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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-pubchemgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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/alterlab-ieu/alterlab-academic-skills/alterlab-pubchem)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pubchem"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pubchem/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/alterlab-ieu/alterlab-academic-skills/alterlab-pubchem"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pubchem.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00089 | $0.01140 |
| Opus 5 | $0.00044 | $0.00570 |
| Sonnet 5 | $0.00018 | $0.00228 |
| Haiku 4.5 | $0.00009 | $0.00114 |
Grade A, and why
alterlab-pubchem scanned grade A with 1 finding 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 6d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) How it starts
The opening of the file, as written. The whole thing — 99 lines — stays where its author put it; the contents beside it link to each section on GitHub.
PubChem Database
Overview
PubChem is the world's largest freely available chemical database with 110M+ compounds and 270M+ bioactivities. Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, and access bioactivity data using the PUG-REST API and PubChemPy.
When to Use This Skill
This skill should be used when:
- Searching for chemical compounds by name, structure (SMILES/InChI), or molecular formula
- Retrieving molecular properties (MW, LogP, TPSA, hydrogen bonding descriptors)
- Performing similarity searches to find structurally related compounds
- Conducting substructure searches for specific chemical motifs
- Accessing bioactivity data from screening assays
- Converting between chemical identifier formats (CID, SMILES, InChI)
- Batch processing multiple compounds for drug-likeness screening or property analysis
Core Capabilities
PubChem access is organized into nine capability areas. Copy-ready snippets for each live in
references/capabilities.md.
- Chemical structure search — by name, CID, SMILES, InChI, or molecular formula.
- Property retrieval — single, specific-list, or batch molecular properties.
- Similarity search — Tanimoto similarity with threshold/MaxRecords.
- Substructure search — find compounds containing a structural motif.
- Format conversion — CID/SMILES/InChI/InChIKey and structure-file download.
- Structure visualization — 2D PNG images via PubChemPy or direct URL.
- Synonym retrieval — all known names for a compound.
- Bioactivity data access — assay summaries via PUG-REST and helper script.
- Comprehensive annotations — full PUG-View records (properties, drug info, safety, toxicity).
Core Workflow
The canonical entry point resolves an identifier to a compound, then reads properties:
import pubchempy as pcp
compound = pcp.get_compounds('aspirin', 'name')[0]
print(compound.cid, compound.molecular_formula, compound.molecular_weight)
print(compound.smiles, compound.xlogp, compound.tpsa)
What ships with it
8 files 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.
- 6d ago First seen · 99 lines · 89 tokens per session scan A 27d584427588
alterlab-pubchem is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 7d ago), licensed MIT. It adds 89 tokens to every session and 1,140 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-05.
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