Core Functions

Auto-generated API documentation for plotlyMol's core visualization functions.

Main Visualization Function

draw_3D_rep

draw_3D_rep(
    smiles=None,
    xyzfile=None,
    charge=0,
    cubefile=None,
    molfile=None,
    pbdfile=None,
    resolution=DEFAULT_RESOLUTION,
    radius=DEFAULT_RADIUS,
    mode="ball+stick",
    orbital_opacity=0.25,
    orbital_colors=None,
    cubedraw="orbitals",
    vibration_file=None,
    vibration_mode=None,
    vibration_display="arrows",
    vibration_amplitude=1.0,
    vibration_arrow_scale=1.0,
    vibration_arrow_color="red",
    ambient=0,
    diffuse=1,
    specular=0,
    roughness=1,
    fresnel=0,
    lightx=1000,
    lighty=1000,
    lightz=1000,
)

Create a complete 3D molecular visualization from various input formats.

This is the main entry point for creating molecular visualizations. Accepts multiple input formats and combines them into a single figure.

Parameters:

Name	Type	Description	Default
smiles	Optional[str]	SMILES string for the molecule.	None
xyzfile	Optional[str]	Path to an XYZ coordinate file.	None
charge	int	Molecular charge (used for XYZ bond perception).	0
cubefile	Optional[str]	Path to a Gaussian cube file (for orbitals).	None
molfile	Optional[str]	Path to a MOL file.	None
pbdfile	Optional[str]	Path to a PDB file (not yet implemented).	None
resolution	int	Mesh resolution for rendering.	DEFAULT_RESOLUTION
radius	Union[float, str]	Atom/bond radius (float, "vdw", or "ball").	DEFAULT_RADIUS
mode	str	Visualization mode - "ball+stick", "ball", "stick", or "vdw".	'ball+stick'
orbital_opacity	float	Opacity for orbital isosurfaces (0-1).	0.25
orbital_colors	Optional[List[str]]	Colors for positive/negative orbital lobes. Defaults to ["darkorange", "skyblue"].	None
cubedraw	str	What to draw from cube file - "orbitals", "molecule", or both.	'orbitals'
vibration_file	Optional[str]	Path to vibration file (.log, .out, .molden).	None
vibration_mode	Optional[int]	Mode number to visualize (1-based).	None
vibration_display	str	"arrows", "heatmap", or "both".	'arrows'
vibration_amplitude	float	Displacement amplitude scale.	1.0
vibration_arrow_scale	float	Visual scale for arrows.	1.0
vibration_arrow_color	str	Color for displacement arrows.	'red'
ambient	float	Ambient light intensity (0-1).	0
diffuse	float	Diffuse light intensity (0-1).	1
specular	float	Specular highlight intensity (0-1).	0
roughness	float	Surface roughness (0-1).	1
fresnel	float	Fresnel effect intensity (0-1).	0
lightx	float	Light position x-coordinate.	1000
lighty	float	Light position y-coordinate.	1000
lightz	float	Light position z-coordinate.	1000

Returns:

Type	Description
Figure	Plotly figure with the molecular visualization.

Example

fig = draw_3D_rep(smiles="CCO", mode="ball+stick", ambient=0.1) fig = draw_3D_rep(cubefile="orbital.cube", cubedraw="orbitals") fig = draw_3D_rep(smiles="O", vibration_file="water.log", vibration_mode=1)

Source code in src/plotlymol3d/plotlyMol3D.py

def draw_3D_rep(
    smiles: Optional[str] = None,
    xyzfile: Optional[str] = None,
    charge: int = 0,
    cubefile: Optional[str] = None,
    molfile: Optional[str] = None,
    pbdfile: Optional[str] = None,
    resolution: int = DEFAULT_RESOLUTION,
    radius: Union[float, str] = DEFAULT_RADIUS,
    mode: str = "ball+stick",
    orbital_opacity: float = 0.25,
    orbital_colors: Optional[List[str]] = None,
    cubedraw: str = "orbitals",
    vibration_file: Optional[str] = None,
    vibration_mode: Optional[int] = None,
    vibration_display: str = "arrows",
    vibration_amplitude: float = 1.0,
    vibration_arrow_scale: float = 1.0,
    vibration_arrow_color: str = "red",
    ambient: float = 0,
    diffuse: float = 1,
    specular: float = 0,
    roughness: float = 1,
    fresnel: float = 0,
    lightx: float = 1000,
    lighty: float = 1000,
    lightz: float = 1000,
) -> go.Figure:
    """Create a complete 3D molecular visualization from various input formats.

    This is the main entry point for creating molecular visualizations.
    Accepts multiple input formats and combines them into a single figure.

    Args:
        smiles: SMILES string for the molecule.
        xyzfile: Path to an XYZ coordinate file.
        charge: Molecular charge (used for XYZ bond perception).
        cubefile: Path to a Gaussian cube file (for orbitals).
        molfile: Path to a MOL file.
        pbdfile: Path to a PDB file (not yet implemented).
        resolution: Mesh resolution for rendering.
        radius: Atom/bond radius (float, "vdw", or "ball").
        mode: Visualization mode - "ball+stick", "ball", "stick", or "vdw".
        orbital_opacity: Opacity for orbital isosurfaces (0-1).
        orbital_colors: Colors for positive/negative orbital lobes.
            Defaults to ["darkorange", "skyblue"].
        cubedraw: What to draw from cube file - "orbitals", "molecule", or both.
        vibration_file: Path to vibration file (.log, .out, .molden).
        vibration_mode: Mode number to visualize (1-based).
        vibration_display: "arrows", "heatmap", or "both".
        vibration_amplitude: Displacement amplitude scale.
        vibration_arrow_scale: Visual scale for arrows.
        vibration_arrow_color: Color for displacement arrows.
        ambient: Ambient light intensity (0-1).
        diffuse: Diffuse light intensity (0-1).
        specular: Specular highlight intensity (0-1).
        roughness: Surface roughness (0-1).
        fresnel: Fresnel effect intensity (0-1).
        lightx: Light position x-coordinate.
        lighty: Light position y-coordinate.
        lightz: Light position z-coordinate.

