Daylight Summer School 2002, June 5-7, Santa Fe, NM

Languages and Applications - Day 1
Lab/Lecture Outline and Links



  • Simple forms
  • SMILES syntax rules
  • Isomeric SMILES
  • Canonical SMILES
  • Reaction SMILES
  • Simple forms
  • SMARTS syntax rules
  • Atom and bond primitives, operators
  • Recursive SMARTS (vectors)
  • SMILES are nomenclature
  • SMARTS are for matching/searching
  • SMIRKS are for transforming
  • Fingerprints are bitmaps
  • Used for similarity and screening
Thor Data Trees (TDTs)
  • Datatypes
  • Root identifiers
  • Cross-reference identifiers
  • Non-identifiers (data)

Database Applications:

xvthor X Thor client
xvmerlin X Merlin client (and Thor client)
MCL Merlin Control Language
Thorfilters command-line Thor/Merlin tools
sthorman serial Thor/Merlin admin tool

Other Applications:

PrintPackage PostScript structure and data output
PCModels (ClogP and CMR) xvpcmodels, clogp and cmr apps
Clustering Package nearneighbors, jarpat, listclusters and showclusters
Rubicon Rule-based Invention of Conformers

Web Applications:

JavaGrins molecular and smarts editor applet and application
DayCGI web apps and tools


Lab Activities - Languages and Applications

  1. SMILES Practice- Compose SMILES, Isomeric SMILES, and Reaction SMILES from depictions, self test w/ smipractice.cgi.
  2. SMARTS Practice - Compose SMARTS for described chemical target substructures / functional groups. Recursive and disconnected SMARTS. Self test using depictmatch.cgi.
  3. TDT Retrieval and editing with xvthor - running xvthor and experimenting with its various features.
  4. Structural, Non-Structural, and Reaction Searching - exploratory data analysis techniques with Merlin including Reaction SMILES and SMARTS
  5. Thorfilters/Sthorman - thorlookup, thorlist, etc. also generating poscript with prado from printpackage
  6. PCModels/PCFilters - running xvpcmodels, clogp and cmr in various modes.
  7. Cluster Package - generating a clustered dataset, jarpat, listclusters, showclusters, etc.
  8. Rubicon - generating 3D coordinates for a TDT file
  9. DayCGI - using the web applications, JavaGrins.

Daylight Chemical Information Systems Inc.