GraphMolecule

Cargo featurefeatures = ["chemistry"]

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GraphMolecule is manim-chemistry’s GraphMolecule with the animations of its GMAnimationBuilder. It draws every atom of a Structure as a ring with its symbol, carbons too, and the bonds as lines, two for a double bond and three for a triple bond, bond_length pixels long. Three lists animate it on the figure’s own seconds, each entry with a start and a duration:

rotations: a BondRotation turns the part of the molecule on the far side of bond bond (the atoms reached from its second atom) by degrees about the bond, as about a shaft. The figure is seen from elevation degrees above the page (15 by default), and atoms nearer the viewer are drawn larger and on top. A bond in a ring turns nothing.
recolors: a Recolor blends the atoms and bonds in parts (MoleculePart::Atom(i), MoleculePart::Bond(i)) to color.
highlights: a GroupHighlight fades in a band of color behind atoms and the bonds between them.

functional_groups(&structure, FunctionalGroup::Carboxyl) finds the atoms of each group in a structure: hydroxyls, carbonyls, carboxyls, esters, amides, amines and ethers, each list starting with the group’s central atom. Gallery scenes: GraphMolecule (acetic acid with its carboxyl group highlighted) and BondRotation (hexan-1-ol, its hydroxyl lit while the end of the chain turns).

GraphMolecule demo, first frame — `GraphMolecule` 4 s

BondRotation demo, first frame — `BondRotation` 4 s

use fframes_kit::prelude::*;

// Prepare the structure once, outside the frame render.
let acid = Structure::from_smiles("CC(=O)O")?;
let carboxyl = functional_groups(&acid, FunctionalGroup::Carboxyl);

fn figure<'a>(ui: &mut Ui<'a, '_, '_>, acid: &'a Structure, carboxyl: &[Vec<usize>]) -> Svgr<'a> {
    let accent = ui.theme.colors.accent;
    ui.show(GraphMolecule {
        structure: Some(acid),
        rotations: vec![BondRotation { bond: 0, degrees: 180.0, start: 1.0, duration: 2.0 }],
        highlights: carboxyl
            .iter()
            .cloned()
            .map(|atoms| GroupHighlight { atoms, color: accent, start: 0.3, duration: 0.5 })
            .collect(),
        ..ui.defaults()
    })
}

API

Components are plain structs. Set the fields you need and fill the rest with ..ui.defaults(): the defaults below come from the current theme (theme. values are fields of Theme).

GraphMolecule

Field	Type	Default	Description
`structure`	`Option<&Structure>`	`None`	The molecule to draw (from SMILES, a molfile or built by hand); `None` draws nothing.
`center`	`(f64, f64)`	`(0.0, 0.0)`	The middle of the molecule’s coordinates, in units of `ui.space`.
`bond_length`	`f32`	`110.0`	Pixels per bond length of the structure’s coordinates.
`atom_radius`	`f32`	`24.0`	Radius in pixels of an atom ring, before the depth scaling of a turn.
`elevation`	`f32`	`15.0`	Degrees the view looks down from above the page: 0 is straight on, where atoms in line hide each other.
`rotations`	`Vec<BondRotation>`	`Vec::new()`	Turns of the part of the molecule beyond a bond; empty for none.
`recolors`	`Vec<Recolor>`	`Vec::new()`	Colour changes of atoms and bonds over time; empty for none.
`highlights`	`Vec<GroupHighlight>`	`Vec::new()`	Soft colour bands behind groups of atoms, fading in over time; empty for none.
`color_atoms`	`bool`	`true`	Colours each ring and symbol by its element; `false` uses `bond_color` for all.
`bond_color`	`Color`	`theme.colors.text`	Colour of the bonds, and of the atoms when `color_atoms` is `false`.
`atom_fill`	`Color`	`theme.colors.surface`	Fill colour inside the atom rings.
`stroke_width`	`f32`	`theme.stroke.regular`	Width in pixels of the bonds and atom rings.
`enter`	`Option<FadeIn>`	`None`	Fade in at the start; `None` for none.
`exit`	`Option<FadeOut>`	`None`	Fade out before the end; `None` for none.

Feature chemistry · Source