    Returns:
        Plotly figure with the molecular visualization.

    Example:
        >>> fig = draw_3D_rep(smiles="CCO", mode="ball+stick", ambient=0.1)
        >>> fig = draw_3D_rep(cubefile="orbital.cube", cubedraw="orbitals")
        >>> fig = draw_3D_rep(smiles="O", vibration_file="water.log", vibration_mode=1)
    """
    if orbital_colors is None:
        orbital_colors = ["darkorange", "skyblue"]

    fig = make_subplots()
    fig = format_figure(fig)

    if smiles is not None:
        rdkitmol = smiles_to_rdkitmol(smiles)
        draw_3D_mol(fig, rdkitmol, resolution=resolution, radius=radius, mode=mode)
    if xyzfile is not None:
        xyzblock = xyzfile_to_xyzblock(xyzfile)
        rdkitmol = xyzblock_to_rdkitmol(xyzblock, charge=0)
        draw_3D_mol(fig, rdkitmol, resolution=resolution, radius=radius, mode=mode)
    if molfile is not None:
        rdkitmol = Chem.MolFromMolFile(molfile)
        draw_3D_mol(fig, rdkitmol, resolution=resolution, radius=radius, mode=mode)
    if cubefile is not None:
        if "molecule" in cubedraw:
            xyzblock, cubecharge = cubefile_to_xyzblock(cubefile)
            print(cubecharge)
            rdkitmol = xyzblock_to_rdkitmol(xyzblock, charge=cubecharge)
            draw_3D_mol(fig, rdkitmol, resolution=resolution, radius=radius, mode=mode)
        if "orbitals" in cubedraw:
            draw_cube_orbitals(fig, cubefile, orbital_opacity, orbital_colors)

    # Add vibration visualization if requested
    if vibration_file is not None and vibration_mode is not None:
        from .vibrations import parse_vibrations, add_vibrations_to_figure

        vib_data = parse_vibrations(vibration_file)
        fig = add_vibrations_to_figure(
            fig=fig,
            vib_data=vib_data,
            mode_number=vibration_mode,
            display_type=vibration_display,
            amplitude=vibration_amplitude,
            arrow_scale=vibration_arrow_scale,
            arrow_color=vibration_arrow_color,
        )

    format_lighting(
        fig,
        ambient=ambient,
        diffuse=diffuse,
        specular=specular,
        roughness=roughness,
        fresnel=fresnel,
        lightx=lightx,
        lighty=lighty,
        lightz=lightz,
    )

    return fig

Drawing from RDKit Mol

draw_3D_mol

draw_3D_mol(
    fig,
    rdkitmol,
    resolution=DEFAULT_RESOLUTION,
    radius=DEFAULT_RADIUS,
    mode="ball+stick",
)

Draw a 3D molecule representation on a Plotly figure.

Parameters:

Name	Type	Description	Default
fig	Figure	Plotly figure to draw on.	required
rdkitmol	Mol	RDKit molecule object with 3D coordinates.	required
resolution	int	Mesh resolution for atoms and bonds.	DEFAULT_RESOLUTION
radius	Union[float, str]	Atom/bond radius (float, "vdw", or "ball").	DEFAULT_RADIUS
mode	str	Visualization mode - "ball+stick", "ball", "stick", or "vdw".	'ball+stick'

Returns:

Type	Description
Figure	The figure with the molecule drawn.

Example

fig = make_subplots() mol = smiles_to_rdkitmol("CCO") fig = draw_3D_mol(fig, mol, mode="ball+stick")

Source code in src/plotlymol3d/plotlyMol3D.py

def draw_3D_mol(
    fig: go.Figure,
    rdkitmol: Chem.Mol,
    resolution: int = DEFAULT_RESOLUTION,
    radius: Union[float, str] = DEFAULT_RADIUS,
    mode: str = "ball+stick",
) -> go.Figure:
    """Draw a 3D molecule representation on a Plotly figure.

    Args:
        fig: Plotly figure to draw on.
        rdkitmol: RDKit molecule object with 3D coordinates.
        resolution: Mesh resolution for atoms and bonds.
        radius: Atom/bond radius (float, "vdw", or "ball").
        mode: Visualization mode - "ball+stick", "ball", "stick", or "vdw".

    Returns:
        The figure with the molecule drawn.

    Example:
        >>> fig = make_subplots()
        >>> mol = smiles_to_rdkitmol("CCO")
        >>> fig = draw_3D_mol(fig, mol, mode="ball+stick")
    """
    atomList, bondList = rdkitmol_to_atoms_bonds_lists(rdkitmol)

    if "ball" in mode:
        fig = draw_atoms(fig, atomList, resolution=resolution, radius="ball")
        if "stick" in mode:
            fig = draw_bonds(
                fig, bondList, atomList, resolution=resolution, radius="ball"
            )
    elif "stick" == mode:
        fig = draw_atoms(fig, atomList, resolution=resolution, radius=radius)
        fig = draw_bonds(fig, bondList, atomList, resolution=resolution, radius=radius)
    elif "vdw" == mode:
        fig = draw_atoms(fig, atomList, resolution=resolution * 4, radius="vdw")

    return fig

Input Processing Functions

SMILES Processing

smiles_to_rdkitmol

smiles_to_rdkitmol(smiles)

Convert a SMILES string to an RDKit molecule with 3D coordinates.

Parses the SMILES string, adds hydrogens, embeds in 3D space, and optimizes the geometry using the Universal Force Field (UFF).

Parameters:

Name	Type	Description	Default
smiles	str	SMILES representation of the molecule.	required

Returns:

Type	Description
Mol	RDKit molecule object with optimized 3D coordinates.

Raises:

Type	Description
ValueError	If the SMILES string is invalid.

