Xpersona
agentCLAWHUBUnverified

Small molecule design

Small-molecule generation workflows combining REINVENT4, PocketXMol, fpocket, and Gnina Score through SciMiner.

OpenClaw
View on ClawHubHomepage

Rank

62

Safety

84

Downloads

1.1k

Updated

Oct 11, 2026

Version

1.0.5

Source

CLAWHUB

About

What it does, and when to use it.

Capability contract not published. No trust telemetry is available yet. 1.1K downloads reported by the source. Last updated 10/11/2026.

Avoid when

  • Contract metadata is missing or unavailable for deterministic execution.

Risk flags: missing_or_unavailable_contract, trust_data_unavailable, schema_references_missing

Public facts

Every fact links back to the source it came from.

Vendor
Clawhubvendor · observed Oct 11, 2026
Protocol compatibility
OpenClawcompatibility · observed Oct 11, 2026
Adoption signal
1.1K downloadsadoption · observed Oct 11, 2026
Latest release
1.0.5release · observed May 31, 2026
Handshake status
UNKNOWNsecurity

Install and run

Setup complexity: low.

clawhub skill install s170qp1q4twz35wa85ppa8894h83w461:small-molecule-design
  1. Install using `clawhub skill install s170qp1q4twz35wa85ppa8894h83w461:small-molecule-design` in an isolated environment before connecting it to live workloads.
  2. No published capability contract is available yet, so validate auth and request/response behavior manually.
  3. Review the upstream CLAWHUB listing at https://clawhub.ai/sciminer/small-molecule-design before using production credentials.

Contract: missing

curl -s "https://www.xpersona.co/api/v1/agents/clawhub-sciminer-small-molecule-design/snapshot"

Documentation

CLAWHUB

62,422 characters of source documentation, loaded on request.

Extracted files

3 files captured from the source.

SKILL.md

---
name: small-molecule-design
description: Small-molecule generation workflows combining REINVENT4, PocketXMol, fpocket, and Gnina Score through SciMiner.
credential_files:
   - ~/.config/sciminer/credentials.json
---

# Small-Molecule Design Skill

This skill groups small-molecule generation and validation workflows, including:

- structure-free de novo generation and optimization with REINVENT4
- structure-based pocket-guided small-molecule design with PocketXMol
- predicted pocket detection with fpocket for structure-based design
- post-generation validation of PocketXMol molecules with Gnina Score

## When to use this skill

- Generate small molecules from scratch without a receptor structure
- Optimize molecules with transfer learning or reinforcement learning in REINVENT4
- Design molecules directly inside a known protein pocket with PocketXMol
- Run fragment linking or fragment growing against a protein structure
- Validate PocketXMol-generated molecules against the target receptor with Gnina Score

## Method selection rule

- If a protein structure file or PDB ID is provided, use `PocketXMol` for molecule design.
- For that structure-based path, use `fpocket` first to predict the binding pocket when the user has no explicit pocket coordinates.
- After PocketXMol generates molecules, validate the generated molecules with `Gnina Score`.
- If no protein structure file or PDB ID is provided, use `REINVENT4`.

## Prerequisites

1. Obtain a free SciMiner API key from `https://sciminer.tech/utility`.
2. Store it outside this repository at `~/.config/sciminer/credentials.json` with JSON shaped as `{"api_key":"your_api_key_here"}`.
3. For SciMiner calls, read the API key from `~/.config/sciminer/credentials.json` and send it as the `X-Auth-Token` header.
4. Never print, persist, or store the API key in prompts, logs, or repository files. Agents should remember only the credential file path.

If `~/.config/sciminer/credentials.json` is not available or does not contain an `api_key` field, stop and tell the user to obtain a free SciMiner API key from `https://sciminer.tech/utility` and store it in that file. Do not try to complete the task by switching to other tools or services.

## Authoritative tool-doc source (required)

The published Markdown files under `https://sciminer.tech/tool_api_files/` are
the single source of truth for `provider_name`, `tool_name`, allowed
`parameters`, file-upload behavior, request encoding, and the example
submission flow for this skill's included tools.

Use these SciMiner Markdown docs:

- `REINVENT4` -> `REINVENT4_api_doc.md`
- `PocketXMol` -> `PocketXMol_api_doc.md`
- `fpocket` -> `fpocket_api_doc.md`
- `Gnina Score` -> `Gnina Score_api_doc.md`

The agent MUST:

1. Resolve the selected tool's Markdown file and read it before every
   invocation.
2. Never invent `provider_name`, `tool_name`, parameter names, enum values,
   upload-field names, content type, or submission flow from memory.
3. Extract and follow t

_meta.json

{
  "ownerId": "kn725br751g8y5tkj1h6d2krf58356et",
  "slug": "small-molecule-design",
  "version": "1.0.5",
  "publishedAt": 1780221806143
}

skill-card.md

## Description:

Small-molecule generation workflows combining REINVENT4, PocketXMol, fpocket, and Gnina Score through SciMiner.

This skill is ready for commercial/non-commercial use.

## Publisher:

[sciminer](https://clawhub.ai/user/sciminer)

### License/Terms of Use:

MIT-0

## Use Case:

Developers and computational chemistry researchers use this skill to generate, optimize, and validate small molecules through SciMiner-hosted REINVENT4, PocketXMol, fpocket, and Gnina Score workflows.

### Deployment Geography for Use:

Global

## Known Risks and Mitigations:

Risk: Mutable remote SciMiner documentation controls authenticated API calls and file uploads.

Mitigation: Review the selected SciMiner documentation before each run, restrict calls to the documented SciMiner endpoints, and prefer versions that vendor fixed schemas or validate remote docs against a strict allowlist.

Risk: SciMiner workflows require an API key and may upload molecular structures or receptor files.

Mitigation: Use a narrowly scoped, revocable SciMiner API key stored outside the repository, avoid exposing it in prompts or logs, and do not upload sensitive unpublished structures unless the SciMiner documentation source is trusted.

## Reference(s):

- [ClawHub skill page](https://clawhub.ai/sciminer/skills/small-molecule-design)
- [SciMiner tool API files](https://sciminer.tech/tool_api_files/)
- [REINVENT4 API documentation](https://sciminer.tech/tool_api_files/REINVENT4_api_doc.md)
- [PocketXMol API documentation](https://sciminer.tech/tool_api_files/PocketXMol_api_doc.md)
- [fpocket API documentation](https://sciminer.tech/tool_api_files/fpocket_api_doc.md)
- [Gnina Score API documentation](https://sciminer.tech/tool_api_files/Gnina%20Score_api_doc.md)
- [SciMiner API key utility](https://sciminer.tech/utility)

## Skill Output:

**Output Type(s):** [text, markdown, code, shell commands, configuration, guidance]

**Output Format:** [Markdown with JSON examples and code or shell command snippets]

**Output Parameters:** [1D]

**Other Properties Related to Output:** [Successful SciMiner task summaries should include task identifiers and share_url links.]

## Skill Version(s):

1.0.5 (source: server release metadata)

## Ethical Considerations:

Users should evaluate whether this skill is appropriate for their environment, review any generated or modified files before relying on them, and apply their organization's safety, security, and compliance requirements before deployment.

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Machine-readable data

The same record, as JSON, for agents and crawlers.

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Record generated Oct 11, 2026.

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