org.openscience.cdk.isomorphism.matchers

Class QueryAtomContainerCreator

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

public class QueryAtomContainerCreator
extends Object

Source code:

master

Belongs to CDK module:

isomorphism

Constructor Summary

Constructors

Constructor and Description
QueryAtomContainerCreator()

Method Summary

Methods

Modifier and Type	Method and Description
static QueryAtomContainer	createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity) Creates a QueryAtomContainer with wildcard atoms and wildcard bonds.
static QueryAtomContainer	createAnyAtomContainer(IAtomContainer container, boolean aromaticity) Creates a QueryAtomContainer with AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.
static QueryAtomContainer	createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
static QueryAtomContainer	createBasicQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's and OrderQueryBond's.
static QueryAtomContainer	createSymbolAndBondOrderQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
static QueryAtomContainer	createSymbolAndChargeQueryContainer(IAtomContainer container) Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and OrderQueryBond's.
static QueryAtomContainer	createSymbolChargeIDQueryContainer(IAtomContainer container)

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 SymbolQueryAtom's, AromaticQueryBond's and OrderQueryBond's. If a IBond of the input container is flagged aromatic, then it disregards bond order information and only match against an aromatic target atom instead.

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 SymbolQueryAtom's and OrderQueryBond's. Unlike createBasicQueryContainer, it disregards aromaticity flags.

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 SymbolAncChargeQueryAtom's and OrderQueryBond's.

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 AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds. It uses the CDKConstants.ISAROMATIC flag to determine the aromaticity of container.

Parameters:

container - The AtomContainer that stands as model

aromaticity - True = use aromaticity flags to create AtomaticAtoms and AromaticQueryBonds

Returns:

The new QueryAtomContainer created from container

createAnyAtomAnyBondContainer

public static QueryAtomContainer createAnyAtomAnyBondContainer(IAtomContainer container,
                                               boolean aromaticity)

Creates a QueryAtomContainer with wildcard atoms and wildcard bonds. This method thus allows the user to search based only on connectivity.

Parameters:

container - The AtomContainer that stands as the model

aromaticity - If True, aromaticity flags are checked to create AromaticAtoms and AromaticQueryBonds

Returns:

The new QueryAtomContainer

createAnyAtomForPseudoAtomQueryContainer

public static QueryAtomContainer createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)

Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's. Each PseudoAtom will be replaced by a AnyAtom

Parameters:

container - The AtomContainer that stands as model

Returns:

The new QueryAtomContainer created from container.