Molecular Visualization

def MolToImage(mol: Mol, size: tuple = (300, 300), kekulize: bool = True,
               wedgeBonds: bool = True, fitImage: bool = False, atomLabels: dict = None,
               bondLabels: dict = None, highlightAtoms: list = None, 
               highlightBonds: list = None, highlightAtomColors: dict = None,
               highlightBondColors: dict = None, highlightRadius: dict = None) -> PIL.Image:
    """
    Generate a PIL Image of a molecule.
    
    Parameters:
    - mol: Input molecule
    - size: Image dimensions as (width, height) tuple (default (300, 300))
    - kekulize: Convert aromatic bonds to alternating single/double (default True)
    - wedgeBonds: Draw wedge/dash bonds for stereochemistry (default True)
    - fitImage: Fit molecule to image bounds (default False)
    - atomLabels: Dictionary mapping atom indices to label strings
    - bondLabels: Dictionary mapping bond indices to label strings
    - highlightAtoms: List of atom indices to highlight
    - highlightBonds: List of bond indices to highlight
    - highlightAtomColors: Dictionary mapping atom indices to highlight colors
    - highlightBondColors: Dictionary mapping bond indices to highlight colors
    - highlightRadius: Dictionary mapping atom indices to highlight radii
    
    Returns:
    PIL Image object
    """

def MolToFile(mol: Mol, filename: str, size: tuple = (300, 300), 
              imageType: str = None, **kwargs) -> None:
    """
    Save molecule image directly to file.
    
    Parameters:
    - mol: Input molecule
    - filename: Output file path (extension determines format)
    - size: Image dimensions as (width, height) tuple (default (300, 300))
    - imageType: Force specific image type ('png', 'svg', etc.)
    - **kwargs: Additional arguments passed to drawing functions
    
    Returns:
    None
    """

def ReactionToImage(rxn, subImgSize: tuple = (200, 200), **kwargs) -> PIL.Image:
    """
    Generate a PIL Image of a chemical reaction.
    
    Parameters:
    - rxn: ChemicalReaction object
    - subImgSize: Size for individual molecule images (default (200, 200))
    - **kwargs: Additional drawing options
    
    Returns:
    PIL Image object showing the complete reaction
    """

def DrawReaction(rxn, **kwargs):
    """
    Draw a chemical reaction using matplotlib backend.
    
    Parameters:
    - rxn: ChemicalReaction object
    - **kwargs: Drawing options
    
    Returns:
    Matplotlib figure object
    """

def MolsToGridImage(mols: list, molsPerRow: int = 4, subImgSize: tuple = (200, 200),
                    legends: list = None, highlightAtomLists: list = None,
                    highlightBondLists: list = None, useSVG: bool = False,
                    returnPNG: bool = True, **kwargs) -> PIL.Image:
    """
    Generate a grid image of multiple molecules.
    
    Parameters:
    - mols: List of molecule objects
    - molsPerRow: Number of molecules per row (default 4)
    - subImgSize: Size of each molecule image (default (200, 200))
    - legends: List of legend strings for each molecule
    - highlightAtomLists: List of atom index lists to highlight for each molecule
    - highlightBondLists: List of bond index lists to highlight for each molecule
    - useSVG: Use SVG rendering (default False)
    - returnPNG: Return PNG format (default True)
    - **kwargs: Additional drawing options
    
    Returns:
    PIL Image object containing the molecule grid
    """

def MolsToImage(mols: list, **kwargs) -> PIL.Image:
    """
    Generate a single image containing multiple molecules.
    
    Parameters:
    - mols: List of molecule objects
    - **kwargs: Drawing options (same as MolsToGridImage)
    
    Returns:
    PIL Image object
    """

def MolToSVG(mol: Mol, size: tuple = (300, 300), kekulize: bool = True,
             drawer: object = None, **kwargs) -> str:
    """
    Generate SVG representation of a molecule.
    
    Parameters:
    - mol: Input molecule
    - size: Image dimensions as (width, height) tuple (default (300, 300))
    - kekulize: Convert aromatic bonds to alternating single/double (default True)
    - drawer: Custom drawer object (default None for auto-selection)
    - **kwargs: Additional drawing options
    
    Returns:
    SVG string representation
    """

def ReactionToSVG(rxn, **kwargs) -> str:
    """
    Generate SVG representation of a chemical reaction.
    
