MolGFX

Documentation

MolGFX is a semantic molecular-rendering library for Python, Rust, and WebGPU. It renders structures supplied by MolFrame as interactive browser scenes or deterministic native images. MolGFX does not parse, fetch, dock, simulate, or open an application window.

Install

macOS builds include native Metal and Vulkan portability. For repeatable headless images on virtual machines, install a software Vulkan adapter and select it with WGPU_BACKEND=vulkan and VK_DRIVER_FILES. Byte-exact rendering is checked on an explicit reference adapter; Apple's hosted paravirtual Metal device produces different pixels for repeated static exposures.

python -m pip install --upgrade molgfx

Render a structure

import molframe
import molgfx

# Infer bonds so atom-and-bond representations have sticks to draw.
structure = molframe.read("structure.cif").infer_bonds()
scene = molgfx.Scene(structure)
scene.add(molgfx.rep.cartoon(target=molgfx.sel.protein(), color=molgfx.color.chain()))
scene.add(molgfx.rep.ball_and_stick(target=molgfx.sel.ligands()))

molgfx.Renderer().render_image(scene, size=(1920, 1080)).save("structure.png")

Cartoon representations accept aspect_ratio (width divided by depth, default 5.0) and arrow_factor (terminal beta-arrow shoulder scale, default 1.5). Set arrow_factor=0.0 to disable arrows. The Rust builder and browser scene contract expose the same controls. helix_profile and nucleic_profile select "elliptical", "rounded" (planar faces with semicircular ends), or "square" cross-sections (helix default: elliptical; nucleic default: square). Rust uses molgfx::rep::CartoonProfile. Profiles change the cross-section while preserving source guide coordinates and picking anchors.

Set direction_wedges=True on molgfx.rep.cartoon(...) to draw a flat N-to-C direction triangle at each selected polymer guide (default: False). The triangle's width and length are half the cartoon width. It follows live source coordinates and picks the guide atom. A selection containing one guide uses the direction of its source polymer; an isolated residue requires N/CA/C (or C5'/C4'/C3' for nucleic acids). Missing direction atoms produce a render error. Glycan cartoon mode rejects this control. Rust uses .direction_wedges(true); commands use direction_wedges=true.

Use gaps="dashed" on cartoon, backbone, trace, tube or putty to connect missing polymer intervals with closed tubes of radius 0.15 Å and 0.5 Å dashes separated by 0.5 Å. The default is "hidden". Chain boundaries and excluded residues remain disconnected. Connectors follow live coordinates and retain source atom identity for picking. Rust uses .gaps(molgfx::rep::GapStyle::Dashed); commands use gaps=dashed.

Presentation effects are explicit values on a render profile:

profile = molgfx.profile.converged().with_effect(molgfx.effect.bloom(intensity=0.8))
renderer = molgfx.Renderer(profile=profile)

molgfx.effect also provides depth cue, depth of field, motion blur, backdrop, lighting, shape cues, display and anti-aliasing constructors. Invalid settings raise an error before rendering. without_effect(kind) restores the quality recipe's default for that kind. Rust exposes the same values under molgfx::profile; WASM Renderer.create accepts an optional effects JSON array of { "kind": ..., "settings": ... } records validated by the shared core.

For native HDR export, retain scene-linear highlights in half-float OpenEXR:

hdr = molgfx.Renderer(profile=molgfx.profile.converged()).render_hdr_image(scene, size=(1920, 1080))
hdr.save("structure.exr")

HdrImage exposes width, height, exr_bytes(), rgba16f() and quality_json(). HDR capture completes the profile's exposure without baking in bloom, exposure, tone mapping, display conversion or screen overlays. Python .save() accepts only .exr filenames and raises ValueError before writing any other format. Rust uses HdrImage::save_exr and also supports an explicit camera through Renderer::render_hdr_image_with_camera.

A structure is optional for a scalar-volume scene. Bind voxel values separately from the portable scene specification; the same grid can drive several presentations without another upload:

import hashlib
import struct
import molgfx

values = [
    max(0.0, 1.0 - ((x - 3.5) ** 2 + (y - 3.5) ** 2 + (z - 3.5) ** 2) ** 0.5 / 4.0)
    for z in range(8)
    for y in range(8)
    for x in range(8)
]
source = molgfx.data.source(hashlib.sha256(struct.pack("<512f", *values)).hexdigest())
scene = molgfx.Scene()
volume = molgfx.density.volume(source=source, dimensions=(8, 8, 8))
volume = volume.isosurface(0.5, color=(220, 40, 70)).direct(
    [
        (0.0, (50, 150, 255), 0.0),
        (1.0, (50, 150, 255), 0.4),
    ]
)
identity = scene.add(volume)
scene.bind_volume(identity, values)
molgfx.Renderer().render_image(scene, size=(640, 480)).save("density.png")

values are indexed with x fastest, then y, then z. For a map read by MolFrame, supply its column-major voxel_to_world affine instead of assuming unit voxels at the origin. Region bounds use half-open voxel indices.

