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Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
SOC 직업 분류 기준
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Extract structured synthesis procedures from a folder of PDFs using the LeMat-Synth GeneralSynthesisOntology schema, producing one JSON file per paper with per-material synthesis records.
Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.
| name | chem-similarity-search |
| description | Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API. |
| category | ["chemistry","drug-discovery"] |
To programmatically find chemical analogs, alternative precursors, and structurally similar compounds for a given target molecule using PubChem's "fastsimilarity_2d" endpoint. The skill retrieves lists of similar compounds ranked by sequence alignment of their 2D molecular fingerprints, providing CIDs, molecular weights, formulas, and SMILES strings.
Search for similar compounds by providing the canonical or isomeric SMILES.
Adjust the --threshold (similarity cutoff 0-100, default is 95) to widen or narrow the search radius. Higher threshold equals higher similarity.
Adjust --max_records to limit the output length.
# Env: base-agent
python .agents/skills/chem-similarity-search/scripts/similarity_search.py \
--smiles "CC(=O)Oc1ccccc1C(=O)O" \
--threshold 95 \
--max_records 5 \
--outdir research/aspirin_similar \
--output aspirin_similar.json
Search directly using an exact compound's CID. This avoids translation steps for SMILES parsing.
# Env: base-agent
python .agents/skills/chem-similarity-search/scripts/similarity_search.py \
--cid 2244 \
--threshold 90 \
--max_records 10 \
--outdir research/aspirin_similar \
--output cid_2244_similar.json
We can test extracting highly similar analogs (Threshold 95) for Aspirin (CID: 2244 or SMILES: CC(=O)Oc1ccccc1C(=O)O).
# Env: base-agent
python .agents/skills/chem-similarity-search/scripts/similarity_search.py \
--cid 2244 \
--threshold 95 \
--max_records 5 \
--outdir .agents/skills/chem-similarity-search/examples/aspirin_analogs \
--output aspirin_analogs.json
HTTP 503 Server Busy errors. The script implements an exponential backoff retry mechanism.Author: Bowen Deng Contact: GitHub @learningmatter-mit