Molecule2D and Molecule

Molecule2D draws a skeletal formula from a Structure: atoms with positions in bond lengths (y up) and bonds between them. It draws the bonds bond_length pixels long:

• single, double and triple bonds;
• a solid Wedge out of the page and a hashed Dash behind it, both wide at the second atom;
• in a ring, the second line of a double bond inside the ring;
• with the same number of neighbours on both sides (a carbonyl), the two lines centred.

Carbons are left out. Other atoms are labelled with their hydrogens (on the side away from their bonds) and their charge, and with color_atoms oxygen, nitrogen, sulfur, phosphorus and the halogens get their own colours. With Create as enter the bonds draw on one after the other. Gallery scene: Molecule2D (a stereocentre with a wedge and a dash).

Molecule2D 3 sPlayUnmuteCopy render command

Molecule takes a SMILES string instead. Structure::from_smiles reads it with chematic, which lays it out in 2D. Aromatic rings become alternating single and double bonds. The layout is computed once per string and kept for the rest of the process. An invalid string draws nothing, so check new strings with Structure::from_smiles, which returns a SmilesError. Gallery scene: Molecule (aspirin and caffeine).

Molecule 3.5 sPlayUnmuteCopy render command

use fframes_kit::prelude::*;

fn water() -> Structure {
    Structure::new(
        vec![
            ChemAtom::new("O", 0.0, 0.0),
            ChemAtom::new("H", -0.8, -0.6),
            ChemAtom::new("H", 0.8, -0.6),
        ],
        vec![
            ChemBond::new(0, 1, BondKind::Single),
            ChemBond::new(0, 2, BondKind::Single),
        ],
    )
}

fn figures<'a>(ui: &mut Ui<'a, '_, '_>, water: &'a Structure) -> Svgr<'a> {
    let water = ui.show(Molecule2D {
        structure: Some(water),
        center: (-4.0, 0.0),
        bond_length: 90.0,
        ..ui.defaults()
    });
    let aspirin = ui.show(Molecule {
        smiles: "CC(=O)Oc1ccccc1C(=O)O".into(),
        center: (2.5, 0.0),
        enter: Some(Create::default().into()),
        ..ui.defaults()
    });
    svgr!(<g>{water}{aspirin}</g>)
}

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).

Molecule2D

A skeletal formula: the bonds of structure bond_length pixels long around center (units of ui.space), double bonds in rings drawn inside the ring, and the labels of the atoms that are not carbons, with their hydrogens and charges (show_hydrogens). The bonds draw on in order with enter (Create draws them one after the other), the labels with parts_enter. With color_atoms oxygen, nitrogen, sulfur, phosphorus and the halogens get their own colours. Without structure nothing is drawn.

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	70.0	Pixels per bond length of the structure’s coordinates.
show_hydrogens	bool	true	Writes the hydrogens and charge after a heteroatom’s symbol (OH, NH2); false writes the symbol alone.
color_atoms	bool	true	Colours the labels of oxygen, nitrogen, sulfur, phosphorus and the halogens; false uses bond_color for all.
bond_color	Color	theme.colors.text	Colour of the bonds, and of the labels of carbon and of every atom when color_atoms is false.
stroke_width	f32	theme.stroke.regular	Width in pixels of the bond lines.
enter	Option<EnterAnim>	None	How the bonds draw on; None shows them from the start.
exit	Option<ExitAnim>	None	How the bonds leave at the end of the container; None stays.
parts_enter	Option<FadeIn>	None	Fade in of the atom labels; None for none.
parts_exit	Option<FadeOut>	None	Fade out of the atom labels before the end; None for none.

Feature chemistry · Source

Molecule

A skeletal formula from a SMILES string ("CC(=O)O"), laid out by chematic and drawn like Molecule2D. The layout is computed once per string and kept for the rest of the process; an invalid string draws nothing (check it with Structure::from_smiles).

Field	Type	Default	Description
smiles	Cow<str>	Cow::Borrowed("c1ccccc1")	The molecule as a SMILES string ("CC(=O)O"); an invalid string draws nothing.
center	(f64, f64)	m.center	The middle of the molecule’s coordinates, in units of ui.space.
bond_length	f32	m.bond_length	Pixels per bond length of the laid-out structure.
show_hydrogens	bool	m.show_hydrogens	Writes the hydrogens and charge after a heteroatom’s symbol (OH, NH2); false writes the symbol alone.
color_atoms	bool	m.color_atoms	Colours the labels of oxygen, nitrogen, sulfur, phosphorus and the halogens; false uses bond_color for all.
bond_color	Color	m.bond_color	Colour of the bonds, and of the labels of carbon and of every atom when color_atoms is false.
stroke_width	f32	m.stroke_width	Width in pixels of the bond lines.
enter	Option<EnterAnim>	None	How the bonds draw on; None shows them from the start.
exit	Option<ExitAnim>	None	How the bonds leave at the end of the container; None stays.
parts_enter	Option<FadeIn>	None	Fade in of the atom labels; None for none.
parts_exit	Option<FadeOut>	None	Fade out of the atom labels before the end; None for none.

Feature chemistry · Source