Package org.openscience.cdk.atomtype
Class CDKAtomTypeMatcher
- java.lang.Object
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- org.openscience.cdk.atomtype.CDKAtomTypeMatcher
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- All Implemented Interfaces:
IAtomTypeMatcher
public class CDKAtomTypeMatcher extends Object implements IAtomTypeMatcher
Atom Type matcher that perceives atom types as defined in the CDK atom type listorg/openscience/cdk/dict/data/cdk-atom-types.owl
. If there is not an atom type defined for the tested atom, then NULL is returned.- Author:
- egonw
- Source code:
- main
- Belongs to CDK module:
- core
- Created on:
- 2007-07-20
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Field Summary
Fields Modifier and Type Field Description static int
REQUIRE_EXPLICIT_HYDROGENS
static int
REQUIRE_NOTHING
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description IAtomType
findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom container.IAtomType[]
findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.static CDKAtomTypeMatcher
getInstance(IChemObjectBuilder builder)
static CDKAtomTypeMatcher
getInstance(IChemObjectBuilder builder, int mode)
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Field Detail
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REQUIRE_NOTHING
public static final int REQUIRE_NOTHING
- See Also:
- Constant Field Values
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REQUIRE_EXPLICIT_HYDROGENS
public static final int REQUIRE_EXPLICIT_HYDROGENS
- See Also:
- Constant Field Values
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Method Detail
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getInstance
public static CDKAtomTypeMatcher getInstance(IChemObjectBuilder builder)
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getInstance
public static CDKAtomTypeMatcher getInstance(IChemObjectBuilder builder, int mode)
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findMatchingAtomTypes
public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CDKException
Method that assigns atom types to atoms in the given atom container.- Specified by:
findMatchingAtomTypes
in interfaceIAtomTypeMatcher
- Parameters:
atomContainer
- AtomContainer for which atom types are perceived- Returns:
- The matching AtomType
- Throws:
CDKException
- when something went wrong with going through the AtomType's
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findMatchingAtomType
public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) throws CDKException
Method that assigns an atom type to a given atom belonging to an atom container.- Specified by:
findMatchingAtomType
in interfaceIAtomTypeMatcher
- Parameters:
atomContainer
- AtomContainer of which theatom
is partatom
- Atom for which a matching atom type is searched- Returns:
- The matching AtomType
- Throws:
CDKException
- when something went wrong with going through the AtomType's
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