    Parameters:
    - rxn: ChemicalReaction object
    - **kwargs: Drawing options
    
    Returns:
    SVG string representation
    """

class DrawingOptions:
    """
    Configuration object for molecular drawing options.
    """
    atomLabelFontSize: int = 12  # Font size for atom labels
    bondLineWidth: float = 2.0   # Width of bond lines
    multipleBondOffset: float = 0.15  # Offset for multiple bonds
    dummiesAreAttachments: bool = False  # Treat dummy atoms as attachment points
    circleAtoms: bool = True     # Draw circles around atoms
    highlightColour: tuple = (1, 1, 0)  # Default highlight color (RGB)
    atomColourPalette: dict = {}  # Custom atom color palette
    includeAtomTags: bool = False  # Include atom tags in drawing
    clearBackground: bool = True  # Use transparent background
    bgColor: tuple = (1, 1, 1)   # Background color (RGB)
    legendFontSize: int = 12     # Font size for legends

def SetDrawingOptions(opts: DrawingOptions) -> None:
    """
    Set global drawing options.
    
    Parameters:
    - opts: DrawingOptions object with configuration
    
    Returns:
    None
    """

def MolFromPNG(pngData: bytes) -> Mol:
    """
    Extract molecule from PNG image data (if embedded).
    
    Parameters:
    - pngData: PNG image data as bytes
    
    Returns:
    Mol object or None if extraction fails
    """

def MolFromSVG(svgData: str) -> Mol:
    """
    Extract molecule from SVG string data (if embedded).
    
    Parameters:
    - svgData: SVG string data
    
    Returns:
    Mol object or None if extraction fails
    """

# External types used in visualization functions
class PIL.Image:
    """Pillow Image object for raster graphics"""
    def save(self, filename: str) -> None: ...
    def show(self) -> None: ...

from rdkit import Chem
from rdkit.Chem import Draw

# Create and draw a molecule
mol = Chem.MolFromSmiles('CCO')  # Ethanol
img = Draw.MolToImage(mol, size=(400, 400))
img.save('ethanol.png')

# Draw with custom options
img = Draw.MolToImage(mol, 
                      size=(500, 500),
                      highlightAtoms=[0, 1],  # Highlight first two carbons
                      highlightAtomColors={0: (1, 0, 0), 1: (0, 1, 0)})  # Red and green
img.save('ethanol_highlighted.png')

from rdkit import Chem
from rdkit.Chem import Draw

# Create a list of molecules
smiles_list = ['CCO', 'CCCO', 'CCCCO', 'CCCCCO']
mols = [Chem.MolFromSmiles(smi) for smi in smiles_list]
legends = ['Ethanol', 'Propanol', 'Butanol', 'Pentanol']

# Create grid image
img = Draw.MolsToGridImage(mols,
                           molsPerRow=2,
                           subImgSize=(250, 250),
                           legends=legends)
img.save('alcohol_series.png')

from rdkit import Chem
from rdkit.Chem import Draw

# Generate SVG for scalable graphics
mol = Chem.MolFromSmiles('c1ccccc1')  # Benzene
svg_string = Draw.MolToSVG(mol, size=(400, 400))

# Save SVG to file
with open('benzene.svg', 'w') as f:
    f.write(svg_string)

from rdkit import Chem
from rdkit.Chem import AllChem, Draw

# Create a chemical reaction
rxn = AllChem.ReactionFromSmarts('[C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3]')

# Draw the reaction
img = Draw.ReactionToImage(rxn, subImgSize=(300, 300))
img.save('amidation_reaction.png')

from rdkit import Chem
from rdkit.Chem import Draw

# Create custom drawing options
opts = Draw.DrawingOptions()
opts.atomLabelFontSize = 18
opts.bondLineWidth = 3.0
opts.highlightColour = (0, 1, 0)  # Green highlights
opts.bgColor = (0.9, 0.9, 0.9)   # Light gray background

# Apply custom options
Draw.SetDrawingOptions(opts)

# Draw with custom styling
mol = Chem.MolFromSmiles('CCO')
img = Draw.MolToImage(mol, size=(400, 400))
img.save('ethanol_custom_style.png')

from rdkit import Chem
from rdkit.Chem import Draw

# Create molecule and define substructure
mol = Chem.MolFromSmiles('CCO')
pattern = Chem.MolFromSmarts('CO')  # Alcohol pattern

# Find matches
matches = mol.GetSubstructMatches(pattern)

if matches:
    # Highlight the first match
    highlight_atoms = list(matches[0])
    img = Draw.MolToImage(mol,
                          highlightAtoms=highlight_atoms,
                          highlightAtomColors={atom: (1, 0, 0) for atom in highlight_atoms})
    img.save('ethanol_alcohol_highlighted.png')

from rdkit import Chem
from rdkit.Chem import Draw

# Create molecule with custom atom labels
mol = Chem.MolFromSmiles('CCO')
atom_labels = {0: 'C1', 1: 'C2', 2: 'O'}

img = Draw.MolToImage(mol,
                      size=(400, 400),
                      atomLabels=atom_labels)
img.save('ethanol_labeled.png')