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 Kdevos12/ALKYL --skill chem-brainstormgit clone --depth 1 https://github.com/Kdevos12/ALKYLWrote 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/kdevos12/alkyl/chem-brainstorm)<a href="https://agentmods.dev/skills/kdevos12/alkyl/chem-brainstorm"><img src="https://agentmods.dev/badge/skills/kdevos12/alkyl/chem-brainstorm/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/kdevos12/alkyl/chem-brainstorm"><img src="https://agentmods.dev/badge/skills/kdevos12/alkyl/chem-brainstorm.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00050 | $0.01755 |
| Opus 5.5 | $0.00020 | $0.00702 |
| Sonnet 5.5 | $0.00010 | $0.00351 |
| Haiku 4.5 | $0.00005 | $0.00176 |
Grade A, and why
chem-brainstorm 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 — 175 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Chem-Brainstorm — Computational Chemistry Thinking Guide
A flexible brainstorming framework for comp chem problems. Not a rigid checklist — activate only the steps relevant to the problem at hand. For complex/recurring workflows, load the appropriate references/protocol-*.md.
Step 1 — Classify the Problem
Identify which mode(s) apply (can be multiple):
| Mode | Keywords | Protocol |
|---|---|---|
| MOL | "evaluate this molecule", "properties of X", "is this drug-like?" | references/protocol-mol-evaluation.md |
| HYP | "why does X work?", "what target?", "generate hypotheses", "SAR" | references/protocol-hypothesis.md |
| RXN | "will this reaction work?", "retrosynthesis", "conditions", "mechanism" | references/protocol-reaction.md |
| PIPE | "screen a library", "build a workflow", "automate", "batch" | references/protocol-pipeline.md |
For simple one-off questions (e.g. "LogP of aspirin"), skip to Step 3 directly.
Step 2 — Audit Inputs
What is available?
| Input type | Examples |
|---|---|
| Structure | SMILES, SDF, MOL, InChI, name |
| Library | .smi, .sdf, CSV with SMILES column |
| Target | Gene name, UniProt ID, PDB ID |
| Reaction | Reaction SMILES, SMARTS, conditions |
| Data | IC50/EC50 table, experimental results |
| None | Starting from a concept only |
Missing inputs → note what to fetch (Step 3 MCPs).
Step 3 — Tool Map
Match inputs and goal to available tools. Order = cost (⚡ fast → ⚡⚡⚡ expensive).
ALKYL Scripts (local, instant)
| Goal | Script | Cost |
|---|---|---|
| Properties, Lipinski, PAINS | chem_props.py |
⚡ |
| Drug-likeness filters (Ro5/Veber/Egan/PAINS) | chem_filter.py |
⚡ |
| Full structural analysis (FG, stereo, QED, SA) | chem_analyze.py |
⚡ |
| Protonation state at pH | chem_pka.py --ph 7.4 |
⚡ |
| CYP450 metabolic soft spots | chem_metabolism.py |
⚡ |
| Scaffold, BRICS fragments | chem_scaffold.py |
⚡ |
| Tautomers, stereoisomers | chem_tautomers.py / chem_enum.py |
⚡ |
| Substructure / similarity search | chem_search.py |
⚡ |
| Compare two molecules (MCS, Δprop) | chem_compare.py |
⚡ |
| Apply reaction SMARTS | chem_react.py |
⚡ |
| Batch process a library | chem_batch.py |
⚡ |
| Diverse subset selection | chem_diversity.py |
⚡ |
| 3D conformer generation | chem_3d.py |
⚡⚡ |
| QM input (ORCA/Gaussian) | chem_qm.py |
⚡⚡⚡ |
What ships with it
4 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.
- 1mo ago First seen · 175 lines · 50 tokens per session scan A d074a12d1687
chem-brainstorm is a skill published in the GitHub repository Kdevos12/ALKYL (7 stars, last pushed 7mo ago), licensed MIT. It adds 50 tokens to every session and 1,755 once invoked, about $0.0002 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 2026-08-31.
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