PyLipidParse

Convert standard lipid shorthand notation (LIPID MAPS, SwissLipids, HMDB) to molecular structures.

What it does

No existing open-source tool converts lipid shorthand notation to SMILES, InChI, or RDKit molecules. PyLipidParse fills this gap.

from pylipidparse import LipidConverter

conv = LipidConverter()

conv.to_smiles("PC 16:0/18:1(9Z)")
# → 'CCCCCCCCCCCCCCCC(=O)OC[C@@H](OC(=O)CCCCCCCC/C=C\\CCCCCCCC)COP(=O)([O-])OCC[N+](C)(C)C'

conv.to_inchikey("FA 18:2(9Z,12Z)")
# → 'OYHQOLUKZRVURQ-HZJYTTRNSA-N'

conv.to_mol("Cer 18:1;O2/16:0")
# → <rdkit.Chem.rdchem.Mol object>

conv.to_sdf(["PC 16:0/18:1(9Z)", "PE 18:0/20:4(5Z,8Z,11Z,14Z)"], path="output.sdf")

Supported lipid classes

Installation

pip

pip install pylipidparse

uv

uv add pylipidparse

From source

git clone https://github.com/MontgomeryBohde/PyLipidParse.git
cd PyLipidParse
pip install -e ".[dev]"

Quick start

from pylipidparse import LipidConverter

conv = LipidConverter()

# SMILES
smiles = conv.to_smiles("FA 18:1(9Z)")        # Oleic acid
smiles = conv.to_smiles("PC 16:0/18:1(9Z)")   # POPC

# InChI / InChIKey
inchi = conv.to_inchi("FA 16:0")
ik = conv.to_inchikey("FA 16:0")   # "IPCSVZSSVZVIGE-UHFFFAOYSA-N"

# RDKit Mol (for downstream cheminformatics)
mol = conv.to_mol("Cer 18:1;O2/16:0")

# Write to file
conv.to_mol_file("PC 16:0/18:1(9Z)", "popc.mol")
conv.to_sdf(["FA 16:0", "FA 18:1(9Z)", "PC 16:0/18:1(9Z)"], "lipids.sdf")

Notation requirements

PyLipidParse requires full structural notation with explicit chain positions. Sum-composition notation (e.g., PC 34:1) is rejected because a unique structure cannot be generated from it.

API reference

LipidConverter(dialect="LipidMaps", cache_size=512)

Exceptions

from pylipidparse.exceptions import (
    LipidParseError,                  # pygoslin couldn't parse the input
    UnsupportedLipidClassError,       # lipid class not yet implemented
    InsufficientStructuralDetailError, # species-level / unknown positions
    StructureGenerationError,         # molecule assembly failed
)

Contributing

Issues and pull requests are welcome at github.com/MontgomeryBohde/PyLipidParse.

Citation

If you use PyLipidParse in published work, please cite this repository and the underlying tools:

• pygoslin: Kopczynski et al., Analytical Chemistry (2022). DOI: 10.1021/acs.analchem.1c05430
• RDKit: Landrum, G. RDKit: Open-source cheminformatics. rdkit.org

License

MIT License — see LICENSE.