Mol Render

mol-render

Generate high-quality 3D ball-and-stick model PNG images from SMILES strings or PDB structures, rendered with POV-Ray ray tracing.

Dependencies

Required:

• rdkit — SMILES parsing & 3D conformer generation
• numpy — coordinate transforms
• povray — ray tracing renderer

Optional (PDB mode only):

• biopython — PDB file parsing

Install:

pip install rdkit numpy
apt-get install -y povray

# For PDB support:
pip install biopython

Usage

SMILES Mode

python3 scripts/smiles_to_3d.py "SMILES" -o output.png

Arguments:

• SMILES — (positional) SMILES string (required)
• -o, --output — output PNG path (default: molecule.png)
• --bg — background color: black / white / blue (default: blue)
• --no-hydrogen — hide hydrogen atoms
• --kekulize — convert aromatic bonds to alternating single/double bonds

Examples:

# Ethanol
python3 scripts/smiles_to_3d.py "CCO" -o ethanol.png

# Benzene (white background, Kekulé style)
python3 scripts/smiles_to_3d.py "c1ccccc1" -o benzene.png --bg white --kekulize

# Caffeine
python3 scripts/smiles_to_3d.py "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -o caffeine.png

# Aspirin (no hydrogens)
python3 scripts/smiles_to_3d.py "CC(=O)OC1=CC=CC=C1C(=O)O" -o aspirin.png --no-hydrogen

PDB Mode

python3 scripts/pdb_to_3d.py --pdb <PDB_ID_or_file> -o output.png

Arguments:

• --pdb — PDB file path or 4-character PDB ID (auto-downloads from RCSB) (required)
• -o, --output — output PNG path (default: pdb_molecule.png)
• --chain — select specific chain (e.g., A)
• --residues — residue range (e.g., 1-50 or 10,20,30-40)
• --ligand-only — render only ligands (HETATM, excluding water)
• --no-hydrogen — hide hydrogen atoms
• --no-water / --keep-water — filter/keep water molecules (default: filter)
• --bg — background color: black / white / blue (default: blue)
• --view — viewing angle: auto / side / top / front or θ,φ in degrees (default: auto)
• --resolution — resolution multiplier, e.g., 0.5 for half, 2.0 for double (default: 1.0)
• --sphere-scale — override sphere scale factor (default: auto)
• --bond-radius — override bond radius (default: auto)

Examples:

# Download and render G-quadruplex from RCSB
python3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen -o g4.png

# Side view
python3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen --view side -o g4_side.png

# Ligands only
python3 scripts/pdb_to_3d.py --pdb 1KF1 --ligand-only -o ligands.png

# Specific chain and residues
python3 scripts/pdb_to_3d.py --pdb 1KF1 --chain A --residues 1-12 -o partial.png

# Local PDB file
python3 scripts/pdb_to_3d.py --pdb structure.pdb -o out.png

# Large protein at lower resolution
python3 scripts/pdb_to_3d.py --pdb 2HYY --no-hydrogen --resolution 0.5 -o protein.png

Output

• 1200×1200 PNG with POV-Ray ray tracing
• CPK color scheme (C=dark gray, O=red, N=blue, H=white, P=orange, S=yellow, K=purple, ...)
• Aromatic bonds rendered as solid + dashed lines (SMILES mode)
• Double bonds rendered as two parallel solid lines
• --kekulize option converts aromatic bonds to alternating single/double
• Metal ions displayed with ionic radius (large spheres), no coordination bonds drawn
• Auto-selects best viewing angle (PCA-based)
• Auto-scales sphere/bond sizes for large molecules
• Water molecules filtered by default (PDB mode)

Known Limitations

• Very large molecules (>2000 atoms) may be slow to render (use --resolution 0.5)
• PDB mode renders all bonds as single bonds (no double/aromatic distinction)
• Metal coordination bonds are not rendered
• POV-Ray must be installed (which povray)
• biopython required only for PDB mode (optional dependency)

License

MIT