OPSIN

Overview

Resolve systematic organic names with the EMBL-EBI OPSIN web service. This skill is for name-to-structure parsing, not synonym search or general compound facts.

When to Use

Use this skill when:

• the prompt contains a clear systematic or IUPAC-like chemical name
• multiple systematic names need consistent structure resolution
• OPSIN parse failures need normalized diagnostics
• a successful OPSIN structure should be checked locally with RDKit

Prefer pubchem instead for trivial names, trade names, abbreviations, or broad synonym lookup.

Scripts

• name_to_structure.py
• batch_name_to_structure.py
• parse_diagnostics.py
• validate_with_rdkit.py

Harbor Trial execution

In a harbor-agent-infra Trial, the allowlisted directory is available at $HOME/.openclaw/skills/opsin and commands start in /workspace. Invoke the skill script directly; do not use the retired benchmark runner or host workspace paths.

python "$HOME/.openclaw/skills/opsin/scripts/<capability>.py" \
  --request-json /workspace/requests/opsin.json \
  --output-dir /workspace/outputs/opsin \
  --json

Each script writes result.json in --output-dir and prints the same payload when --json is set.

Read references/contracts.md for request and response details.