ChemNames

A CLI utility to retrieve chemical data (SMILES, InChI, Full Names) from PubChem and map Compound names to their corresponding identifiers.

Installation

This package is managed with standard Python tools and can be installed via pip.

1. Clone the repository.
2. Install the package in editable mode (or normal mode):

pip install .

Or using uv to manage the environment:

uv pip install .

After installation, the CLI tool addchemnames will be available in your path.

Usage

1. Retrieve Chemical Data

The main utility reads a CSV file containing a Compound column, queries PubChem, and outputs a new CSV with added SMILES, InChI, and Full Name columns.

Input CSV Format: The input file MUST contain a column named Compound.

Example input.csv:

Compound,ID
Aspirin,1
Caffeine,2

Run the command:

addchemnames input.csv output.csv

Output: The tool will generate output.csv with the enriched data. If a compound is not found, "xxxxxx" will be used as the placeholder.

2. Add KEGG IDs

If you have a CSV file that already contains PubChem CIDs (e.g., from a previous step or source), you can use add_keggs.py (located in the root of the repository) to append KEGG IDs.

Run the command:

python add_keggs.py input_with_cids.csv output_with_keggs.csv

Notes

• Network Requests: This tool makes network requests to PubChem. Large files may take some time to process.
• Rate Limiting: The tool uses threading to speed up requests, but be mindful of PubChem's usage policies.
• Data Accuracy: Data is fetched "as is" from PubChem.

License

MIT