Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add InternScience/MolClaw --skill molclaw-interaction-visualizergit clone --depth 1 https://github.com/InternScience/MolClawWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/internscience/molclaw/molclaw-interaction-visualizer)<a href="https://agentmods.dev/skills/internscience/molclaw/molclaw-interaction-visualizer"><img src="https://agentmods.dev/badge/skills/internscience/molclaw/molclaw-interaction-visualizer/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/internscience/molclaw/molclaw-interaction-visualizer"><img src="https://agentmods.dev/badge/skills/internscience/molclaw/molclaw-interaction-visualizer.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium analysis-evasion · line 1 Suspicious Unicode normalization or mixed-script contentFix: Review the flagged content for security risks. Ensure no credentials, secrets, or sensitive data are exposed.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00121 | $0.06114 |
| Opus 5.5 | $0.00048 | $0.02446 |
| Sonnet 5.5 | $0.00024 | $0.01223 |
| Haiku 4.5 | $0.00012 | $0.00611 |
Grade A, and why
molclaw-interaction-visualizer scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 423 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Interaction Visualizer — MCP and Local Analysis
Invocation
Use the exact tool name and parameter schema exposed by the current harness. Tool names in SDK examples below are raw MCP names, not model-facing aliases. Local files must be uploaded with molclaw-file-transfer before a server tool can use them. Repair PDB inputs first when the workflow requires it.
[!NOTE] The current MolClaw server exposes this capability as the MCP tool
interaction_visualizer. The bundledmolclaw_interaction_visualizer.pyremains available as an optional local CLI; it does not need to be uploaded to the server.
When To Use This Skill
This is the PRIMARY tool for all single-structure interaction analysis. ProLIF is only needed for batch docking fingerprint comparison or MD trajectory dynamics.
| Scenario | Use this skill | Use ProLIF instead |
|---|---|---|
| Single complex structure interaction analysis | ✅ PRIMARY | Only if this tool unavailable |
| Peptide or protein-protein interface analysis (single structure) | ✅ PRIMARY | Only if this tool unavailable |
| Need Schrödinger-style 2D interaction diagram | ✅ | ❌ |
| Need PyMOL 3D multi-angle renderings | ✅ | ❌ |
| Need residue role annotations (Hinge/Gatekeeper/DFG) | ✅ | ❌ |
| Need decision-ready JSON with top residues + hot sites | ✅ | ❌ |
Need partner_site.csv for ligand atom modification diagnosis |
✅ | ❌ |
| Need interaction fingerprint across MD trajectory frames | ❌ | ✅ prolif_md |
| Need batch docking pose fingerprint comparison (≥ 2 poses) | ❌ | ✅ prolif_docking |
| Need protein-protein trajectory interface profiling | ❌ | ✅ prolif_protein_protein |
Interaction Types Detected
| # | Type | Key Geometry | Default Cutoff |
|---|---|---|---|
| 1 | Hydrogen bond | D-H···A angle ≥ 130° | 3.5 Å |
| 2 | Hydrophobic contact | C···C distance | 4.5 Å |
| 3 | π-π stacking (Face-to-Face) | Ring plane ∠ ≤ 35° | 5.5 Å |
| 4 | π-π stacking (Edge-to-Face) | Ring plane ∠ 50°–90° | 6.5 Å |
| 5 | Salt bridge | Charge center distance | 5.5 Å |
| 6 | Cation-π | Cation-centroid + normal ∠ | 6.0 Å |
| 7 | Halogen bond | X···A with A-X-D geometry | 3.5 Å |
| 8 | Metal coordination | Metal···coordinating atom | 3.0 Å |
| 9 | van der Waals | Sum of VdW radii + tolerance | +0.5 Å |
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago Changed · -7 lines · +9 tokens per session 7af5ff2c848e
- 1mo ago First seen · 430 lines · 112 tokens per session scan A fc747d3a9935
molclaw-interaction-visualizer is a skill published in the GitHub repository InternScience/MolClaw (38 stars, last pushed 1mo ago), licensed MIT. It adds 121 tokens to every session and 6,114 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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