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chem-similarity-search

Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.

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Prix non confirmé★ 161 Stars GitHubRegistre mis à jour · 6 sept. 2026agent-skill

Vue d’ensemble

Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.

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Documentation source, pas des instructions pour ce site. Vérifiez les permissions avant d’exécuter des commandes.

Chemical Similarity Search

Goal

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.

Instructions

1. Search by SMILES String

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

2. Search by PubChem CID

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

Examples

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

Constraints

Rate Limiting: PubChem PUG REST API enforces per-user throttling limits. Heavy bursts will result in HTTP 503 Server Busy errors. The script implements an exponential backoff retry mechanism.
2D Similarity: Uses exact structural bit-vector fingerprints. Stereochemical and 3D properties do not strongly affect the score.
Network: Internet access is required.

Author: Bowen Deng Contact: GitHub @learningmatter-mit

Voir la source ↗

Métadonnées du fichier

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]

Voir le texte original

---
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]
---

# Chemical Similarity Search

## Goal
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.

## Instructions

### 1. Search by SMILES String
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.

```bash
# 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
```

### 2. Search by PubChem CID
Search directly using an exact compound's CID. This avoids translation steps for SMILES parsing.

```bash
# 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
```

## Examples

We can test extracting highly similar analogs (Threshold 95) for Aspirin (CID: 2244 or SMILES: `CC(=O)Oc1ccccc1C(=O)O`).

```bash
# 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
```

## Constraints
- **Rate Limiting**: PubChem PUG REST API enforces per-user throttling limits. Heavy bursts will result in `HTTP 503 Server Busy` errors. The script implements an exponential backoff retry mechanism.
- **2D Similarity**: Uses exact structural bit-vector fingerprints. Stereochemical and 3D properties do not strongly affect the score.
- **Network**: Internet access is required.

---
---

**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

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Licence: MIT
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Réviser avant installation: Éviter l’installation automatique

Licence: MIT

Dependency or permission surface needs review
Permission surface may require sandboxing
The SKILL.md excerpt shows an incomplete line in the script (e.g., 'elif' with no following code), but this is likely due to truncation in the provided excerpt and not a real issue.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

Ouvrir l’audit complet

Les outils sont des indications de métadonnées, pas une compatibilité testée. Les prompts sont des suggestions.

Commencer par une petite tâche

1Lisez la source et confirmez entrées, résultats, dépendances et permissions.
2Demandez un plan à l’agent. Approuvez la configuration et les coûts avant un test isolé.
3Vérifiez résultats et fichiers modifiés. Signalez uniquement ce qui a été exécuté et conservez la révision source.

Vérifiez les dépendances, clés API et frais externes dans la source. Un dépôt public ne rend pas tous les services gratuits.

Source et conseils d’utilisation

Répertorié

Métadonnées et examens sont indicatifs. Popularité, découverte et exécution réussie sont des faits distincts.

Dépôt source: learningmatter-mit/AtomisticSkills
Licence: MIT
Version: 1.0.0
Dernier push GitHub: 3 sept. 2026
Registre mis à jour: 6 sept. 2026
Chemin des instructions: .agents/skills/chem-similarity-search/SKILL.md @ d1f7ecfda2cd

Version déclarée dans le registre ; vérifiez les versions de la source.

Qualité

66/100

Prometteur

Confiance

60/100

Sandbox uniquement

Audit

73/100

Revue nécessaire

Ouvrir l’audit complet Voir le rapport d’évaluation

Dependency or permission surface needs review
Permission surface may require sandboxing
The SKILL.md excerpt shows an incomplete line in the script (e.g., 'elif' with no following code), but this is likely due to truncation in the provided excerpt and not a real issue.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

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Résultats: —

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Plus de détails

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Source: learningmatter-mit/AtomisticSkills
Indexé par: Index communautaire OpenAgentSkill

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