ambit2.reactions.retrosynth

Class ReactionSequence

java.lang.Object

ambit2.reactions.retrosynth.ReactionSequence

public class ReactionSequence
extends Object

Author:

nick This is sequence of reactions represented in tree data structure and it represents a partucula solution of the retro-synthesis problem

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ReactionSequence.InchiEntry
static class	ReactionSequence.MoleculeStatus
static class	ReactionSequence.SortingMethod

Field Summary

Fields

Modifier and Type	Field and Description
static String	MoleculeInChIKeyProperty
static String	MoleculeStatusProperty

Constructor Summary

Constructors

Constructor and Description
ReactionSequence()

Method Summary

Modifier and Type	Method and Description
static int	compare(GenericReactionInstance inst0, GenericReactionInstance inst1, ReactionSequence.SortingMethod sortMethod)
Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>>	generateAllReactionInstances(org.openscience.cdk.interfaces.IAtomContainer mol)
Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>>	generateAllReactionInstances(org.openscience.cdk.interfaces.IAtomContainer mol, List<GenericReaction> reactions)
void	generateSequenceStepForReactionInstance(ReactionSequenceLevel level, int moleculeIndex, GenericReactionInstance gri)
void	generateSequenceStepForReactionInstance(ReactionSequenceLevel level, int moleculeIndex, GenericReaction reaction, List<org.openscience.cdk.interfaces.IAtom> reactionInstance)
GenericReactionInstance	getBestInstance(List<GenericReactionInstance> griList)
ReactionSequenceLevel	getFirstLevel()
String	getInchiKey(org.openscience.cdk.interfaces.IAtomContainer mol)
List<net.sf.jniinchi.INCHI_OPTION>	getInchiOptions()
ReactionSequenceLevel	getLevel(int levIndex)
List<ReactionSequenceLevel>	getLevels()
static ReactionSequence.MoleculeStatus	getMoleculeStatus(org.openscience.cdk.interfaces.IAtomContainer mol)
ReactionDataBase	getReactDB()
IReactionSequenceHandler	getReactionSequenceHandler()
SMIRKSManager	getSmrkMan()
StartingMaterialsDataBase	getStartMatDB()
SyntheticStrategy	getStrategy()
org.openscience.cdk.interfaces.IAtomContainer	getTarget()
Map<String,ReactionSequence.InchiEntry>	getUsedInchies()
List<GenericReactionInstance>	handleReactionInstances(Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>> instances, org.openscience.cdk.interfaces.IAtomContainer target)
void	initilize()
boolean	isFlagExplicitHAtoms()
void	iterateLevelMolecules(ReactionSequenceLevel level)
void	iterateLevelMoleculesRandomly(ReactionSequenceLevel level)
void	reset()
void	setFlagExplicitHAtoms(boolean flagExplicitHAtoms)
void	setInchiOptions(List<net.sf.jniinchi.INCHI_OPTION> inchiOptions)
void	setLevels(List<ReactionSequenceLevel> levels)
String	setMoleculeInchiKey(org.openscience.cdk.interfaces.IAtomContainer mol)
static void	setMoleculeStatus(org.openscience.cdk.interfaces.IAtomContainer mol, ReactionSequence.MoleculeStatus status)
void	setReactDB(ReactionDataBase reactDB)
void	setReactionSequenceHandler(IReactionSequenceHandler reactionSequenceHandler)
void	setSmrkMan(SMIRKSManager smrkMan)
void	setStartMatDB(StartingMaterialsDataBase startMatDB)
void	setStrategy(SyntheticStrategy strategy)
void	setTarget(org.openscience.cdk.interfaces.IAtomContainer target)
static int[]	sortReactionInstances(List<GenericReactionInstance> griList)
static int[]	sortReactionInstances(List<GenericReactionInstance> griList, ReactionSequence.SortingMethod sortMethod)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

MoleculeStatusProperty

public static final String MoleculeStatusProperty

See Also:

Constant Field Values

MoleculeInChIKeyProperty

public static final String MoleculeInChIKeyProperty

See Also:

Constant Field Values

Constructor Detail

ReactionSequence

public ReactionSequence()

