AutoMapper User's Guide


    AutoMapper is a tool that performs automated chemical reaction mapping. It assigns atom maps to the atoms of a reaction, so that the same map number will identify the corresponding atoms on the two sides of the reaction arrow (reactant side and product side). Atom mapping reflects the mechanism of the reaction.


    AutoMapper provides the following features:

    • Map reactions in various mapping styles;

      • Complete : All atoms of a reaction will be mapped.

      • Changing : Atoms connected to forming, breaking, or modified bonds, and orphan atoms (they have no matching pair on the other side of the reaction arrow) will be mapped.

      • Matching : Atoms present on both sides of the reaction will be mapped.

    • Preserve the original maps of a partially mapped reaction;

    • Mark reaction center. The following bonds will be marked:

      • images/download/thumbnails/5312999/make_or_break16.png Make or break: bond is made or broken in the reaction;

      • images/download/thumbnails/5312999/change16.png Change: type of the bond has changed during the reaction (e.g., single bond to double bond).


    Automapper is integrated into and used by the following ChemAxon products:


    AutoMapper is a licensed ChemAxon product.

    • batch mode usage requires Standardizer license

    • single reactions can be mapped in MarvinSketch without license


    AutoMapper algorithm is based on Maximum Common Substructure (MCS) and Minimal Chemical Distance (MCD) algorithms.


    Example 1: Comparison of different mapping styles

    images/download/attachments/5312999/example01.png images/download/attachments/5312999/example02.png images/download/attachments/5312999/example03.png images/download/attachments/5312999/example04.png

    Example 2: Demonstration of reaction center bond marks and Changing mapping style