xpict

Molecule depiction for publication-quality vector graphics — Rust, Python, or the web with JavaScript. Shared paint in Rust (xpict-core); each language owns RDKit layout at its edge.

Public API

Two first-class surfaces — same paint:

1. Single molecule — mol → render → toSvg (JS, Rust): one structure, options, align_to.
2. Declarative document — nested JSON (type: "mol" / group + children): batching and a document model that is still expanding toward full PictSpec.

Chem label markup: docs/label-markup.md.
Full walkthrough with images: https://swamidasslab.github.io/xenosite-pict/

Single molecule

import { xpict } from "@xenosite/xpict";

const benzene = xpict.mol("c1ccccc1");
const rendered = await xpict.render(benzene, {
  color: "#0b6e4f",
  atom_shade: [0, 0, 0.2, 0, 0, 0.9],
  star_labels: ["$R_1$"], // when the mol has *
});
const svg = xpict.toSvg(rendered.scene);

const aligned = await xpict.render(xpict.mol("Cc1ccccc1"), {
  align_to: benzene, // or align_to: rendered
});

use xpict::{mol, MolRenderOptions};

let mut m = mol("CCO")?;
let rendered = m.render(MolRenderOptions {
    color: Some("#0b6e4f".into()),
    atom_shade: Some(vec![0.0, 0.2, 0.9]),
    ..Default::default()
})?;
let svg = rendered.to_svg();

render options

When star_labels is omitted, CXSMILES |$…$| aliases apply by atom index.

Declarative document

const [r] = await xpict.depict({
  type: "mol",
  smiles: "CCO",
  color: "#0b6e4f",
  shade: { atoms: [0.0, 0.2, 0.9], vmin: 0, vmax: 1 },
});
const svg = xpict.toSvg(r.scene);

const batch = await xpict.depict({
  type: "group",
  children: [
    { type: "mol", cxsmiles: "*c1ccccc1Cl |$R1;;;;;$|" },
    { type: "mol", cxsmiles: "*c1ccc(O)cc1 |$R1;;;;;$|" },
  ],
});

from xpict import render

svg = render({
    "type": "mol",
    "smiles": "CCO",
    "shade": {"atoms": [0.0, 0.2, 0.9], "vmin": 0.0, "vmax": 1.0},
})

use xpict::{depict, DepictSpec, MolNode};

let results = depict(&DepictSpec::Group {
    id: None,
    children: vec![
        MolNode {
            smiles: Some("CCO".into()),
            ..Default::default()
        },
    ],
})?;

Contract: DepictSpec / MolNode in xpict.contracts.depict. Document fields today: structure, id, color, shade. Nested diagrams / ELK / reaction chrome stay under xpict.future until they graduate.

Docs & demo

https://swamidasslab.github.io/xenosite-pict/
JS align demo: https://swamidasslab.github.io/xenosite-pict/js/demo/

Architecture

                    ┌─────────────────┐
                    │   xpict-core    │  paint (no RDKit)
                    └────────┬────────┘
         ┌───────────────────┼───────────────────┐
         ▼                   ▼                   ▼
   xpict-py / WASM      @xenosite/xpict       xpict (native)
   (Python / JS)         (RDKit.js)         (RDKit + FFI)

License

MIT