Package org.openscience.cdk.isomorphism.matchers

Class QueryAtomContainerCreator

java.lang.Object
org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
public class QueryAtomContainerCreator extends Object
Utilities for creating queries from 'real' molecules. Note that most of this functionality has now been replaced by the QueryAtomContainer.create(IAtomContainer, Expr.Type...) method and the documentation simply indicates what settings are used.

  • Constructor Details

    • QueryAtomContainerCreator

      public QueryAtomContainerCreator()

  • Method Details

    • createBasicQueryContainer

      public static QueryAtomContainer createBasicQueryContainer(IAtomContainer container)
      Creates a QueryAtomContainer with the following settings: 
       QueryAtomContainer.create(container,
                           Expr.Type.ALIPHATIC_ELEMENT,
                           Expr.Type.AROMATIC_ELEMENT,
                           Expr.Type.IS_AROMATIC,
                           Expr.Type.ALIPHATIC_ORDER,
                           Expr.Type.STEREOCHEMISTRY);
      Parameters:
      container - The AtomContainer that stands as model
      Returns:
      The new QueryAtomContainer created from container.

    • createSymbolAndBondOrderQueryContainer

      public static QueryAtomContainer createSymbolAndBondOrderQueryContainer(IAtomContainer container)
      Creates a QueryAtomContainer with the following settings: 
       QueryAtomContainer.create(container,
                           Expr.Type.ELEMENT,
                           Expr.Type.ORDER);
      Parameters:
      container - The AtomContainer that stands as model
      Returns:
      The new QueryAtomContainer created from container.

    • createSymbolAndChargeQueryContainer

      public static QueryAtomContainer createSymbolAndChargeQueryContainer(IAtomContainer container)
      Creates a QueryAtomContainer with the following settings: 
       QueryAtomContainer.create(container,
                           Expr.Type.ELEMENT,
                           Expr.Type.FORMAL_CHARGE,
                           Expr.Type.IS_AROMATIC,
                           Expr.Type.ORDER);
      Parameters:
      container - The AtomContainer that stands as model
      Returns:
      The new QueryAtomContainer created from container.

    • createSymbolChargeIDQueryContainer

      public static QueryAtomContainer createSymbolChargeIDQueryContainer(IAtomContainer container)

    • createAnyAtomContainer

      public static QueryAtomContainer createAnyAtomContainer(IAtomContainer container, boolean aromaticity)
      Creates a QueryAtomContainer with the following settings: 
       // aromaticity = true
 QueryAtomContainer.create(container,
                           Expr.Type.IS_AROMATIC,
                           Expr.Type.ALIPHATIC_ORDER);
 // aromaticity = false
 QueryAtomContainer.create(container,
                           Expr.Type.ORDER);
      Parameters:
      container - The AtomContainer that stands as model
      aromaticity - option flag
      Returns:
      The new QueryAtomContainer created from container.

    • createAnyAtomAnyBondContainer

      public static QueryAtomContainer createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity)
      Creates a QueryAtomContainer with the following settings: 
       // aromaticity = true
 QueryAtomContainer.create(container,
                           Expr.Type.IS_AROMATIC);
 // aromaticity = false
 QueryAtomContainer.create(container);
      Parameters:
      container - The AtomContainer that stands as model
      aromaticity - option flag
      Returns:
      The new QueryAtomContainer created from container.

    • createAnyAtomForPseudoAtomQueryContainer

      public static QueryAtomContainer createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
      Creates a QueryAtomContainer with the following settings: 
       QueryAtomContainer.create(container,
                           Expr.Type.ELEMENT,
                           Expr.Type.IS_AROMATIC,
                           Expr.Type.ALIPHATIC_ORDER);
      Parameters:
      container - The AtomContainer that stands as model
      Returns:
      The new QueryAtomContainer created from container.

    • suppressQueryHydrogens

      public static IAtomContainer suppressQueryHydrogens(IAtomContainer mol)