AutoMapper User's Guide

• Introduction
• Features
• Usage
• Licensing
• Algorithm
• Examples
• Links

Introduction

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.

Features

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:

  • Make or break: bond is made or broken in the reaction;

  • Change: type of the bond has changed during the reaction (e.g., single bond to double bond).

Usage

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

• MarvinSketch: Map Atoms action in case of reactions (menu Structure > Mapping > Map Atoms);

• Standardizer: Action Map Reaction (actionstring: mapreaction);

• Structure Checker: Fixer of Reaction Map Error Checker (actionstring: mapreaction).

Licensing

AutoMapper is a licensed Chemaxon product.

• batch mode usage requires Standardizer license

• single reactions can be mapped in MarvinSketch without license

Algorithm

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

Examples

Example 1: Comparison of different mapping styles

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

Links

• AutoMapper API Documentation