MolFile

MolFile::parse reads a V2000 molfile (.mol), or the first record of an .sdf file: the title, the atoms with their positions and charges (M CHG lines replace the charges of the atom block) and the bonds. V3000 files return MolError::V3000; save them as V2000.

• structure() gives the skeletal formula for Molecule2D. Hydrogens bonded to another atom are counted on it instead of drawn, and aromatic bonds become alternating single and double bonds. A 2D file keeps its positions, scaled so bonded atoms are one bond length apart, with its wedges and hashes. A file without positions, or with 3D ones, is laid out by chematic like a SMILES string.
• structure_3d() (with the 3d feature) gives every atom, hydrogens too, at its position in the file for Molecule3D. It returns None when the file has no positions.

Gallery scene: MolFile (paracetamol from a 2D file, ethanol from a 3D SDF record).

MolFile 3 sPlayUnmuteCopy render command

use fframes_kit::prelude::*;

fn read(text: &str) -> Result<Structure, MolError> {
    Ok(MolFile::parse(text)?.structure())
}

fn figure<'a>(ui: &mut Ui<'a, '_, '_>, structure: &'a Structure) -> Svgr<'a> {
    ui.show(Molecule2D {
        structure: Some(structure),
        bond_length: 90.0,
        enter: Some(Create::default().into()),
        ..ui.defaults()
    })
}