EuroMUG'01 - Sept. 12-14, 2001 - Cambridge, UK

Glossary of Daylight Terms

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 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
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
Web tools. JavaGRINS = molecular and graphical SMARTS editor DayCGI Manual
JavaGRINS Manual
CEX Chemical EXchange mechanism for interprocess communication CEX Home Page


Daylight Chemical Information Systems