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Daylight theory

Skill Kdevos12/ALKYL/skills/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.From its SKILL.md

Install
npx -y skills add Kdevos12/ALKYL --skill daylight-theory

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SKILL.md

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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

TopicReference
Molecular graph model, aromaticity, chirality, SSSR, reaction representationreferences/molecules.md
SMILES syntax: atoms, bonds, branches, rings, stereochemistry, reactionsreferences/smiles.md
SMARTS query language: primitives, operators, recursive SMARTS, reaction queriesreferences/smarts.md
SMIRKS reaction transforms: atom maps, grammar, stereochemistryreferences/smirks.md
Fingerprints: structural keys, path-based FP, folding, Tanimoto, Tversky, all similarity measuresreferences/fingerprints.md
Chemical database concepts: hash tables, identifiers, in-memory search, pools, hitlistsreferences/cheminformatics-databases.md

Core Languages at a Glance

LanguagePurposeExample
SMILESEncode a specific moleculeCC(=O)Oc1ccccc1C(=O)O
SMARTSDescribe a molecular pattern[OH]c1ccccc1 (phenol)
SMIRKSEncode 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: O in 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 Python
  • scientific-skills:matchms — spectrum similarity (same mathematical ideas)

What ships with it: 6 files

39.8 KB alongside SKILL.md

references/

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