# Molclaw Mol Topology Metrics

> Compute a comprehensive set of topological descriptors for a list of SMILES strings, returning the Topological Polar Surface Area (TPSA), a series of valence and non-valence molecular connectivity indices (Chi0–Chi4), the Hall–Kier alpha value, and Kappa shape indices (Kappa1–Kappa3) for each input molecule.

- Skill: `internscience/molclaw-mol-topology-metrics` (Agent Skill)
- Install (CLI): `npx skillmds@latest add internscience/molclaw-mol-topology-metrics`
- Raw SKILL.md: https://api.skillmd.com/api/skills/internscience/molclaw-mol-topology-metrics/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: MIT license
- Author: internscience (https://skillmd.com/u/internscience)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/internscience/molclaw-mol-topology-metrics

---


# Molecular Topology Properties 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.

The description of tool *calculate_mol_topology*.

```tex
Compute a set of topological descriptors for each SMILES.
Args:
    smiles_list (List[str]): List of input SMILES strings, (e.g., ["N[C@@H](Cc1ccc(O)cc1)C(=O)O", "CC(C)C1=CC=CC=C1"])
Return:
    status (str): success/error
    msg (str): message
    metrics (List[dict]): List of dict, each containing several feature keys.
        --smiles (str): A SMILES string of smiles_list
        --tpsa (float): Topological polar surface area
        --chi0v (float): Non-valence molecular connectivity index
        --chi1v (float): Non-valence molecular connectivity index
        --chi2v (float): Non-valence molecular connectivity index
        --chi3v (float): Non-valence molecular connectivity index
        --chi4v (float): Non-valence molecular connectivity index
        --chi0n (float): Non-valence molecular connectivity index
        --chi1n (float): Non-valence molecular connectivity index
        --chi2n (float): Non-valence molecular connectivity index
        --chi3n (float): Non-valence molecular connectivity index
        --chi4n (float): Non-valence molecular connectivity index
        --hall_kier_alpha (float): Hall–Kier alpha value
        --kappa1 (float): Kappa shape index
        --kappa2 (float): Kappa shape index
        --kappa3 (float): Kappa shape index
```

How to use tool *calculate_mol_topology*:

```python
response = await client.session.call_tool(
    "calculate_mol_topology",			
    arguments={
        "smiles_list": smiles_list
    }
)
result = client.parse_result(response)
metrics = result["metrics"]
```