AFGen: Fragment-based Descriptors for Chemical Compounds

History of Changes

Ver: 2.0.0, 5/12/08
  • A new descriptor space based on all bounded size subgraphs (GF descriptor space) has been added as the default option.
  • Added the option to generate a set of descriptors that are limited to a pre-determined set (descriptor-space projection mode). This is useful for projecting a new library on the set of descriptors obtained from another library.
  • Enhanced the information stored with each discovered fragment.
  • Added options to explicitly remove hydrogen atoms and to label the aromatic bonds in SDF files.
  • Various optimizations resulting in a 10x-20x performance improvements and lower memory footprint. For reference, the GF descriptors with 3--7 bonds (314720 in total) of the MLSMR library (~246K compounds) can be obtained in 165 seconds on a 2.4Ghz Core 2 duo processor.