Method Detail

getReactDB

public ReactionDataBase getReactDB()

setReactDB

public void setReactDB(ReactionDataBase reactDB)

getStartMatDB

public StartingMaterialsDataBase getStartMatDB()

setStartMatDB

public void setStartMatDB(StartingMaterialsDataBase startMatDB)

getStrategy

public SyntheticStrategy getStrategy()

setStrategy

public void setStrategy(SyntheticStrategy strategy)

getTarget

public org.openscience.cdk.interfaces.IAtomContainer getTarget()

setTarget

public void setTarget(org.openscience.cdk.interfaces.IAtomContainer target)

getLevels

public List<ReactionSequenceLevel> getLevels()

setLevels

public void setLevels(List<ReactionSequenceLevel> levels)

getFirstLevel

public ReactionSequenceLevel getFirstLevel()

getUsedInchies

public Map<String,ReactionSequence.InchiEntry> getUsedInchies()

getSmrkMan

public SMIRKSManager getSmrkMan()

setSmrkMan

public void setSmrkMan(SMIRKSManager smrkMan)

isFlagExplicitHAtoms

public boolean isFlagExplicitHAtoms()

setFlagExplicitHAtoms

public void setFlagExplicitHAtoms(boolean flagExplicitHAtoms)

getInchiOptions

public List<net.sf.jniinchi.INCHI_OPTION> getInchiOptions()

setInchiOptions

public void setInchiOptions(List<net.sf.jniinchi.INCHI_OPTION> inchiOptions)

getReactionSequenceHandler

public IReactionSequenceHandler getReactionSequenceHandler()

setReactionSequenceHandler

public void setReactionSequenceHandler(IReactionSequenceHandler reactionSequenceHandler)

initilize

public void initilize()

getLevel

public ReactionSequenceLevel getLevel(int levIndex)

reset

public void reset()

generateAllReactionInstances

public Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>> generateAllReactionInstances(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                                                   throws EmptyMoleculeException

Throws:

EmptyMoleculeException

generateAllReactionInstances

public Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>> generateAllReactionInstances(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                                                          List<GenericReaction> reactions)
                                                                                                   throws EmptyMoleculeException

Throws:

EmptyMoleculeException

handleReactionInstances

public List<GenericReactionInstance> handleReactionInstances(Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>> instances,
                                                             org.openscience.cdk.interfaces.IAtomContainer target)
                                                      throws Exception

Throws:

Exception

sortReactionInstances

public static int[] sortReactionInstances(List<GenericReactionInstance> griList)

sortReactionInstances

public static int[] sortReactionInstances(List<GenericReactionInstance> griList,
                                          ReactionSequence.SortingMethod sortMethod)

compare

public static int compare(GenericReactionInstance inst0,
                          GenericReactionInstance inst1,
                          ReactionSequence.SortingMethod sortMethod)

Parameters:

inst0 -

inst1 -

sortMethod -

Returns:

negatine value if inst0 < inst1, 0 if inst0 = inst1, positive value if inst0 > inst1

getBestInstance

public GenericReactionInstance getBestInstance(List<GenericReactionInstance> griList)

generateSequenceStepForReactionInstance

public void generateSequenceStepForReactionInstance(ReactionSequenceLevel level,
                                                    int moleculeIndex,
                                                    GenericReaction reaction,
                                                    List<org.openscience.cdk.interfaces.IAtom> reactionInstance)
                                             throws Exception

Throws:

Exception

generateSequenceStepForReactionInstance

public void generateSequenceStepForReactionInstance(ReactionSequenceLevel level,
                                                    int moleculeIndex,
                                                    GenericReactionInstance gri)
                                             throws Exception

Throws:

Exception

iterateLevelMolecules

public void iterateLevelMolecules(ReactionSequenceLevel level)
                           throws Exception

Throws:

Exception

iterateLevelMoleculesRandomly

public void iterateLevelMoleculesRandomly(ReactionSequenceLevel level)
                                   throws Exception

Throws:

Exception

getMoleculeStatus

public static ReactionSequence.MoleculeStatus getMoleculeStatus(org.openscience.cdk.interfaces.IAtomContainer mol)

setMoleculeStatus

public static void setMoleculeStatus(org.openscience.cdk.interfaces.IAtomContainer mol,
                                     ReactionSequence.MoleculeStatus status)

getInchiKey

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

setMoleculeInchiKey

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

toString

public String toString()

Overrides:

toString in class Object