Class QueryAtomContainerCreator
java.lang.Object
org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
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functionality has now been replaced by the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 -
Method Summary
Modifier and TypeMethodDescriptionstatic 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
Creates a QueryAtomContainer with the following settings:static QueryAtomContainer
createBasicQueryContainer
(IAtomContainer container) Creates a QueryAtomContainer with the following settings:static QueryAtomContainer
Creates a QueryAtomContainer with the following settings:static QueryAtomContainer
Creates a QueryAtomContainer with the following settings:static QueryAtomContainer
createSymbolChargeIDQueryContainer
(IAtomContainer container) static IAtomContainer
-
Constructor Details
-
QueryAtomContainerCreator
public QueryAtomContainerCreator()
-
-
Method Details
-
createBasicQueryContainer
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
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
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
-
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 modelaromaticity
- 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 modelaromaticity
- option flag- Returns:
- The new QueryAtomContainer created from container.
-
createAnyAtomForPseudoAtomQueryContainer
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
-