Daylight Theory
Use when working with SMILES, SMARTS, SMIRKS, molecular fingerprints, or cheminformatics fundamentals. Covers the complete Daylight theory: molecular graph representation, SMILES specification, SMARTS query language, SMIRKS reaction transforms, and fingerprint-based similarity. Based on the Daylight Theory Manual.
Install
$ agentstack add skill-kdevos12-alkyl-daylight-theory ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/skill-kdevos12-alkyl-daylight-theory) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.
How agent discovery & health will work →About
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)
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: Kdevos12
- Source: Kdevos12/ALKYL
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.