Package org.openscience.cdk.atomtype
Class MMFF94AtomTypeMatcher
- java.lang.Object
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- org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
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- All Implemented Interfaces:
IAtomTypeMatcher
@Deprecated public class MMFF94AtomTypeMatcher extends Object implements IAtomTypeMatcher
Deprecated.use the newer Mmff.assignAtomTypes()Class implements methods to assign mmff94 atom types for a specific atom in an molecule. The full list of mmff94 atom types is defined in the file cdk/config/data/mmff94_atomtypes.xml.
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Constructor Summary
Constructors Constructor Description MMFF94AtomTypeMatcher()
Deprecated.Constructor for the MMFF94AtomTypeMatcher object.
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description IAtomType
findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)
Deprecated.Assign the mmff94 atom type to a given atom.IAtomType[]
findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.Method that assigns atom types to atoms in the given atom container.
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Method Detail
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findMatchingAtomTypes
public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CDKException
Deprecated.Description copied from interface:IAtomTypeMatcher
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 atomInterface) throws CDKException
Deprecated.Assign the mmff94 atom type to a given atom. Before this method can be called the following has to be done: atomContainer=(AtomContainer)atomTypeTools.assignAtomTypePropertiesToAtom(new Molecule(atomContainer));- Specified by:
findMatchingAtomType
in interfaceIAtomTypeMatcher
- Parameters:
atomContainer
- AtomContaineratomInterface
- the target atom- Returns:
- the matching AtomType (AtomType class)
- Throws:
CDKException
- Description of the Exception
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