PDB to SMILES converter

Convert PDB to SMILES locally in your browser with COSMolKit, Rust, and WebAssembly.

COSMolKit 0.3.0 / Rust / WASM

Input formatProtein Data Bank

Output format.smi

Source

263 characters

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Converted output

1 atoms / 0 bonds

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Converted locally. No structure data is uploaded.

SUPPORTED FORMATS

Formats available in this converter

COSMolKit reads and writes the molecular graph locally. Coordinate-dependent exports use the coordinates available in the source or generated by the selected workflow.

Input formats

SMILES; MOL or SDF V2000/V3000; Tripos MOL2; PDB; PDBx/mmCIF; XYZ.

Output formats

SMILES; MOL V2000/V3000; SDF V2000/V3000; PDB; SVG depiction.

Common molecular file conversions

Convert files to SMILES: SDF to SMILES, MOL to SMILES, MOL2 to SMILES, PDB to SMILES, mmCIF to SMILES, and XYZ to SMILES.

Export from SMILES: SMILES to SDF V2000/V3000, SMILES to MOL V2000/V3000, SMILES to PDB, and SMILES to SVG.

Convert molecular structure files: MOL2 to SDF, MOL2 to PDB, SDF to MOL, SDF to PDB, PDB to SDF, mmCIF to PDB, and XYZ to SDF.

Create a 2D structure image: Render SMILES, MOL, SDF, MOL2, PDB, mmCIF, or XYZ input as a scalable SVG molecular depiction.

PYTHON BACKEND

Run the same conversion with COSMolKit

The example tracks the formats and source currently selected above.

COSMolKit Python 0.3.0

INSTALLpip install cosmolkit==0.3.0

Python 3.9+ / Rust-native wheel

convert_molecule.py

from pathlib import Path
from cosmolkit import Molecule

source = "HETATM    1  O   HOH A   1       0.000   0.000   0.000  1.00 20.00           O\nHETATM    2  H1  HOH A   1       0.957   0.000   0.000  1.00 20.00           H\nHETATM    3  H2  HOH A   1      -0.240   0.927   0.000  1.00 20.00           H\nCONECT    1    2    3\nEND\n"
mol = Molecule.from_pdb_block(source)
output = mol.to_smiles()

Path("molecule.smi").write_text(output, encoding="utf-8")