Package org.openscience.cdk.isomorphism.matchers

Class RGroupQuery

  • All Implemented Interfaces:
    Cloneable, ICDKObject, IChemObject, IRGroupQuery
    public class RGroupQuery
extends QueryChemObject
implements IChemObject, IRGroupQuery
    Represents information contained in a Symyx RGfile (R-group query file).
    It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points. The attachment points define a connection order for the substitutes, which is relevant when an Rgroup is connected to the scaffold with more than one bond.

    This class can also be used to produce all the valid configurations for the combination of its root,definitions and conditions.

    This Javadoc does not contain a code sample how to create a new RGroupQuery from scratch, because a sensible RGroupQuery has quite a few attributes to be set including a root plus a bunch of substituents, which are all atom containers. So that would be a lot of sample code here.
    The best way to get a feel for the way the RGroup objects are populated is to run the RGroupQueryReaderTest and look at the sample input RGroup query files contained in the CDK and how they translate into RGroupXX objects. The JChempaint application can visualize the input files for you.

    Author:
    Mark Rijnbeek
    Source code:
    main
    Belongs to CDK module:
    isomorphism
    Keywords:
    Rgroup, R group, R-group