Examples Gallery¶

Collection of molecular visualization examples using plotlyMol.

Basic Examples¶

Simple Molecules¶

Ethanol (C₂H₆O)¶

Ball-and-stick representation of ethanol:

from plotlymol3d import draw_3D_rep

fig = draw_3D_rep(
    smiles="CCO",
    mode="ball+stick",
    ambient=0.15
)
fig.show()

Benzene (C₆H₆)¶

Aromatic ring with dashed bonds:

fig = draw_3D_rep(
    smiles="c1ccccc1",
    mode="ball+stick",
    ambient=0.1,
    bgcolor="white"
)
fig.show()

Visualization Modes¶

Compare different rendering modes:

Ball and StickStick OnlyVan der Waals

fig = draw_3D_rep(smiles="CC(C)O", mode="ball+stick")
fig.show()

fig = draw_3D_rep(smiles="CC(C)O", mode="stick")
fig.show()

fig = draw_3D_rep(smiles="CC(C)O", mode="vdw")
fig.show()

Drug Molecules¶

Aspirin (Acetylsalicylic Acid)¶

fig = draw_3D_rep(
    smiles="CC(=O)OC1=CC=CC=C1C(=O)O",
    mode="ball+stick",
    resolution=48,
    ambient=0.12,
    title="Aspirin"
)
fig.write_html("aspirin.html")

Caffeine (C₈H₁₀N₄O₂)¶

fig = draw_3D_rep(
    smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C",
    mode="ball+stick",
    ambient=0.1,
    title="Caffeine"
)
fig.show()

Ibuprofen¶

fig = draw_3D_rep(
    smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O",
    mode="ball+stick",
    title="Ibuprofen"
)
fig.show()

Amino Acids¶

Glycine¶

fig = draw_3D_rep(
    smiles="C(C(=O)O)N",
    mode="ball+stick",
    ambient=0.15,
    title="Glycine"
)
fig.show()

Phenylalanine¶

fig = draw_3D_rep(
    smiles="C1=CC=C(C=C1)CC(C(=O)O)N",
    mode="ball+stick",
    title="Phenylalanine"
)
fig.show()

Complex Molecules¶

Glucose (β-D-Glucose)¶

fig = draw_3D_rep(
    smiles="C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O",
    mode="ball+stick",
    resolution=64,
    ambient=0.1,
    title="β-D-Glucose"
)
fig.show()

Cholesterol¶

fig = draw_3D_rep(
    smiles="CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C",
    mode="ball+stick",
    resolution=48,
    ambient=0.1,
    title="Cholesterol"
)
fig.show()

From Files¶

XYZ File¶

fig = draw_3D_rep(
    xyzfile="data/benzene.xyz",
    mode="ball+stick",
    ambient=0.1
)
fig.show()

MOL File¶

fig = draw_3D_rep(
    molfile="data/molecule.mol",
    mode="stick",
    resolution=48
)
fig.show()

PDB File¶

fig = draw_3D_rep(
    pdbfile="data/protein_fragment.pdb",
    mode="stick",
    ambient=0.2
)
fig.show()

Orbital Visualization¶

HOMO Visualization¶

fig = draw_3D_rep(
    molfile="benzene.mol",
    cubefile="benzene_HOMO.cube",
    mode="stick",
    cubedraw="orbitals",
    orbital_isovalue=0.02,
    orbital_colors=["red", "blue"],
    orbital_opacity=0.3,
    ambient=0.1,
    bgcolor="white",
    title="Benzene HOMO"
)
fig.show()

Electron Density¶

fig = draw_3D_rep(
    molfile="molecule.mol",
    cubefile="density.cube",
    mode="ball+stick",
    cubedraw="orbitals",
    orbital_isovalue=0.01,
    orbital_colors=["purple", "orange"],
    orbital_opacity=0.25,
    title="Electron Density"
)
fig.show()

Custom Styling¶

High-Quality Publication Figure¶

fig = draw_3D_rep(
    smiles="CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
    mode="ball+stick",
    resolution=64,
    ambient=0.08,
    diffuse=0.92,
    specular=0.6,
    roughness=0.25,
    bgcolor="white"
)

fig.update_layout(
    title=dict(
        text="Aspirin (Acetylsalicylic Acid)",
        font=dict(size=20, family="Arial")
    ),
    scene=dict(
        camera=dict(eye=dict(x=1.3, y=1.3, z=1.3))
    )
)

fig.write_image("aspirin_publication.png", width=1600, height=1200, scale=2)

Dark Theme¶

fig = draw_3D_rep(
    smiles="c1ccccc1",
    mode="ball+stick",
    ambient=0.3,
    bgcolor="rgb(17, 17, 17)",  # Dark background
    resolution=48
)

fig.update_layout(
    title=dict(
        text="Benzene",
        font=dict(color="white")
    ),
    scene=dict(
        xaxis=dict(
            backgroundcolor="rgb(17, 17, 17)",
            gridcolor="rgb(50, 50, 50)"
        ),
        yaxis=dict(
            backgroundcolor="rgb(17, 17, 17)",
            gridcolor="rgb(50, 50, 50)"
        ),
        zaxis=dict(
            backgroundcolor="rgb(17, 17, 17)",
            gridcolor="rgb(50, 50, 50)"
        )
    )
)

fig.show()

Batch Processing¶

Multiple Molecules¶

molecules = {
    "Methanol": "CO",
    "Ethanol": "CCO",
    "Propanol": "CCCO",
    "Butanol": "CCCCO"
}

for name, smiles in molecules.items():
    fig = draw_3D_rep(
        smiles=smiles,
        mode="ball+stick",
        title=name
    )
    fig.write_html(f"{name.lower()}.html")
    print(f"Created {name}.html")

Conformer Gallery¶

# Generate multiple conformers (requires RDKit)
from rdkit import Chem
from rdkit.Chem import AllChem

mol = Chem.MolFromSmiles("CCCCCC")
mol = Chem.AddHs(mol)

# Generate conformers
AllChem.EmbedMultipleConfs(mol, numConfs=5)
AllChem.MMFFOptimizeMoleculeConfs(mol)

# Visualize each conformer
for i in range(mol.GetNumConformers()):
    fig = draw_3D_rep(
        mol=mol,
        mode="stick",
        title=f"Hexane Conformer {i+1}"
    )
    fig.write_html(f"hexane_conformer_{i+1}.html")

Interactive Features¶

Custom Camera Angle¶

fig = draw_3D_rep(smiles="c1ccccc1", mode="ball+stick")

fig.update_layout(
    scene_camera=dict(
        eye=dict(x=2, y=2, z=0.5),
        center=dict(x=0, y=0, z=0),
        up=dict(x=0, y=0, z=1)
    )
)

fig.show()

Add Annotations¶

fig = draw_3D_rep(smiles="CCO", mode="ball+stick")

fig.add_annotation(
    text="Hydroxyl Group",
    x=0.5, y=0.5, z=0.5,
    showarrow=True,
    arrowhead=2
)

fig.show()

Complete Example Script¶

See examples/demo_visualizations.py in the repository for a comprehensive demo script showing all features.

# Run demo script
python examples/demo_visualizations.py

Download Examples¶

All example code is available in the GitHub repository.

Contributing Examples¶

Have a cool visualization to share? We'd love to see it!

Create your example
Add it to examples/ directory
Submit a pull request

See the Contributing Guide for details.

Need help recreating these examples? Check the Quick Start guide or API Reference.