Example

mol = smiles_to_rdkitmol("CCO") mol.GetNumAtoms() 9

Source code in src/plotlymol3d/plotlyMol3D.py

def smiles_to_rdkitmol(smiles: str) -> Chem.Mol:
    """Convert a SMILES string to an RDKit molecule with 3D coordinates.

    Parses the SMILES string, adds hydrogens, embeds in 3D space,
    and optimizes the geometry using the Universal Force Field (UFF).

    Args:
        smiles: SMILES representation of the molecule.

    Returns:
        RDKit molecule object with optimized 3D coordinates.

    Raises:
        ValueError: If the SMILES string is invalid.

    Example:
        >>> mol = smiles_to_rdkitmol("CCO")
        >>> mol.GetNumAtoms()
        9
    """
    mol = Chem.MolFromSmiles(smiles)
    mol = Chem.AddHs(mol)
    AllChem.EmbedMolecule(mol, randomSeed=42)
    AllChem.UFFOptimizeMolecule(mol)
    return mol

XYZ File Processing

xyzfile_to_xyzblock

xyzfile_to_xyzblock(file)

Read an XYZ file and return its contents as a string.

Parameters:

Name	Type	Description	Default
file	str	Path to the XYZ file.	required

Returns:

Type	Description
str	Contents of the XYZ file as a string block.

Example

xyzblock = xyzfile_to_xyzblock("molecule.xyz")

Source code in src/plotlymol3d/plotlyMol3D.py

def xyzfile_to_xyzblock(file: str) -> str:
    """Read an XYZ file and return its contents as a string.

    Args:
        file: Path to the XYZ file.

    Returns:
        Contents of the XYZ file as a string block.

    Example:
        >>> xyzblock = xyzfile_to_xyzblock("molecule.xyz")
    """
    xyzblock = ""
    with open(file, "r") as f:
        for line in f:
            xyzblock = xyzblock + line
    return xyzblock

xyzblock_to_rdkitmol

xyzblock_to_rdkitmol(xyzblock, charge=0)

Convert an XYZ coordinate block to an RDKit molecule with bonds.

Parses XYZ coordinates and uses RDKit's bond perception algorithms to determine connectivity and bond orders.

Parameters:

Name	Type	Description	Default
xyzblock	str	String containing XYZ format coordinates.	required
charge	int	Total molecular charge (used for bond order determination).	0

Returns:

Type	Description
Mol	RDKit molecule object with perceived bonds.

Note

Bond perception may fail for certain functional groups (e.g., nitro groups). For problematic molecules, consider using a MOL file instead.

Example

xyzblock = "3\n\nO 0.0 0.0 0.0\nH 0.96 0.0 0.0\nH -0.24 0.93 0.0" mol = xyzblock_to_rdkitmol(xyzblock)

Source code in src/plotlymol3d/plotlyMol3D.py

def xyzblock_to_rdkitmol(xyzblock: str, charge: int = 0) -> Chem.Mol:
    """Convert an XYZ coordinate block to an RDKit molecule with bonds.

    Parses XYZ coordinates and uses RDKit's bond perception algorithms
    to determine connectivity and bond orders.

    Args:
        xyzblock: String containing XYZ format coordinates.
        charge: Total molecular charge (used for bond order determination).

    Returns:
        RDKit molecule object with perceived bonds.

    Note:
        Bond perception may fail for certain functional groups (e.g., nitro groups).
        For problematic molecules, consider using a MOL file instead.

    Example:
        >>> xyzblock = "3\\n\\nO  0.0 0.0 0.0\\nH  0.96 0.0 0.0\\nH -0.24 0.93 0.0"
        >>> mol = xyzblock_to_rdkitmol(xyzblock)
    """
    raw_mol = Chem.MolFromXYZBlock(xyzblock)
    conn_mol = Chem.Mol(raw_mol)
    rdDetermineBonds.DetermineConnectivity(conn_mol)
    rdDetermineBonds.DetermineBondOrders(conn_mol, charge=charge)
    return conn_mol

Cube File Processing

cubefile_to_xyzblock

cubefile_to_xyzblock(cubefile)

Extract atomic coordinates from a Gaussian cube file.

Parses a cube file and extracts the molecular geometry in XYZ format. Cube files contain volumetric data (e.g., electron density, orbitals) along with atomic coordinates.

Parameters:

Name	Type	Description	Default
cubefile	str	Path to the cube file.	required

Returns:

Type	Description
Tuple[str, int]	A tuple containing: - xyzblock: String in XYZ format with atom count, blank line, and atomic coordinates. - total_charge: Sum of nuclear charges (integer).

Example

xyzblock, charge = cubefile_to_xyzblock("orbital.cube") print(xyzblock[:50]) 12

C 0.00000 0.00000 0.00000

Source code in src/plotlymol3d/plotlyMol3D.py

def cubefile_to_xyzblock(cubefile: str) -> Tuple[str, int]:
    """Extract atomic coordinates from a Gaussian cube file.

    Parses a cube file and extracts the molecular geometry in XYZ format.
    Cube files contain volumetric data (e.g., electron density, orbitals)
    along with atomic coordinates.

    Args:
        cubefile: Path to the cube file.

    Returns:
        A tuple containing:
            - xyzblock: String in XYZ format with atom count, blank line,
              and atomic coordinates.
            - total_charge: Sum of nuclear charges (integer).

