pylipidparse — Claude Code plugin: lipid structures and setup
This MCP server turns full lipid shorthand into SMILES, InChI, InChIKey, MOL, and SDF outputs. Use it to inspect chemical structures from Claude Code.
/plugin marketplace add anthropics/claude-plugins-community
/plugin install pylipidparse@claude-communityWhat pylipidparse does
pylipidparse exposes PyLipidParse in Claude Code as an MCP server. Give it a complete lipid notation such as PC 16:0/18:1(9Z) or Cer 18:1;O2/16:0, and it can return canonical SMILES, InChI, and InChIKey values. It can also produce MOL files with 2D coordinates and SDF output for a batch of lipids.
The plugin accepts LIPID MAPS, Goslin, SwissLipids, and HMDB notation dialects. Its supported classes include fatty acids, glycerolipids, glycerophospholipids, sphingolipids, and sterols. A shorthand such as PC 34:1 is insufficient; the structural form must include the required detail.
You need uv before using the server. It runs through uvx, which installs pylipidparse[mcp] on the first request and reuses the cached environment later. The initial setup may take 30–60 seconds. Without uv, the MCP server will not start.
What it helps with
- convert full lipid notation into SMILES
- look up an InChIKey for PubChem or LIPID MAPS
- export a lipid structure as a MOL file
- generate an SDF file for several lipids
Example prompts for the agent
- Convert
PC 16:0/18:1(9Z)into a SMILES string. - Find the InChIKey for oleic acid, written as
FA 18:1(9Z). - Create an SDF file from this list of ceramides: ...
How to install pylipidparse
Plugin marketplace
/plugin marketplace add anthropics/claude-plugins-community/plugin install pylipidparse@claude-communityStep by step, with commands for each platform: Claude Code plugins: marketplaces, installing, and building your own
Questions about pylipidparse
How do I install pylipidparse in Claude Code?
Add the marketplace with /plugin marketplace add anthropics/claude-plugins-community, then install the plugin with /plugin install pylipidparse@claude-community.
What does pylipidparse do?
It connects PyLipidParse to Claude Code through MCP and converts complete lipid notation into SMILES, InChI, InChIKey, MOL, or SDF output. It accepts LIPID MAPS, Goslin, SwissLipids, and HMDB dialects.
What lipid notation does pylipidparse require?
Use a full structural form such as PC 16:0/18:1(9Z). A compact entry like PC 34:1 is not sufficient.
Source text
claude-code-plugin · MIT
# PyLipidParse Claude Code Plugin
This plugin exposes [PyLipidParse](https://github.com/MontgomeryBohde/PyLipidParse) as an MCP server inside Claude Code, letting you convert lipid shorthand notation to molecular structures directly in your AI assistant.
## What it does
Converts lipid names like `PC 16:0/18:1(9Z)` or `Cer 18:1;O2/16:0` into:
- Canonical **SMILES** strings
- **InChI** identifiers
- **InChIKey** hashes (for PubChem / LIPID MAPS database lookups)
- **MOL files** with 2D coordinates
- **SDF files** for multiple lipids at once
Supports LIPID MAPS, Goslin, SwissLipids, and HMDB notation dialects.
## Requirements
- [uv](https://docs.astral.sh/uv/) must be installed (used to run the server without pre-installation)
## Installation
Install this plugin from the Claude Code plugins directory, or manually:
```bash
claude --plugin-dir /path/to/PyLipidParse/claude-code-plugin
```
The MCP server runs via `uvx` and installs `pylipidparse[mcp]` automatically on first use. Subsequent runs use the cached environment.
## Manual MCP configuration (without the plugin)
Add to your `.mcp.json` or Claude Code MCP config:
```json
{
"mcpServers": {
"pylipidparse": {
"command": "uvx",
"args": ["--from", "pylipidparse[mcp]", "pylipidparse-mcp"]
}
}
}
```
Or if you have `pylipidparse[mcp]` already installed:
```json
{
"mcpServers": {
"pylipidparse": {
"command": "pylipidparse-mcp"
}
}
}
```
## Example prompts
- *"Convert PC 16:0/18:1(9Z) to SMILES"*
- *"What is the InChIKey for oleic acid (FA 18:1(9Z))?"*
- *"Give me SMILES and InChIKey for these 10 lipids: ..."*
- *"Generate an SDF file for this list of ceramides"*
## Supported lipid classes
Fatty acids (FA), glycerolipids (MAG/DAG/TAG), glycerophospholipids (PC/PE/PA/PI/PS/PG and lyso variants), sphingolipids (Cer/SM/HexCer/LacCer/SPB), and sterols (Cholesterol/CE/bile acids).
## Notes
- **Full structural notation required** — use `PC 16:0/18:1(9Z)`, not `PC 34:1`
- First run may take 30–60 seconds while `uvx` installs dependencies
- Source: [github.com/MontgomeryBohde/PyLipidParse](https://github.com/MontgomeryBohde/PyLipidParse)
© MontgomeryBohde · MIT · MontgomeryBohde/PyLipidParse
