lipid-convert

name	lipid-convert
description	Convert lipid shorthand notation to molecular structures (SMILES, InChI, InChIKey, MOL files, SDF files). Use when the user asks about lipid structures, needs to look up a lipid by name, wants SMILES or InChIKey for database searches, or needs structure files for visualization or cheminformatics tools.

Lipid Structure Conversion

Use the pylipidparse MCP tools to convert lipid shorthand notation to molecular structures.

Available Tools

Tool	Use for
lipid_to_smiles	Single lipid → canonical SMILES string
lipid_to_inchi	Single lipid → InChI string
lipid_to_inchikey	Single lipid → InChIKey (27-char hash for database lookups)
batch_convert_lipids	Multiple lipids → SMILES/InChI/InChIKey in one call
lipid_to_mol_file	Single lipid → MDL MOL file content (2D coords)
lipids_to_sdf	Multiple lipids → SDF file content (2D coords + metadata)

Input Format Requirements

Lipid names must use full structural notation with explicit chain positions.

Valid (full structural)	Invalid (species-level)
PC 16:0/18:1(9Z)	PC 34:1
FA 18:2(9Z,12Z)	FA 18:2
Cer 18:1;O2/16:0	Cer 18:1/16:0
TAG 16:0/18:1(9Z)/18:2(9Z,12Z)	TG 52:2

Special cases that work without chain notation: Cholesterol, FC, CHOL.

Supported Dialects

• LipidMaps (default) — LIPID MAPS shorthand notation
• Goslin — Goslin shorthand
• SwissLipids — SwissLipids notation
• HMDB — Human Metabolome Database notation

Example Usage

Single conversion:

Convert PC 16:0/18:1(9Z) to SMILES
→ Use lipid_to_smiles with lipid_name="PC 16:0/18:1(9Z)"

Batch conversion with multiple formats:

Get SMILES and InChIKey for a list of lipids
→ Use batch_convert_lipids with output_formats=["smiles", "inchikey"]

Structure file for visualization:

Give me a MOL file for FA 18:1(9Z)
→ Use lipid_to_mol_file; the mol_content field contains the file text

Export multiple lipids for a cheminformatics tool:

Generate an SDF file for these 5 lipids
→ Use lipids_to_sdf; the sdf_content field contains the full SDF text

Error Handling

If a conversion fails, the tool returns an error field instead of the structure. Common errors:

• parse_error — name not recognized; check notation and dialect
• insufficient_detail — species-level notation; use full structural notation
• unsupported_class — lipid class not yet supported by PyLipidParse
• structure_error — parsed but could not generate a valid 3D structure