    Example:
        >>> xyzblock, charge = cubefile_to_xyzblock("orbital.cube")
        >>> print(xyzblock[:50])
        12

        C          0.00000       0.00000       0.00000
    """
    total_charge: float = 0.0
    xyzblock = ""
    with open(cubefile, "r") as cf:
        for i, line in enumerate(cf):
            if i == 2:
                num_atoms = int(line.strip().split()[0])
                xyzblock = xyzblock + str(num_atoms) + "\n \n"
                stopat = 2 + 3 + num_atoms

            elif i > 5 and i <= stopat:
                if i <= stopat:
                    parts = line.strip().split()
                    atom_symbol = atom_symbols[int(parts[0])]
                    total_charge = total_charge + float(parts[1])
                    x = float(parts[2])
                    y = float(parts[3])
                    z = float(parts[4])

                    xyzblock = (
                        xyzblock
                        + f"{atom_symbol:<3} {x:>14.5f} {y:>14.5f} {z:>14.5f} \n"
                    )
                else:
                    break
    xyzblock = xyzblock + "\n"
    print(xyzblock)
    print(f"total charge = {total_charge}")
    return xyzblock, int(total_charge)

Molecule Processing

rdkitmol_to_atoms_bonds_lists

rdkitmol_to_atoms_bonds_lists(mol)

Convert an RDKit molecule to lists of Atom and Bond objects.

Extracts atom and bond information from an RDKit molecule object, including 3D coordinates, element types, and van der Waals radii.

Parameters:

Name	Type	Description	Default
mol	Mol	RDKit molecule object with 3D coordinates (must have a conformer).	required

Returns:

Type	Description
Tuple[List[Atom], List[Bond]]	A tuple containing: - atomList: List of Atom dataclass objects. - bondList: List of Bond dataclass objects.

Raises:

Type	Description
ValueError	If the molecule has no conformer (3D coordinates).

Example

mol = Chem.MolFromSmiles("CCO") AllChem.EmbedMolecule(mol) atoms, bonds = rdkitmol_to_atoms_bonds_lists(mol) len(atoms) 9

Source code in src/plotlymol3d/plotlyMol3D.py

def rdkitmol_to_atoms_bonds_lists(mol: Chem.Mol) -> Tuple[List[Atom], List[Bond]]:
    """Convert an RDKit molecule to lists of Atom and Bond objects.

    Extracts atom and bond information from an RDKit molecule object,
    including 3D coordinates, element types, and van der Waals radii.

    Args:
        mol: RDKit molecule object with 3D coordinates (must have a conformer).

    Returns:
        A tuple containing:
            - atomList: List of Atom dataclass objects.
            - bondList: List of Bond dataclass objects.

    Raises:
        ValueError: If the molecule has no conformer (3D coordinates).

    Example:
        >>> mol = Chem.MolFromSmiles("CCO")
        >>> AllChem.EmbedMolecule(mol)
        >>> atoms, bonds = rdkitmol_to_atoms_bonds_lists(mol)
        >>> len(atoms)
        9
    """
    atoms = mol.GetAtoms()
    bonds = mol.GetBonds()
    conf = mol.GetConformer()

    atomList = []
    for a in atoms:
        atomList.append(
            Atom(
                atom_id=a.GetIdx(),
                atom_number=a.GetAtomicNum(),
                atom_symbol=a.GetSymbol(),
                atom_xyz=[
                    conf.GetAtomPosition(a.GetIdx()).x,
                    conf.GetAtomPosition(a.GetIdx()).y,
                    conf.GetAtomPosition(a.GetIdx()).z,
                ],
                atom_vdw=vdw_radii[a.GetAtomicNum()],
            )
        )

    bondList = []
    for b in bonds:
        # Get bond order: SINGLE=1, DOUBLE=2, TRIPLE=3, AROMATIC=1.5
        bond_type = b.GetBondType()
        if bond_type == Chem.BondType.SINGLE:
            bond_order = 1.0
        elif bond_type == Chem.BondType.DOUBLE:
            bond_order = 2.0
        elif bond_type == Chem.BondType.TRIPLE:
            bond_order = 3.0
        elif bond_type == Chem.BondType.AROMATIC:
            bond_order = 1.5
        else:
            bond_order = 1.0  # Default to single for other types

        bondList.append(
            Bond(
                a1_id=b.GetBeginAtomIdx(),
                a2_id=b.GetEndAtomIdx(),
                a1_number=b.GetBeginAtom().GetAtomicNum(),
                a2_number=b.GetEndAtom().GetAtomicNum(),
                a1_xyz=atomList[b.GetBeginAtomIdx()].atom_xyz,
                a2_xyz=atomList[b.GetEndAtomIdx()].atom_xyz,
                a1_vdw=atomList[b.GetBeginAtomIdx()].atom_vdw,
                a2_vdw=atomList[b.GetEndAtomIdx()].atom_vdw,
                bond_order=bond_order,
            )
        )

    return atomList, bondList

Mesh Generation Functions

Sphere Tessellation

make_fibonacci_sphere

make_fibonacci_sphere(center, radius=DEFAULT_RADIUS, resolution=DEFAULT_RESOLUTION)

Generate points on a sphere using the Fibonacci lattice method.

Creates evenly distributed points on a sphere surface, which produces better visual results than latitude/longitude grids.

Parameters:

Name	Type	Description	Default
center	Sequence[float]	Center point [x, y, z] of the sphere.	required
radius	float	Radius of the sphere.	DEFAULT_RADIUS
resolution	int	Number of points to generate on the sphere.	DEFAULT_RESOLUTION

Returns:

Type	Description
Tuple[ndarray, ndarray, ndarray]	Tuple of (x, y, z) numpy arrays containing point coordinates.

Source code in src/plotlymol3d/plotlyMol3D.py

def make_fibonacci_sphere(
    center: Sequence[float],
    radius: float = DEFAULT_RADIUS,
    resolution: int = DEFAULT_RESOLUTION,
) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
    """Generate points on a sphere using the Fibonacci lattice method.

    Creates evenly distributed points on a sphere surface, which produces
    better visual results than latitude/longitude grids.

    Args:
        center: Center point [x, y, z] of the sphere.
        radius: Radius of the sphere.
        resolution: Number of points to generate on the sphere.

