| Term | Definition | Key algorithm(s) | Refs |
| SMILES | Language for representation of molecules | SMILES canonicalization: Generate unique SMILES for any molecule. Thus, SMILES is a nomenclature for chemistry and viable primary key for databases. |
SMILES Manual SMILES Home Page SMILES paper #2 |
| SMARTS | Language for molecular pattern matching | Recognize generic molecular substructures (e.g., functional groups). |
SMARTS Manual SMARTS Examples |
| Reaction SMILES | Language for representation of reactions | Handle reactants/agents/products, optional atom-mappings. | Theory Manual |
| Reaction SMARTS | Language for reaction/molecular pattern matching | SMARTS w/ reaction role recognition. | Theory Manual |
| SMIRKS | Language for reaction transforms | Virtual chemistry: transform reactants to products. |
Theory Manual SMIRKS Examples |
| CHUCKLES, CHORTLES, & CHARTS | Language for monomers, mixtures, and pattern matching, respectively | Enumerate combinatorial mixtures only when needed. | Theory Manual |
| THOR | THesaurus-Oriented Retreival chemical DBMS. Disk-based data archival. Works with Merlin. | Hashing-based for fast, constant-time exact lookups. | Admin Manual |
| TDT | THOR Data Tree; data structure for Thor. | Handle ambiguous and overlapping identifiers. | Admin Manual |
| MERLIN | High-speed exploratory data analysis; read-only; works with Thor. | RAM intensive. | Admin Manual |
| MCL | MERLIN Control Language | English-language scripting. | MCL Manual |
| Fingerprint | Compact structural descriptor stored as bitmap (bit-array). | Similarity (Tanimoto, Euclidean, Tversky) and fast-screening computataions. | Theory Manual |
| Clustering and Diversity | Clustering is grouping of a set of compounds based on structural or other similarity. Diversity is non-similarity. | Jarvis-Patrick clustering. Parallelized nearneighbor calculation. | Clustering Package Manual |
| toolkit | The Daylight Toolkit is a set of programming libraries which are available commercially and the basis for Daylight application software. | OOP-ish, stable API. | Toolkit Programmer's Guide |
| Contrib | Repository of open-source Daylight toolkit code | E.g.: Stigmata, TPSA (polar surface), chifinger, make_parents, etc. | Contrib at www.daylight.com |
| DayCart | Daylight cartridge (plugin) for Oracle. Extends Oracle with chemistry capabilities. | Indices for chemical searching. | DayCart Manual |
| ClogP | Octanol/water partition coefficient calculator. | Fragment based w/ corrections and new frag-calc capability. | ClogP Manual BioByte Home Page |
| Rubicon | 3D conformation generation and analysis | Distance geometry methods (DGEOM). SMARTS-based customizable rules. | Rubicon Manual |
| DayCGI, JavaGRINS | Web tools. JavaGRINS = molecular and graphical SMARTS editor | DayCGI Manual JavaGRINS Manual | |
| CEX | Chemical EXchange mechanism for interprocess communication | CEX Home Page |
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