Class QueryAtomContainerCreator
- java.lang.Object
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- org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
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public class QueryAtomContainerCreator extends Object
Utilities for creating queries from 'real' molecules. Note that most of this functionality has now been replaced by theQueryAtomContainer.create(IAtomContainer, Expr.Type...)
method and the documentation simply indicates what settings are used.
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Constructor Summary
Constructors Constructor Description QueryAtomContainerCreator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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)
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Method Detail
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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.
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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.
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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.
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createSymbolChargeIDQueryContainer
public static QueryAtomContainer createSymbolChargeIDQueryContainer(IAtomContainer container)
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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.
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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.
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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.
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suppressQueryHydrogens
public static IAtomContainer suppressQueryHydrogens(IAtomContainer mol)
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