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 Note that most of this functionality has now been replaced by the QueryAtomContainer.create(IAtomContainer, Expr.Type...)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 Summary

Constructors

Constructor and Description
QueryAtomContainerCreator()

Method Summary

Modifier and Type	Method and Description
static QueryAtomContainer	createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity) Creates a QueryAtomContainer with the following settings:
static QueryAtomContainer	createAnyAtomContainer(IAtomContainer container, boolean aromaticity) Creates a QueryAtomContainer with the following settings:
static QueryAtomContainer	createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with the following settings:
static QueryAtomContainer	createBasicQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with the following settings:
static QueryAtomContainer	createSymbolAndBondOrderQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with the following settings:
static QueryAtomContainer	createSymbolAndChargeQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with the following settings:
static QueryAtomContainer	createSymbolChargeIDQueryContainer(IAtomContainer container)
static IAtomContainer	suppressQueryHydrogens(IAtomContainer mol)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

QueryAtomContainerCreator

public QueryAtomContainerCreator()

Method Detail

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)