    Returns:
        Tuple of (x, y, z) numpy arrays containing point coordinates.
    """
    num_points = resolution
    indices = np.arange(0, num_points, dtype=float) + 0.5
    phi = np.arccos(1 - 2 * indices / num_points)
    theta = np.pi * (1 + 5**0.5) * indices

    x = radius * np.sin(phi) * np.cos(theta) + center[0]
    y = radius * np.sin(phi) * np.sin(theta) + center[1]
    z = radius * np.cos(phi) + center[2]

    return x, y, z

Cylinder Meshes

generate_cylinder_mesh_rectangles

generate_cylinder_mesh_rectangles(
    point1, point2, radius=DEFAULT_RADIUS, resolution=DEFAULT_RESOLUTION
)

Generate mesh vertices for a cylinder between two points.

Creates vertices for the top and bottom circles of a cylinder, which can be used to draw bonds between atoms.

Parameters:

Name	Type	Description	Default
point1	Union[List[float], ndarray]	Starting point [x, y, z] of the cylinder.	required
point2	Union[List[float], ndarray]	Ending point [x, y, z] of the cylinder.	required
radius	float	Radius of the cylinder.	DEFAULT_RADIUS
resolution	int	Number of vertices around the circular cross-section.	DEFAULT_RESOLUTION

Returns:

Type	Description
Tuple[ndarray, ndarray, ndarray]	Tuple of (x, y, z) numpy arrays containing vertex coordinates.

Source code in src/plotlymol3d/plotlyMol3D.py

def generate_cylinder_mesh_rectangles(
    point1: Union[List[float], np.ndarray],
    point2: Union[List[float], np.ndarray],
    radius: float = DEFAULT_RADIUS,
    resolution: int = DEFAULT_RESOLUTION,
) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
    """Generate mesh vertices for a cylinder between two points.

    Creates vertices for the top and bottom circles of a cylinder,
    which can be used to draw bonds between atoms.

    Args:
        point1: Starting point [x, y, z] of the cylinder.
        point2: Ending point [x, y, z] of the cylinder.
        radius: Radius of the cylinder.
        resolution: Number of vertices around the circular cross-section.

    Returns:
        Tuple of (x, y, z) numpy arrays containing vertex coordinates.
    """
    point1 = np.array(point1)
    point2 = np.array(point2)

    v = point2 - point1
    height = np.linalg.norm(v)
    v = v / height  # Normalize the vector

    # Find two vectors orthogonal to the axis of the cylinder
    if np.allclose(v, np.array([0, 0, 1])) or np.allclose(v, np.array([0, 0, -1])):
        not_v = np.array([1, 0, 0])
    else:
        not_v = np.array([0, 0, 1])

    n1 = np.cross(v, not_v)
    n1 /= np.linalg.norm(n1)
    n2 = np.cross(v, n1)

    # Generate the angles for the circular cross-section
    theta = np.linspace(0, 2 * np.pi, resolution, endpoint=False)
    circle = np.array([np.cos(theta), np.sin(theta)])

    # Generate the points for the bottom and top circles of the cylinder
    bottom_circle = point1[:, None] + radius * (
        n1[:, None] * circle[0] + n2[:, None] * circle[1]
    )
    top_circle = point2[:, None] + radius * (
        n1[:, None] * circle[0] + n2[:, None] * circle[1]
    )

    x = np.concatenate([bottom_circle[0], top_circle[0]])
    y = np.concatenate([bottom_circle[1], top_circle[1]])
    z = np.concatenate([bottom_circle[2], top_circle[2]])

    return x, y, z

Trace Creation Functions

Atom Traces

make_atom_mesh_trace

make_atom_mesh_trace(
    atom, radius=DEFAULT_RADIUS, resolution=DEFAULT_RESOLUTION, color="grey"
)

Create a Plotly Mesh3d trace for a single atom.

Generates a spherical mesh representing an atom at its 3D position.

Parameters:

Name	Type	Description	Default
atom	Atom	Atom object containing position and element information.	required
radius	Union[float, str]	Sphere radius. Can be a float, "vdw" for van der Waals radius, or "ball" for scaled VDW radius (0.2x).	DEFAULT_RADIUS
resolution	int	Number of points for sphere generation.	DEFAULT_RESOLUTION
color	str	Fallback color (actual color is determined by element).	'grey'

Returns:

Type	Description
Mesh3d	Plotly Mesh3d trace object for the atom.

Source code in src/plotlymol3d/plotlyMol3D.py

def make_atom_mesh_trace(
    atom: Atom,
    radius: Union[float, str] = DEFAULT_RADIUS,
    resolution: int = DEFAULT_RESOLUTION,
    color: str = "grey",
) -> go.Mesh3d:
    """Create a Plotly Mesh3d trace for a single atom.

    Generates a spherical mesh representing an atom at its 3D position.

    Args:
        atom: Atom object containing position and element information.
        radius: Sphere radius. Can be a float, "vdw" for van der Waals radius,
            or "ball" for scaled VDW radius (0.2x).
        resolution: Number of points for sphere generation.
        color: Fallback color (actual color is determined by element).

    Returns:
        Plotly Mesh3d trace object for the atom.
    """
    if radius == "vdw":
        radius_value = atom.atom_vdw
    elif radius == "ball":
        radius_value = atom.atom_vdw * 0.2
    else:
        radius_value = float(radius)

    x, y, z = make_fibonacci_sphere(
        atom.atom_xyz, radius=radius_value, resolution=resolution * a_res_scale
    )

    atom_trace = go.Mesh3d(
        x=x,
        y=y,
        z=z,
        color=atom_colors[atom.atom_number],
        opacity=1,
        alphahull=0,
        name=f"{atom.atom_symbol}{atom.atom_id}",
        hoverinfo="name",
    )
    return atom_trace

draw_atoms

draw_atoms(fig, atomList, resolution=DEFAULT_RESOLUTION, radius=DEFAULT_RADIUS)

Add atom traces to a Plotly figure.

Parameters:

Name	Type	Description	Default
fig	Figure	Plotly figure to add atoms to.	required
atomList	List[Atom]	List of Atom objects to draw.	required
resolution	int	Sphere resolution for each atom.	DEFAULT_RESOLUTION
radius	Union[float, str]	Atom sphere radius (float, "vdw", or "ball").	DEFAULT_RADIUS

Returns:

Type	Description
Figure	The figure with atom traces added.

