org.openscience.cdk.atomtype

Class CDKAtomTypeMatcher

java.lang.Object

org.openscience.cdk.atomtype.CDKAtomTypeMatcher

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 list org/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:

master

Belongs to CDK module:

core

Created on:

2007-07-20

Field Summary

Fields

Modifier and Type	Field and Description
static int	REQUIRE_EXPLICIT_HYDROGENS
static int	REQUIRE_NOTHING

Method Summary

Modifier and Type	Method and 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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

REQUIRE_NOTHING

public static final int REQUIRE_NOTHING

See Also:

Constant Field Values

REQUIRE_EXPLICIT_HYDROGENS

public static final int REQUIRE_EXPLICIT_HYDROGENS

See Also:

Constant Field Values

Method Detail

getInstance

public static CDKAtomTypeMatcher getInstance(IChemObjectBuilder builder)

getInstance

public static CDKAtomTypeMatcher getInstance(IChemObjectBuilder builder,
                                             int mode)

findMatchingAtomTypes

public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer)
                                  throws CDKException

Method that assigns atom types to atoms in the given atom container.

Specified by:

findMatchingAtomTypes in interface IAtomTypeMatcher

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

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 interface IAtomTypeMatcher

Parameters:

atomContainer - AtomContainer of which the atom is part

atom - 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