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Estimate structural complexity


TopoPlex is a software tool for estimating molecular structure complexity based on a user-provided starting material database. The structural complexity analysis performed by TopoPlex provides a rapid and effective ranking technique which can be used for estimating synthetic accessibility, or for elimination of structures with unfeasible molecular motifs.

The method is based upon the common assumption that a structure has low structural complexity if it contains chain and ring structural motifs (patterns) which frequently occur in existing drugs or commercially available starting materials.

The diagram on the right demonstrates the enumeration of chain and ring patterns of an input structure.


  • Is an easy-to-use command-line tool
  • Estimates molecular structure complexity
  • Comes with two complexity databases and the combination of these two:
    • a database built from commercially available starting materials
    • a database derived from existing drugs
  • Comes with a complexity database builder to allow users to generate their own complexity database
  • Provides several options to control the workings of TopoPlex
  • Reads input structures from MDL SDfiles
  • Saves structures with complexity scores into MDL SDfiles


Supported operating systems:

  • Linux