Intro to Daylight

The purpose of this talk is to set the stage for the presentations of new developments at Daylight and user research projects to follow.

In lieu of introductory tutorials on the Daylight suite of software tools, I will attempt to provide an overview of the Daylight system and approach so new users will have perhaps an adequate background for making sense of the presentations to follow. For those already expert in Daylight, this will be a review.

I will then briefly list the new developments at Daylight and featured at this meeting by Daylight and our partners.

Views of the Daylight System

It is possible to view a software system from several distinct perspectives. The programmer must be concerned with every line of source code. A user requires some higher level of abstraction which is:

Meaningful in relating to the science.
Powerful enough to do the task and more.
Flexible to evolve and adapt with users and tasks.
Simple enough to be used widely and productively.

(... and last but not least, has a cute name.)

For many simple tasks, accomplished with Daylight X-windows or web applications, the user interface requires only that the user draw a chemical structure and click a submit button.

It is a goal of some that computers learn to interact with humans via natural language and thereby merge the means of human-human and human-machine communication. But for now, point-and-click GUI's are generally agreed to be the user-friendliest.

But to achieve Power and Flexibility we need to appreciate the system on a deeper level.

The Application View:

The Object/Toolkit View:

The Language View:

The Languages of Daylight

Date Language and... Toolkits (4.5x) Applications (4.5x)
1983 SMILES Simplified Molecular Input Line Entry System introduced (at EPA by David Weininger) SMILES, etc. All!
1984 SMILES Canonicalization algorithm makes Thor possible. SMILES, Thor, etc. Thor, Merlin



Recursive SMARTS

SMILES ARbitrary TargetS introduced, subgraph pattern language, superset of SMILES SMARTS, Merlin Merlin
1986 TD T Thor Data Trees introduced Thor Thor
1987 Fingerprints Fingerprints and their ASCII encoding makes Merlin possible. Fingerprint, Merlin Merlin, MCL
1989 Isomeric SMILES Stereoisomeric and isotopic SMILES introduced. SMILES, etc. Thor, Merlin , etc.
1990 C port (4.1) allows arbitrary length SMILES (>512)
1990 Daylight Toolkit API - Stable toolkit function libraries.
1993 Chuckles
Combinatorial chemistry tools introduced. SMILES, Monomer Thor, Merlin
1994 MCL Merlin Control Language Merlin MCL
1995 CEX Free CEX tools from CEX consortium.    
1996 Reaction SMILES Reaction SMILES introduced SMILES, Reaction Thor, Merlin
1996 DayPerl DayPerl contributed by Alex Wong and Chiron.
1996 HTML/CGI DayHTML and DayCGI tools introduced. DayCGI Thor, Merlin, custom apps
1998 Daylight Java Tools introduced.

What's New at Daylight


  • Informix
  • Oracle
  • MSI (Diversity Explorer, etc.)
  • Synopsys (Accord)
  • Derwent (Patents)
  • CambridgeSoft
  • Bioreason
  • NetGenics
  • DataAspects
  • BioByte
  • CAS


  • New code:

  • Daylight JavaGRINS and Java Tools
  • SMIRKS 4.6 extensions ("SMART-er")
  • FPP Reaction searching
  • ClogP update
  • Daylight scripting wrappers
  • 64-bit clean port
  • PC Remote Toolkit Update (Win95/NT)

    New Databases:

  • WDI 98.1 (Derwent)
  • ACD 97.2 (MDL)
  • CCR 98.1 (soon) (ISI)
  • Asinex
  • Interbioscreen Natural Products
  • Interbioscreen Synthetic Chemicals
  • Spresi Reactions (Infochem)
  • Index Chemicus 1961-87 (ISI)
  • Index Chemicus 98.1 (soon) (ISI)

  • Daylight Chemical Information Systems Inc.