Conversion & Optimization of Molecular Database Queries

SMACK [1] efficiently converts substructure and reaction queries expressed in MDL file format to SMARTS strings. SMACK subsequently optimizes each resulting query for pattern-matching performance. Typical transformations simplify redundant atom and bond expressions and reorder atoms for faster matching against medicinal/organic chemistry databases [2].

Features

• Reads queries in MDL file formats - Mol, RG, Rxn - from programs such as MDL's ISIS/Draw or CambridgeSoft's ChemDraw [3]
• Reads and writes SMARTS and SMIRKS queries for instance for Daylight's DayCart or Merlin database systems [4]
• Converts queries from MDL to SMARTS
• Optimizes queries for database searching [2]
• Optimizes a SMARTS query for output in the same format
• Support for Linux, Windows, Mac OS X and many flavors of Unix in both 32 and 64 bit.

[1] Because after something is SMACKed, it SMARTS.

[2] "1st-Class SMARTS Patterns", Roger Sayle, Daylight EuroMUG 97, Verona, Italy, October 1997.

[3] MDL CTFile formats

[4] Daylight SMARTS and SMIRKS