Molecular Grids

Use molecular grid helpers when you already have molecules, coordinate files, or reaction objects and want a quick notebook visualization.

Works without a FRUST workflow

MolTo3DGrid, RxnTo3DGrid, and DrawMolSvg are available from frust.vis so notebooks can use one visualization import path.

3D Molecule Grids

MolTo3DGrid accepts RDKit molecules, SMILES strings, .xyz paths, or mixed lists of those inputs. It renders an interactive py3Dmol grid.

from frust.vis import MolTo3DGrid

MolTo3DGrid(
    ["CCO", "CC(=O)O", "c1ccccc1"],
    legends=["ethanol", "acetic acid", "benzene"],
    highlightAtoms=[[1], [1, 2], [0, 1, 2, 3, 4, 5]],
    show_labels=True,
    show_charges=True,
    cell_size=(320, 320),
    columns=3,
    linked=True,
)

Interactive inspection

In the exported viewer, click atoms to toggle labels. Ctrl-click two atoms to measure a distance, and Shift-click three atoms to measure an angle.

Export a reusable HTML viewer

MolTo3DGrid(
    ["reactant.xyz", "transition_state.xyz", "product.xyz"],
    legends=["Reactant", "TS", "Product"],
    export_HTML="docs/assets/reaction-snapshot.html",
)

The exported file can be embedded with the same iframe pattern used above.

Common options include:

Option	Use
legends	Add a label to each viewer cell
highlightAtoms	Highlight atoms in each molecule
show_labels	Draw atom labels before rendering
show_charges	Show formal charges as annotations
show_confs	Show all conformers instead of only one
bonds_to_remove	Hide selected bonds before rendering
linked	Rotate and zoom all cells together
export_HTML	Write the interactive viewer to an HTML file

Reaction Grids

RxnTo3DGrid renders a reaction as reactants, an arrow cell, and products. It accepts an RDKit reaction object or a reaction SMILES/SMARTS string.

from frust.vis import RxnTo3DGrid

RxnTo3DGrid(
    "CCO>>CC=O",
    legends=["ethanol", "acetaldehyde"],
    show_labels=True,
    show_charges=True,
    cell_size=(320, 320),
    linked=True,
)

Show mapped reaction changes

If the reaction is atom-mapped, RxnTo3DGrid can highlight changed bonds and charges:

RxnTo3DGrid(
    mapped_reaction,
    show_bond_changes=True,
    show_charge_changes=True,
    check_reaction_stoichiometry=True,
)

Output is the same three-cell reaction viewer, with colored annotations for the mapped bond and charge changes.

Useful reaction options include:

Option	Use
show_bond_changes	Highlight formed, broken, or changed-order bonds
show_charge_changes	Highlight atoms with changed formal charge
h_mode	Control hydrogen display around reactive atoms
check_reaction_stoichiometry	Warn when mapped atoms are not balanced
linked	Rotate and zoom the reaction cells together
export_HTML	Write the interactive reaction viewer to HTML

Unique Aromatic C-H Positions

DrawUniqueChGrid highlights symmetry-unique aromatic C-H positions. This is useful before selecting reactive positions for substrate-scope runs.

Highlight unique positions from SMILES

from frust.vis import DrawUniqueChGrid

DrawUniqueChGrid("COc1ccccc1")

Highlight positions from a DataFrame

from frust.vis import DrawUniqueChGrid

DrawUniqueChGrid(df, smiles_col="smiles")

2D Molecule SVGs

DrawMolSvg is useful when a static 2D depiction is clearer than an interactive 3D viewer. It can highlight atoms, draw atom indices, dim the rest of the molecule, and return SVG for reports or notebooks.

from frust.vis import DrawMolSvg

DrawMolSvg(
    "COc1ccccc1",
    add_atom_indices=True,
    highlight_atom_indices=[4, 5, 6],
    highlight_as_circles=True,
)