ambit2.core.processors.structure

Class HydrogenAdderProcessor

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.core.processors.structure.AtomConfigurator

ambit2.core.processors.structure.HydrogenAdderProcessor

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

public class HydrogenAdderProcessor
extends AtomConfigurator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	addEexplicitHydrogens
protected org.openscience.cdk.tools.CDKHydrogenAdder	adder

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
HydrogenAdderProcessor()

Method Summary

Modifier and Type	Method and Description
static void	convertImplicitToExplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer) Deprecated.
boolean	isAddEexplicitHydrogens()
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setAddEexplicitHydrogens(boolean addEexplicitHydrogens)

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

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

Field Detail

adder

protected org.openscience.cdk.tools.CDKHydrogenAdder adder

addEexplicitHydrogens

protected boolean addEexplicitHydrogens

Constructor Detail

HydrogenAdderProcessor

public HydrogenAdderProcessor()

Method Detail

isAddEexplicitHydrogens

public boolean isAddEexplicitHydrogens()

setAddEexplicitHydrogens

public void setAddEexplicitHydrogens(boolean addEexplicitHydrogens)

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                      throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

process in class AtomConfigurator

Throws:

net.idea.modbcum.i.exceptions.AmbitException

convertImplicitToExplicitHydrogens

@Deprecated
public static void convertImplicitToExplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Deprecated.