toxtree.tree

Class Reactor

java.lang.Object

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

toxtree.tree.Reactor

All Implemented Interfaces:

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

public class Reactor
extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainerSet>
implements IImplementationDetails

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ambit2.smarts.SMIRKSManager	smrkMan

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

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
Reactor()
Reactor(String[][] smirks)

Method Summary

Modifier and Type	Method and Description
String	getImplementationDetails()
String[][]	getSmirks()
org.openscience.cdk.interfaces.IAtomContainerSet	process(org.openscience.cdk.interfaces.IAtomContainer molecule)
void	setSmirks(String[][] smirks) String[][] smirks = { { "Aliphatic hydroxylation", "[C;X4:1][H:2]>>[C:1][O][H:2]" }, { "Aromatic hydroxylation", "[c:1][H:2]>>[c:1][O][H:2]" } }

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

smrkMan

protected final transient ambit2.smarts.SMIRKSManager smrkMan

Constructor Detail

Reactor

public Reactor()

Reactor

public Reactor(String[][] smirks)

Method Detail

getSmirks

public String[][] getSmirks()

setSmirks

public void setSmirks(String[][] smirks)

 String[][] smirks = {
                        { "Aliphatic hydroxylation", "[C;X4:1][H:2]>>[C:1][O][H:2]" },
                        { "Aromatic hydroxylation", "[c:1][H:2]>>[c:1][O][H:2]" }
                        }
 

Parameters:

smirks -

process

public org.openscience.cdk.interfaces.IAtomContainerSet process(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                                         throws ReactionException,
                                                                CloneNotSupportedException

Specified by:

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

Throws:

ReactionException

CloneNotSupportedException

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails