Task tutorial

Canonicalize SMILES before matching local records

Send one SMILES to the local MCP process and retain chematic's canonical representation beside the original input.

You will make

A versioned local record containing input SMILES and the canonical form returned by chematic.

Steps

Start the local MCP server from the source checkout.
Send the canonical_smiles JSON-RPC request below.
Store the input, returned canonical field, and chematic version together before comparing records.

git clone https://github.com/kent-tokyo/chematic.git
cd chematic
printf '%s\n' \
  '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{}}}' \
  '{"jsonrpc":"2.0","method":"notifications/initialized","params":{}}' \
  '{"jsonrpc":"2.0","id":3,"method":"tools/call","params":{"name":"canonical_smiles","arguments":{"smiles":"C1=CC=CC=C1"}}}' \
  | cargo run -p chematic-mcp --release --quiet

Expected result

The response has a canonical field containing a valid SMILES representation. The checked C1=CC=CC=C1 example returns a canonical string without sending the molecule to a network service.

If it does not work

Canonical SMILES is a representation from a particular library and version, not a universal chemical identifier or proof that two records are equivalent. Preserve stereochemistry, salts, and the original input; do not compare strings from different tools or releases without validating that workflow.

Next action

Read the local MCP integration guide