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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',
    boundaries=None,
)

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).
`boundaries`keyword only	`None`	Increasing values that split the scale into bands, one fewer than colors; None interpolates.

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
hydropathy()class method	Hydrophilic blue, neutral near-white, hydrophobic orange; symmetric about 0.
conservation()class method	ConSurf's palette from variable (turquoise) through white to conserved (maroon).
plddt()class method	AlphaFold's four confidence bands, split at pLDDT 50, 70 and 90.
pae()class method	Predicted aligned error in Å: confident dark green to uncertain near-white.
distance()class method	Current endpoint distance in ångströms, regardless of the label unit.
difference()class method	A signed change in Å: closer in blue, unchanged near-white, farther in red.
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).

hydropathy()

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ColorScale.hydropathy(scale='kyte-doolittle')

Hydrophilic blue, neutral near-white, hydrophobic orange; symmetric about 0.

Parameter	Default	Description
`scale`	`'kyte-doolittle'`	"kyte-doolittle" or "eisenberg".

conservation()

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ColorScale.conservation(vmin=0.0, vmax=1.0)

ConSurf's palette from variable (turquoise) through white to conserved (maroon).

Parameter	Default	Description
`vmin`	`0.0`	Score drawn turquoise (variable).
`vmax`	`1.0`	Score drawn maroon (conserved).

plddt()

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ColorScale.plddt()

AlphaFold's four confidence bands, split at pLDDT 50, 70 and 90.

pae()

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ColorScale.pae(max_error=31.75)

Predicted aligned error in Å: confident dark green to uncertain near-white.

Parameter	Default	Description
`max_error`	`31.75`	Error in ångströms drawn near white.

distance()

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ColorScale.distance(max_distance=40.0)

Current endpoint distance in ångströms, regardless of the label unit.

Parameter	Default	Description
`max_distance`	`40.0`	Distance in ångströms drawn darkest.

difference()

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ColorScale.difference(limit=10.0)

A signed change in Å: closer in blue, unchanged near-white, farther in red.

Parameter	Default	Description
`limit`	`10.0`	Change in ångströms at either end of the symmetric scale.

from_values()

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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()

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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()

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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.