Molecular format converter

Convert between SMILES, SDF, MOL, MOL2, PDB, mmCIF, XYZ, and SVG locally while preserving the chemical graph and available coordinates.

COSMolKit 0.2.12 / Rust / WASM

Input formatLine notation

Output format.sdf

Source

21 characters

Choose file

Converted output

13 atoms / 13 bonds

Download

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 0.2.12

INSTALLpip install cosmolkit==0.2.12

Python 3.9+ / Rust-native wheel

convert_molecule.py

from pathlib import Path
from cosmolkit import Molecule

source = "CC(=O)Oc1ccccc1C(=O)O"
mol = Molecule.from_smiles(source)
try:
    mol_2d = mol.with_2d_coordinates()
except (ValueError, NotImplementedError):
    mol_2d = Molecule.from_smiles(mol.to_smiles()).with_2d_coordinates()
output = mol_2d.to_2d_sdf_string(format="v2000")

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