ColorScale

A fixed linear scale mapping scalar values to RGB colors.

from proteinmotion import ColorScale

Constructor

ColorScale(vmin, vmax, *, colors=('#355f9e', '#56c5bd', '#f5d477'), missing='#87909c')

Parameters

Parameter	Default	Description
`vmin`	Required	Finite lower limit of the fixed color scale.
`vmax`	Required	Finite upper limit, greater than vmin.
`colors`keyword only	`('#355f9e', '#56c5bd', '#f5d477')`	Two or more RGB colors, interpolated between equally spaced stops.
`missing`keyword only	`'#87909c'`	Color for missing values (NaN).

Notes

Values outside the limits use endpoint colors. NaN uses the missing color. Intermediate colors interpolate between equally spaced stops.

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

"""Map 1UBQ Cα B factors to residue color and cartoon thickness."""

from pathlib import Path

from proteinmotion import (
    ColorByProperty,
    ColorLegend,
    ColorScale,
    Protein,
    ProteinScene,
    Representation,
    ResidueValues,
    Rotate,
    Text,
)

DATA = Path(__file__).parent / "data"


class NumericalProperties(ProteinScene):
    def construct(self):
        protein = Protein.from_file(DATA / "1ubq.cif").center()
        values = ResidueValues.b_factors(protein)
        scale = ColorScale(0, 40)
        self.add(protein)
        self.camera.frame(protein, margin=1.08)
        self.add(Text("Residue properties", position=(0.06, 0.07), font_size=42))
        self.add(Text("Ubiquitin · Cα B factors", position=(0.06, 0.13), font_size=25))
        self.add(ColorLegend(scale, title="B factor", unit="Å²", position=(0.06, 0.8)))
        self.play(
            ColorByProperty(protein, values, scale=scale, thickness=(0.6, 1.8), residue_delay=0.012),
            Rotate(protein, 0.25),
            run_time=2.5,
        )
        self.wait(0.5)
        self.play(Representation(protein, "ball_and_stick"), run_time=1.5)
        self.play(Rotate(protein, 0.3), run_time=1)
        self.play(Representation(protein, "surface"), run_time=1.5)
        self.play(Rotate(protein, 0.25), run_time=1.5)

Output Preview · 8.5 s · 60 fps

B factors across representations

1UBQ B factors control residue color and cartoon thickness.

Full source: NumericalProperties Download MP4

Methods and properties

Name	Description
from_values()class method	Choose limits from finite values; expand a constant range by ±0.5.
normalize()method	Clip values to [0, 1], keeping NaN for missing data.
map()method	Map values to an RGB array shaped (*values.shape, 3).

from_values()

View source

ColorScale.from_values(values, **kwargs)

Choose limits from finite values; expand a constant range by ±0.5.

Parameter	Default	Description
`values`	Required	Numerical input values; see the shape and missing-value rules for this object.
`**kwargs`	—	Additional keyword options described below or in the linked constructor.

normalize()

View source

ColorScale.normalize(values)

Clip values to [0, 1], keeping NaN for missing data.

Parameter	Default	Description
`values`	Required	Numerical input values; see the shape and missing-value rules for this object.

map()

View source

ColorScale.map(values)

Map values to an RGB array shaped (*values.shape, 3).

Parameter	Default	Description
`values`	Required	Numerical input values; see the shape and missing-value rules for this object.