Targets are MolFrame queries, and a small command language works around them through molgfx.Session:

show cartoon, protein
select pocket, byres (within 5 of resname HEM) and protein
show licorice, $pocket
color orange, $pocket

Named snapshots capture the complete authored scene (camera, styles, interaction state, assemblies and overlays), not coordinates, pixels or renderer buffers:

session.snapshot_save("overview")
session.execute("color orange, protein")
session.snapshot_restore("overview")
session.undo()  # Return to the state immediately before restoration.
session.snapshot_remove("overview")

The same operations are commands: snapshot save|restore|remove NAME. Named captures round-trip in Session.to_json() and Session.from_json(scene, json). Restoration requires local bindings with matching content identities; missing or mismatched assets leave the live scene unchanged. Revisions advance on restore and undo rather than returning to the captured revision. Rust uses the canonical interop::SceneSnapshot, Scene::snapshot, Scene::restore_snapshot and PatchOperation::RestoreSnapshot. Frame export remains render_sequence or render_camera_path; no retained movie request is an export implementation.

The Rust engine opens no window and owns no application panels. This repository also supplies the official browser host: a canvas, navigation and semantic picks, not a Workbench, console, toolbar or file picker. Session remains the sole command and undo/redo authority. Python notebooks use this same frontend through AnyWidget, a normal package dependency.

session = molgfx.Session(structure)
session.execute("show cartoon, protein")
viewer = molgfx.Viewer(session)
viewer  # Display in Jupyter.

Browser SDK

npm install molgfx

import { Viewer } from "molgfx";
import "molgfx/viewer.css";

const viewer = await Viewer.create(document.getElementById("scene")!);
await viewer.load(await fetch("structure.cif").then(r => r.arrayBuffer()), { name: "structure.cif" });
viewer.execute("show cartoon, protein");
// On host teardown:
await viewer.dispose();

The one npm package exports molgfx, molgfx/viewer, molgfx/anywidget and molgfx/react. The React adapter owns viewer mount/dispose, not molecular state. Public TypeScript declarations never expose the raw wasm ABI.

"use client";
import { MolGFXViewer } from "molgfx/react";
import "molgfx/viewer.css";

export function Protein({ bytes }: { bytes: Uint8Array }) {
  return <MolGFXViewer structure={bytes} name="protein.cif"
    style={{ width: "100%", height: 480 }}
    onError={error => console.error(error.message)} />;
}

Keep the input byte object stable between unchanged React renders. The adapter reuses its Viewer for structure updates and disposes it on unmount; it does not duplicate Scene, Session or rendering semantics.

Shared frontend build

nix develop -c npm ci --prefix web
nix develop -c npm run build --prefix web
nix develop -c npm test --prefix web
nix develop -c npm pack ./web --pack-destination web

web/scripts/build.mjs runs wasm-pack into ignored web/generated, then emits the official package into ignored web/dist and copies identical artifacts to Python static assets. The documentation site imports the public npm package; Next.js emits its WASM asset rather than loading a private runtime directory. A content-hash manifest and archive-level checks prove that npm tarballs and Python wheels carry identical runtime bytes. Build before running maturin from a source checkout; PyPI source distributions include the prebuilt runtime and need Python >=3.12, Rust and dependency fetching, but no Node, wasm-pack or adjacent MolFrame checkout. Cargo, Python and npm versions must match. Native wheel builds repair external libraries; release gates rebuild the source archive and exercise fresh installed wheels before publication.

Python and npm have separate release workflows. Published versions are immutable; release 0.4.1 supersedes the existing PyPI 0.4.0 package. npm trusted publishing requires the package owner to authorize this repository and release workflow. Until the first registry publication, the docs use the public package through a local npm dependency, exercising the same exports and bundler asset resolution.

Cross-engine gallery

The optional Mol* adapter runs the requested local Mol* source checkout in real Chromium/WebGL2. Install its locked Node transport dependencies, then provide a real Chromium executable and PyMOL binary:

nix develop -c npm ci --prefix crates/molgfx-bench/parity
MOLSTAR_CHROMIUM=/path/to/chrome nix develop -c cargo run -p molgfx-bench --bin parity -- \
  --manifest crates/molgfx-bench/parity/gallery.json --cache ~/.cache/molgfx-corpus \
  --output target/gallery --case P2-iso-solid-skewMRC \
  --recipe molgfx-converged --recipe pymol-ray --recipe molstar-imagepass \
  --molstar-root ../molstar --pymol /path/to/pymol

The manifest records explicit omissions for recipes that cannot faithfully represent a case; failures are never counted as omissions. Review visual semantics before blessing golden images. Motion-blur orbit cases also require --ffmpeg /path/to/ffmpeg.

Writing queries and commands walks through both, and the MolFrame query reference lists every keyword.

Status

Beta. Public APIs are available through the molgfx facade; MolFrame provides structure input and molecular selection semantics.

License

MIT