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 agentmods add skills/kdevos12/alkyl/daylight-theorynpx skills add Kdevos12/ALKYL --skill daylight-theorygit 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/daylight-theory)<a href="https://agentmods.dev/skills/kdevos12/alkyl/daylight-theory"><img src="https://agentmods.dev/badge/skills/kdevos12/alkyl/daylight-theory.svg" alt="Measured on agentmods" 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 | $0.00067 | $0.00615 |
| Opus 5 | $0.00034 | $0.00308 |
| Sonnet 5 | $0.00013 | $0.00123 |
| Haiku 4.5 | $0.00007 | $0.00061 |
Grade A, and why
daylight-theory 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 4d 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 — 41 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Daylight Theory — Cheminformatics Fundamentals
The Daylight Theory Manual is the canonical reference for the molecular languages underlying modern cheminformatics: SMILES, SMARTS, SMIRKS, and fingerprints. These are not Daylight-proprietary — they are industry-standard formats implemented in RDKit, OpenBabel, CDK, and every major cheminformatics toolkit.
Router — What to Read
| Topic | Reference |
|---|---|
| Molecular graph model, aromaticity, chirality, SSSR, reaction representation | references/molecules.md |
| SMILES syntax: atoms, bonds, branches, rings, stereochemistry, reactions | references/smiles.md |
| SMARTS query language: primitives, operators, recursive SMARTS, reaction queries | references/smarts.md |
| SMIRKS reaction transforms: atom maps, grammar, stereochemistry | references/smirks.md |
| Fingerprints: structural keys, path-based FP, folding, Tanimoto, Tversky, all similarity measures | references/fingerprints.md |
| Chemical database concepts: hash tables, identifiers, in-memory search, pools, hitlists | references/cheminformatics-databases.md |
Core Languages at a Glance
| Language | Purpose | Example |
|---|---|---|
| SMILES | Encode a specific molecule | CC(=O)Oc1ccccc1C(=O)O |
| SMARTS | Describe a molecular pattern | [OH]c1ccccc1 (phenol) |
| SMIRKS | Encode a reaction transform | [C:1][Br:2]>>[C:1][I:2] |
Key Principles
- Molecular graph: atoms = nodes, bonds = edges; properties are explicit or derived
- Aromaticity: Hückel 4N+2 rule, all ring atoms sp² — a derived, not stored, property
- SMILES organic subset: B, C, N, O, P, S, F, Cl, Br, I — no brackets needed at normal valence
- SMARTS unspecified = unrestricted:
Oin SMARTS matches any aliphatic oxygen; in SMILES it means water - Tanimoto: c/(a+b+c) — the standard fingerprint similarity; double-zero independent
Related ALKYL Skills
rdkit— implementation of these concepts in Pythonscientific-skills:matchms— spectrum similarity (same mathematical ideas)
What ships with it
6 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.
- 4d ago First seen · 41 lines · 0 tokens per session scan A b2fe956c62d6
daylight-theory is a skill published in the GitHub repository Kdevos12/ALKYL (6 stars, last pushed 5mo ago), licensed MIT. It adds 67 tokens to every session and 615 once invoked, about $0.0003 per session on Opus 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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rdkit
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