Source code in src/plotlymol3d/plotlyMol3D.py

def draw_atoms(
    fig: go.Figure,
    atomList: List[Atom],
    resolution: int = DEFAULT_RESOLUTION,
    radius: Union[float, str] = DEFAULT_RADIUS,
) -> go.Figure:
    """Add atom traces to a Plotly figure.

    Args:
        fig: Plotly figure to add atoms to.
        atomList: List of Atom objects to draw.
        resolution: Sphere resolution for each atom.
        radius: Atom sphere radius (float, "vdw", or "ball").

    Returns:
        The figure with atom traces added.
    """
    for a in atomList:
        a_trace = make_atom_mesh_trace(a, resolution=resolution, radius=radius)
        fig.add_trace(a_trace)
    return fig

Bond Traces

make_bond_mesh_trace

make_bond_mesh_trace(
    point1,
    point2,
    radius=DEFAULT_RADIUS,
    resolution=DEFAULT_RESOLUTION,
    color="grey",
    add_caps=True,
)

Create a Plotly Mesh3d trace for a bond (cylinder).

Parameters:

Name	Type	Description	Default
point1	Union[List[float], ndarray]	Starting point [x, y, z] of the bond.	required
point2	Union[List[float], ndarray]	Ending point [x, y, z] of the bond.	required
radius	float	Radius of the bond cylinder.	DEFAULT_RADIUS
resolution	int	Number of vertices around the cylinder.	DEFAULT_RESOLUTION
color	str	Color of the bond.	'grey'

Returns:

Type	Description
Mesh3d	Plotly Mesh3d trace object for the bond segment.

Source code in src/plotlymol3d/plotlyMol3D.py

def make_bond_mesh_trace(
    point1: Union[List[float], np.ndarray],
    point2: Union[List[float], np.ndarray],
    radius: float = DEFAULT_RADIUS,
    resolution: int = DEFAULT_RESOLUTION,
    color: str = "grey",
    add_caps: bool = True,
) -> go.Mesh3d:
    """Create a Plotly Mesh3d trace for a bond (cylinder).

    Args:
        point1: Starting point [x, y, z] of the bond.
        point2: Ending point [x, y, z] of the bond.
        radius: Radius of the bond cylinder.
        resolution: Number of vertices around the cylinder.
        color: Color of the bond.

    Returns:
        Plotly Mesh3d trace object for the bond segment.
    """
    p1 = np.array(point1)
    p2 = np.array(point2)
    x, y, z = generate_cylinder_mesh_rectangles(p1, p2, radius, resolution)

    # Append center points for the two end-cap disks
    x = np.append(x, [p1[0], p2[0]])
    y = np.append(y, [p1[1], p2[1]])
    z = np.append(z, [p1[2], p2[2]])

    res = resolution
    c_bottom = 2 * res  # center of bottom cap (at p1)
    c_top = 2 * res + 1  # center of top cap (at p2)

    i, j, k = [], [], []

    # Side wall: two triangles per quad segment
    for n in range(res):
        nxt = (n + 1) % res
        i.extend([n, n])
        j.extend([n + res, nxt + res])
        k.extend([nxt + res, nxt])

    if add_caps:
        # Bottom cap (fan from c_bottom into bottom-circle rim)
        for n in range(res):
            nxt = (n + 1) % res
            i.append(c_bottom)
            j.append(nxt)
            k.append(n)

        # Top cap (fan from c_top into top-circle rim)
        for n in range(res):
            nxt = (n + 1) % res
            i.append(c_top)
            j.append(n + res)
            k.append(nxt + res)

    bond_trace = go.Mesh3d(
        x=x,
        y=y,
        z=z,
        i=i,
        j=j,
        k=k,
        color=color,
        opacity=1,
        hoverinfo="skip",
    )
    return bond_trace

draw_bonds

draw_bonds(
    fig, bondList, atomList=None, resolution=DEFAULT_RESOLUTION, radius=DEFAULT_RADIUS
)

Add bond traces to a Plotly figure.

Draws bonds as two half-cylinders colored by each atom's element. Double and triple bonds are shown as multiple parallel cylinders. Aromatic bonds are shown as 1.5 bonds (one full + one thinner).

Parameters:

Name	Type	Description	Default
fig	Figure	Plotly figure to add bonds to.	required
bondList	List[Bond]	List of Bond objects to draw.	required
atomList	Optional[List[Atom]]	List of Atom objects (used for calculating ring centers).	None
resolution	int	Cylinder resolution for each bond.	DEFAULT_RESOLUTION
radius	Union[float, str]	Bond cylinder radius. Can be float or "ball" for ball+stick mode.	DEFAULT_RADIUS

Returns:

Type	Description
Figure	The figure with bond traces added.

Source code in src/plotlymol3d/plotlyMol3D.py

def draw_bonds(
    fig: go.Figure,
    bondList: List[Bond],
    atomList: Optional[List[Atom]] = None,
    resolution: int = DEFAULT_RESOLUTION,
    radius: Union[float, str] = DEFAULT_RADIUS,
) -> go.Figure:
    """Add bond traces to a Plotly figure.

    Draws bonds as two half-cylinders colored by each atom's element.
    Double and triple bonds are shown as multiple parallel cylinders.
    Aromatic bonds are shown as 1.5 bonds (one full + one thinner).

    Args:
        fig: Plotly figure to add bonds to.
        bondList: List of Bond objects to draw.
        atomList: List of Atom objects (used for calculating ring centers).
        resolution: Cylinder resolution for each bond.
        radius: Bond cylinder radius. Can be float or "ball" for ball+stick mode.

