# Molclaw Mol Similarity

> Calculate both Tanimoto similarities and the count of shared structural fragments between a target molecule and a list of candidate molecules via Morgan fingerprints.

- **Type:** Skill
- **Install:** `agentstack add skill-internscience-molclaw-molclaw-mol-similarity`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [InternScience](https://agentstack.voostack.com/s/internscience)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [InternScience](https://github.com/InternScience)
- **Source:** https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-mol-similarity

## Install

```sh
agentstack add skill-internscience-molclaw-molclaw-mol-similarity
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Molecule Similarity Calculation

Note: 
- Local files are not directly accessible by the server. Please upload them to the server using `molclaw-file-transfer` before execution. 
- For PDB file inputs, it is recommended to preprocess them using `molclaw-pdbfixer` before execution.
- Please refer to skill `molclaw-scp-server` to complete tool invocation.

**Scene 1**: Compute the Tanimoto similarities between a target molecule and a list of candidate molecules using Morgan fingerprints. Need to use the tool *calculate_morgan_fingerprint_similarity*.

The description of tool *calculate_morgan_fingerprint_similarity*.

```tex
Compute the Tanimoto similarities between a target molecule and a list of candidate molecules using Morgan fingerprints.
Args:
    target_smiles (str): SMILES string of the target molecule
    candidate_smiles_list (List[str]): List of candidate molecule SMILES strings
    radius (int): Morgan fingerprint radius, default is 2
    nBits (int): Morgan fingerprint vector bits number, default is 2048
Return:
    status (str): success/error
    msg (str): message
    similarities (List[dict]): List of dict, each containing the keys 'smiles' and 'score'.
        --smiles (str): A SMILES string of candidate_smiles_list
        --score (float): Similarity value between the candidate SMILES and the target SMILES
```

How to use tool *calculate_morgan_fingerprint_similarity* :

```python
response = await client.session.call_tool(
    "calculate_morgan_fingerprint_similarity",
    arguments={
        "target_smiles": target_smiles,
        "candidate_smiles_list": candidate_smiles_list,
        "radius": radius,
        "nBits": nBits
    }
)
result = client.parse_result(response)
similarities = result["similarities"]
```

**Scene 2**: Compute the count of shared structural fragments between a target molecule and a list of candidate molecules using Morgan fingerprints. Need to use the tool *calculate_common_fragments*.

The description of tool *calculate_common_fragments*.

```tex
Compute the count of shared structural fragments between a target molecule and a list of candidate molecules using Morgan fingerprints.
Args:
    target_smiles (str): SMILES string of the target molecule
    candidate_smiles_list (List[str]): List of candidate molecule SMILES strings
    radius (int): Morgan fingerprint radius, default is 2
Return:
    status (str): success/error
    msg (str): message
    fragments_info (List[dict]): List of dict, each containing the keys 'smiles' and 'common_fragment_count'.
        --smiles (str): A SMILES string of candidate_smiles_list
        --common_fragment_count (float): Number of structural fragments shared between the candidate SMILES and the target SMILES
```

How to use tool *calculate_common_fragments* :

```python
response = await client.session.call_tool(
    "calculate_common_fragments",
    arguments={
        "target_smiles": target_smiles,
        "candidate_smiles_list": candidate_smiles_list,
        "radius": radius
    }
)
result = client.parse_result(response)
fragments_info = result["fragments_info"]
```

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [InternScience](https://github.com/InternScience)
- **Source:** [InternScience/MolClaw](https://github.com/InternScience/MolClaw)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-internscience-molclaw-molclaw-mol-similarity
- Seller: https://agentstack.voostack.com/s/internscience
- Browse the marketplace: https://agentstack.voostack.com/browse

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