ambit2.reactions.reactor

Class Reactor

java.lang.Object

ambit2.reactions.reactor.Reactor

public class Reactor
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected IDescriptorSolver	descriptorSolver
protected boolean	FlagReactRecursively
protected org.openscience.cdk.inchi.InChIGeneratorFactory	igf
protected static Logger	logger
protected TreeSet<String>	nodeHashCodes
static String	PropertyInchiKey
static String	PropertyReactionIds
protected ReactionDataBase	reactionDataBase
protected Stack<ReactorNode>	reactorNodes
protected ReactorResult	reactorResult
protected SMIRKSManager	smrkMan
protected ReactorStrategy	strategy

Constructor Summary

Constructors

Constructor and Description
Reactor()

Method Summary

Modifier and Type	Method and Description
IDescriptorSolver	getDescriptoSolver()
ReactionDataBase	getReactionDataBase()
SMIRKSManager	getSMIRKSManager()
ReactorStrategy	getStrategy()
int	initializeReactor(org.openscience.cdk.interfaces.IAtomContainer target)
boolean	isFlagReactRecursively()
String	molToSmiles(org.openscience.cdk.interfaces.IAtomContainer mol)
ReactorResult	react(org.openscience.cdk.interfaces.IAtomContainer target)
String	reactionPathToString(org.openscience.cdk.interfaces.IAtomContainer mol, boolean printName)
List<ReactorNode>	reactNext(int numNodes)
protected void	setDescriptoSolverForReactDB()
void	setFlagReactRecursively(boolean flagReactRecursively)
void	setReactionDataBase(ReactionDataBase reactionDataBase)
void	setStrategy(ReactorStrategy strategy)
protected void	setupDescriptoSolver()
protected void	setupInchiGenerator()

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static Logger logger

PropertyInchiKey

public static final String PropertyInchiKey

See Also:

Constant Field Values

PropertyReactionIds

public static final String PropertyReactionIds

See Also:

Constant Field Values

reactionDataBase

protected ReactionDataBase reactionDataBase

strategy

protected ReactorStrategy strategy

smrkMan

protected SMIRKSManager smrkMan

reactorNodes

protected Stack<ReactorNode> reactorNodes

nodeHashCodes

protected TreeSet<String> nodeHashCodes

igf

protected org.openscience.cdk.inchi.InChIGeneratorFactory igf

descriptorSolver

protected IDescriptorSolver descriptorSolver

reactorResult

protected ReactorResult reactorResult

FlagReactRecursively

protected boolean FlagReactRecursively

Constructor Detail

Reactor

public Reactor()
        throws Exception

Throws:

Exception

Method Detail

setupInchiGenerator

protected void setupInchiGenerator()
                            throws Exception

Throws:

Exception

setupDescriptoSolver

protected void setupDescriptoSolver()

getSMIRKSManager

public SMIRKSManager getSMIRKSManager()

isFlagReactRecursively

public boolean isFlagReactRecursively()

setFlagReactRecursively

public void setFlagReactRecursively(boolean flagReactRecursively)

getReactionDataBase

public ReactionDataBase getReactionDataBase()

setReactionDataBase

public void setReactionDataBase(ReactionDataBase reactionDataBase)

getStrategy

public ReactorStrategy getStrategy()

setStrategy

public void setStrategy(ReactorStrategy strategy)

getDescriptoSolver

public IDescriptorSolver getDescriptoSolver()

setDescriptoSolverForReactDB

protected void setDescriptoSolverForReactDB()

initializeReactor

public int initializeReactor(org.openscience.cdk.interfaces.IAtomContainer target)

react

public ReactorResult react(org.openscience.cdk.interfaces.IAtomContainer target)
                    throws Exception

Throws:

Exception

reactNext

public List<ReactorNode> reactNext(int numNodes)
                            throws Exception

Throws:

Exception

molToSmiles

public String molToSmiles(org.openscience.cdk.interfaces.IAtomContainer mol)

reactionPathToString

public String reactionPathToString(org.openscience.cdk.interfaces.IAtomContainer mol,
                                   boolean printName)