    Returns:
        The figure with bond traces added.
    """
    # Convert string radius to numeric value
    if isinstance(radius, str):
        if radius == "ball":
            radius = DEFAULT_RADIUS  # Use default for ball+stick mode
        else:
            radius = DEFAULT_RADIUS

    for bond in bondList:
        # Calculate bond vector and midpoint
        a1 = np.array(bond.a1_xyz)
        a2 = np.array(bond.a2_xyz)
        bond_vec = a2 - a1
        midpoint = (a1 + a2) / 2

        # Get perpendicular offset vector for multiple bonds
        # Find a vector perpendicular to the bond
        if np.allclose(bond_vec / np.linalg.norm(bond_vec), [0, 0, 1]) or np.allclose(
            bond_vec / np.linalg.norm(bond_vec), [0, 0, -1]
        ):
            perp = np.array([1, 0, 0])
        else:
            perp = np.cross(bond_vec, [0, 0, 1])
        perp = perp / np.linalg.norm(perp)

        # Determine bond offsets based on bond order
        bond_order = bond.bond_order
        offset_distance = radius * 1.8  # Spacing between parallel bonds

        # Initialize dashed flags (default: all solid)
        is_dashed = None

        if bond_order == 1.0:
            # Single bond: one cylinder at center
            offsets = [np.zeros(3)]
            radii = [radius]
        elif bond_order == 2.0:
            # Double bond: two parallel cylinders
            offsets = [perp * offset_distance * 0.5, -perp * offset_distance * 0.5]
            radii = [radius * 0.7, radius * 0.7]
        elif bond_order == 3.0:
            # Triple bond: three parallel cylinders
            offsets = [
                np.zeros(3),
                perp * offset_distance * 0.7,
                -perp * offset_distance * 0.7,
            ]
            radii = [radius * 0.6, radius * 0.6, radius * 0.6]
        elif bond_order == 1.5:
            # Aromatic bond: one solid + one dashed (indicating resonance)
            # Calculate ring center to determine correct offset direction
            ring_center_direction = perp  # Default direction

            if atomList is not None and bondList is not None:
                # Find atoms connected to both bond atoms via AROMATIC bonds only
                # This excludes substituents and gives a better ring center
                connected_atoms = []
                for other_bond in bondList:
                    # Only consider other aromatic bonds (same ring)
                    if other_bond.bond_order != 1.5:
                        continue

                    # Find atoms connected to a1 (excluding a2)
                    if (
                        other_bond.a1_id == bond.a1_id
                        and other_bond.a2_id != bond.a2_id
                    ):
                        connected_atoms.append(np.array(other_bond.a2_xyz))
                    elif (
                        other_bond.a2_id == bond.a1_id
                        and other_bond.a1_id != bond.a2_id
                    ):
                        connected_atoms.append(np.array(other_bond.a1_xyz))
                    # Find atoms connected to a2 (excluding a1)
                    if (
                        other_bond.a1_id == bond.a2_id
                        and other_bond.a2_id != bond.a1_id
                    ):
                        connected_atoms.append(np.array(other_bond.a2_xyz))
                    elif (
                        other_bond.a2_id == bond.a2_id
                        and other_bond.a1_id != bond.a1_id
                    ):
                        connected_atoms.append(np.array(other_bond.a1_xyz))

                # Calculate average position of connected atoms (ring center approximation)
                if len(connected_atoms) >= 2:
                    ring_center_approx = np.mean(connected_atoms, axis=0)
                    to_ring_center = ring_center_approx - midpoint

                    # Determine which perpendicular direction points toward ring center
                    # Use dot product to see if perp points toward or away from ring center
                    if np.dot(perp, to_ring_center) < 0:
                        ring_center_direction = -perp  # Flip direction
                    else:
                        ring_center_direction = perp

            # Place solid at center and dashed offset inward toward ring center
            offsets = [np.zeros(3), ring_center_direction * offset_distance * 0.7]
            radii = [radius * 0.7, radius * 0.5]
            is_dashed = [False, True]  # Second bond is dashed for aromatic
        else:
            # Default to single
            offsets = [np.zeros(3)]
            radii = [radius]

        # If no dashed flags set, default to all solid
        if is_dashed is None:
            is_dashed = [False] * len(offsets)

        # Draw each sub-bond
        for idx, (offset, r) in enumerate(zip(offsets, radii)):
            p1 = a1 + offset
            p2 = a2 + offset
            mid = midpoint + offset

            if is_dashed[idx]:
                # Dashed bond: draw segments with gaps
                num_dashes = 5  # Number of dash segments per half-bond

                # First half of bond (atom 1 color) - dashed
                for dash_idx in range(num_dashes):
                    t_start = dash_idx / num_dashes
                    t_end = (
                        dash_idx + 0.75
                    ) / num_dashes  # 75% dash, 25% gap (longer dashes)
                    dash_start = p1 + (mid - p1) * t_start
                    dash_end = p1 + (mid - p1) * t_end
                    bond_trace = make_bond_mesh_trace(
                        dash_start.tolist(),
                        dash_end.tolist(),
                        color=atom_colors[bond.a1_number],
                        resolution=resolution,
                        radius=r,
                    )
                    fig.add_trace(bond_trace)

                # Second half of bond (atom 2 color) - dashed
                for dash_idx in range(num_dashes):
                    t_start = dash_idx / num_dashes
                    t_end = (
                        dash_idx + 0.75
                    ) / num_dashes  # 75% dash, 25% gap (longer dashes)
                    dash_start = mid + (p2 - mid) * t_start
                    dash_end = mid + (p2 - mid) * t_end
                    bond_trace = make_bond_mesh_trace(
                        dash_start.tolist(),
                        dash_end.tolist(),
                        color=atom_colors[bond.a2_number],
                        resolution=resolution,
                        radius=r,
                    )
                    fig.add_trace(bond_trace)
            else:
                # Solid bond: single cylinder per half
                use_oval_caps = bond_order in (2.0, 3.0)
                # First half of bond (atom 1 color)
                bond_trace = make_bond_mesh_trace(
                    p1.tolist(),
                    mid.tolist(),
                    color=atom_colors[bond.a1_number],
                    resolution=resolution,
                    radius=r,
                    add_caps=not use_oval_caps,
                )
                fig.add_trace(bond_trace)

