bind()

View source

Inherited from torsions.SetTorsions.

RotateTorsions.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

Inherited from torsions.SetTorsions.

RotateTorsions.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.

RotateTorsions.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.

targets

View source

Inherited from animation.Animation.

RotateTorsions.targets

Objects whose state this animation changes.