stspeck

The Speck molecule viewer for Streamlit, with the same renderer and settings as the ipyspeck Jupyter widget: ambient occlusion, cartoons, molecular surfaces (optionally transparent), metallic and glossy materials, shadows, fog, outlines, highlighting, trajectories and unit cells.

pip install stspeck      # Python 3.8+, Streamlit 1.20+

import streamlit as st
import stspeck

# Any structure as PDB, mmCIF, SDF / MOL or (extended) XYZ text (detected from the content)
stspeck.speck(data=open("1ubq.cif").read(), cartoon=True, surface=True, surfaceOpacity=0.35)
stspeck.speck(**stspeck.read_file("conformers.sdf.gz"), frame=2)

# Loaders return keyword arguments to splat into speck()
stspeck.speck(**stspeck.fetch_alphafold("Q8W3K0"), preset="cover", height=500)
stspeck.speck(**stspeck.fetch_pdb("4HHB"), highlight={"resName": "HEM"}, ghost=0.6)
stspeck.speck(**stspeck.from_ase(atoms), preset="metal")   # also from_rdkit, from_pymatgen

• Settings: every ipyspeck setting is a keyword argument; see stspeck.SETTINGS for names and defaults, and stspeck.PRESETS for named looks (preset="cover").
• Toolbar: styles, a looks menu, cartoon / surface / ligand toggles, standard views, auto-rotate, tap to focus (or Alt-click), a depth-of-field toggle, a color menu for cartoon, surface and atoms, and a camera button that downloads a high-resolution PNG (export_width=3000, export_scale=...). Toolbar choices persist across reruns.
• Studio floor, illustration, cutaway: floor=0.9, floorReflection=0.3; preset="goodsell" (flat colors per chain, outlines between molecules), atomColor="type", palette="colorblind"; cutaway=0.5 slices off the front to show the inside (cutawayAxis="z" fixes the plane on the molecule, cutawayLight=0.6 lights the inside).
• Colors: colorScheme="jmol" (speck, jmol, rasmol, newcpk) and per-element atomColors={"Au": "#ffcc33"} ('#rrggbb' or [r, g, b] in 0 - 1).
• Touch and keyboard: one finger rotates, two fingers pinch to zoom and pan; arrows rotate, Shift+arrows pan, + / - zoom, 0 recenters, F focuses at the center.
• State: with return_state=True the call returns the camera, the current settings and nframes; pass the camera back as camera= to restore a view.
• Formats: fetch_pdb downloads mmCIF, which also covers entries too large for PDB files (e.g. the 4V6X ribosome); format="pdb" gets the legacy file, and assembly=1 a biological assembly (fetch_pdb("1STM", assembly=1): a complete virus capsid). Bonds listed in the file (CONECT, _struct_conn, SDF / MOL bonds) are always drawn.
• Trajectories: multi-frame XYZ, multi-model PDB or mmCIF, or SDF conformers; drive frame= with a slider. MD: stspeck.speck(**stspeck.from_mdtraj(traj), frame=f) (or from_mdanalysis); frames go as binary coordinates (trajectory=), and count_frames(data, trajectory) gives the slider range (stspeck.count_frames(data) gives the range).

Run the demo with streamlit run example/app.py.

Gallery

Rendered with the ipyspeck / stspeck renderer (see example/showcase.ipynb for the settings behind these looks). Click an image to open that scene in the live demo.

Macro photography (depth of field)

Gold nanoparticle, 923 atoms	Copper surface	Heme in hemoglobin (4HHB)
Imatinib in ABL kinase (1IEP)	Nucleosome DNA (1KX5)	AlphaFold RPP7 repeat domain

Proteins and complexes

AlphaFold RPP7, by pLDDT	Hemoglobin, glass surface (4HHB)	SARS-CoV-2 spike (6VXX)
IgG antibody (1IGT)	Green fluorescent protein (1EMA)	GroEL–GroES chaperonin (1AON)
KcsA K⁺ channel (1BL8)	CRISPR-Cas9 with guide RNA (4OO8)	HIV protease + saquinavir (1HXB)
Streptavidin–biotin (1STP)	Myoglobin, toon style (1MBN)	Collagen triple helix (1BKV)
Ubiquitin surface (1UBQ)	Human 80S ribosome, 237,685 atoms (4V6X)	Virus capsid, all 60 copies (1STM)
Bacteriophage MS2 capsid, 180 copies (2MS2)

Nucleic acids

Nucleosome (1KX5)

Transfer RNA (1EHZ)

G-quadruplex with K⁺ (1KF1)

Studio floor, illustration and cutaway

Hemoglobin on the studio floor (4HHB)	Gold–thiolate cluster on the studio floor	Hemoglobin, Goodsell style (4HHB)
Virus capsid, Goodsell style (1STM)	Ribosome large subunit, Goodsell style (1FFK)	Virus capsid, cut open (1STM)

Chemistry and materials

Gold–thiolate cluster	Copper crystal and unit cell	SrTiO₃ perovskite
MoS₂ monolayer	Graphene	Carbon nanotube
C₆₀ buckminsterfullerene	Taxol (paclitaxel)	Chlorophyll a
Caffeine

For Jupyter, use ipyspeck, which has the same settings.

Development

The frontend (frontend/) bundles the viewer shared with ipyspeck (../core). Build it with cd frontend && npm install && npm run build, which also compiles ../core. pip install . runs the same build when stspeck/static is missing.

License

BSD-3-Clause (see LICENSE). stspeck is based on Speck by wwwtyro, which is in the public domain (see LICENSE-SPECK).