                # Second half of bond (atom 2 color)
                bond_trace = make_bond_mesh_trace(
                    mid.tolist(),
                    p2.tolist(),
                    color=atom_colors[bond.a2_number],
                    resolution=resolution,
                    radius=r,
                    add_caps=not use_oval_caps,
                )
                fig.add_trace(bond_trace)

        # Oval end caps for double and triple bonds
        if bond_order in (2.0, 3.0):
            bond_dir = bond_vec / np.linalg.norm(bond_vec)
            max_offset = max(np.linalg.norm(o) for o in offsets)
            r0 = radii[0]
            semi_a = max_offset + r0
            semi_b = r0
            for center, color_num in [(a1, bond.a1_number), (a2, bond.a2_number)]:
                fig.add_trace(
                    _make_oval_cap(
                        center,
                        bond_dir,
                        perp,
                        semi_a,
                        semi_b,
                        resolution,
                        atom_colors[color_num],
                    )
                )

    return fig

Formatting Functions

Figure Formatting

format_figure

format_figure(fig, bgcolor='rgba(0,0,0,0)')

Apply default formatting to a molecular visualization figure.

Hides axes and grid lines for a clean molecular visualization. Sets aspectmode='data' to ensure spheres aren't distorted.

Parameters:

Name	Type	Description	Default
fig	Figure	Plotly figure to format.	required
bgcolor	str	Background color for the 3D scene (default: transparent).	'rgba(0,0,0,0)'

Returns:

Type	Description
Figure	The formatted figure.

Source code in src/plotlymol3d/plotlyMol3D.py

def format_figure(fig: go.Figure, bgcolor: str = "rgba(0,0,0,0)") -> go.Figure:
    """Apply default formatting to a molecular visualization figure.

    Hides axes and grid lines for a clean molecular visualization.
    Sets aspectmode='data' to ensure spheres aren't distorted.

    Args:
        fig: Plotly figure to format.
        bgcolor: Background color for the 3D scene (default: transparent).

    Returns:
        The formatted figure.
    """
    fig.update_layout(
        scene=dict(
            xaxis=dict(
                visible=False, showbackground=False, showgrid=False, zeroline=False
            ),
            yaxis=dict(
                visible=False, showbackground=False, showgrid=False, zeroline=False
            ),
            zaxis=dict(
                visible=False, showbackground=False, showgrid=False, zeroline=False
            ),
            aspectmode="data",  # Ensure equal scaling on all axes
            bgcolor=bgcolor,  # Transparent background to match theme
        ),
        margin=dict(l=0, r=0, t=0, b=0),
    )

    return fig

Lighting Control

format_lighting

format_lighting(
    fig,
    ambient=0,
    diffuse=1,
    specular=0,
    roughness=1,
    fresnel=0,
    lightx=1000,
    lighty=1000,
    lightz=1000,
)

Configure lighting for 3D mesh traces.

Parameters:

Name	Type	Description	Default
fig	Figure	Plotly figure to configure.	required
ambient	float	Ambient light intensity (0-1).	0
diffuse	float	Diffuse light intensity (0-1).	1
specular	float	Specular highlight intensity (0-1).	0
roughness	float	Surface roughness (0-1).	1
fresnel	float	Fresnel effect intensity (0-1).	0
lightx	float	Light position x-coordinate.	1000
lighty	float	Light position y-coordinate.	1000
lightz	float	Light position z-coordinate.	1000

Returns:

Type	Description
Figure	The figure with updated lighting settings.

Source code in src/plotlymol3d/plotlyMol3D.py

def format_lighting(
    fig: go.Figure,
    ambient: float = 0,
    diffuse: float = 1,
    specular: float = 0,
    roughness: float = 1,
    fresnel: float = 0,
    lightx: float = 1000,
    lighty: float = 1000,
    lightz: float = 1000,
) -> go.Figure:
    """Configure lighting for 3D mesh traces.

    Args:
        fig: Plotly figure to configure.
        ambient: Ambient light intensity (0-1).
        diffuse: Diffuse light intensity (0-1).
        specular: Specular highlight intensity (0-1).
        roughness: Surface roughness (0-1).
        fresnel: Fresnel effect intensity (0-1).
        lightx: Light position x-coordinate.
        lighty: Light position y-coordinate.
        lightz: Light position z-coordinate.

    Returns:
        The figure with updated lighting settings.
    """
    fig.update_traces(
        lighting=dict(
            ambient=ambient,
            diffuse=diffuse,
            specular=specular,
            roughness=roughness,
            fresnel=fresnel,
        ),
        lightposition=dict(x=lightx, y=lighty, z=lightz),
    )

    return fig

Data Classes

Atom

@dataclass
class Atom:
    """Represents an atom with position and properties.

    Attributes:
        atom_id: 0-indexed unique identifier
        atom_number: Atomic number (e.g., 6 for carbon)
        atom_symbol: Element symbol (e.g., "C")
        atom_xyz: [x, y, z] coordinates in Angstroms
        atom_vdw: Van der Waals radius in Angstroms
    """
    atom_id: int
    atom_number: int
    atom_symbol: str
    atom_xyz: List[float]
    atom_vdw: float

Bond

@dataclass
class Bond:
    """Represents a bond between two atoms.

    Attributes:
        a1_id, a2_id: Atom IDs
        a1_number, a2_number: Atomic numbers
        a1_xyz, a2_xyz: Atomic coordinates
        a1_vdw, a2_vdw: Van der Waals radii
        bond_order: 1.0 (single), 1.5 (aromatic), 2.0 (double), 3.0 (triple)
    """
    a1_id: int
    a2_id: int
    a1_number: int
    a2_number: int
    a1_xyz: List[float]
    a2_xyz: List[float]
    a1_vdw: float
    a2_vdw: float
    bond_order: float