ambit2.reactions

Class GenericReaction

java.lang.Object

ambit2.reactions.GenericReaction

public class GenericReaction
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GenericReaction.ReactionConfigStatus
static class	GenericReaction.ReactionType
static class	GenericReaction.TransformType

Field Summary

Fields

Modifier and Type	Field and Description
protected List<ICondition>	applicationConditions
protected double	basicScore
protected List<ICondition>	conditions
protected List<Double>	conditionScores
protected GenericReaction.ReactionConfigStatus	configStatus
protected String	experimentalConditionsInfo
protected double	experimentalConditionsScore
protected String	externId
protected boolean	FlagUse
protected int	id
protected String	info
protected String	name
protected double	priorityScore
protected int[]	reactionCenterIndices
protected String	reactionClass
protected GenericReaction.ReactionType	reactionType
protected double	reliabilityScore
protected String	smirks
protected Map<SmirksTransformationFlag,Boolean>	smirksFlag
protected SMIRKSReaction	smirksReaction
protected GenericReaction.TransformType	transformType
protected double	yieldHi
protected double	yieldLo

Constructor Summary

Constructors

Constructor and Description
GenericReaction()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IAtomContainer	applyAtInstance(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> instance, SMIRKSManager smrkMan)
org.openscience.cdk.interfaces.IAtomContainer	applyAtInstance(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> instance, SMIRKSManager smrkMan, boolean FlagClone)
org.openscience.cdk.interfaces.IAtomContainer	applyAtInstancesSimultaneously(org.openscience.cdk.interfaces.IAtomContainer target, List<List<org.openscience.cdk.interfaces.IAtom>> instances, SMIRKSManager smrkMan, boolean FlagClone)
boolean	checkConditionsForTarget(Object target)
void	configure(SMIRKSManager smrkMan)
List<List<org.openscience.cdk.interfaces.IAtom>>	findReactionInstances(org.openscience.cdk.interfaces.IAtomContainer target, SMIRKSManager smrkMan)
List<List<org.openscience.cdk.interfaces.IAtom>>	findReactionInstances(org.openscience.cdk.interfaces.IAtomContainer target, SMIRKSManager smrkMan, SmartsConst.SSM_MODE SSMode)
List<ICondition>	getApplicationConditions()
double	getBasicScore()
List<ICondition>	getConditions()
List<Double>	getConditionScores()
GenericReaction.ReactionConfigStatus	getConfigStatus()
static Double	getDouble(String s)
String	getExperimentalConditionsInfo()
double	getExperimentalConditionsScore()
String	getExternId()
int	getId()
String	getInfo()
static Integer	getInt(String s)
String	getName()
double	getPriorityScore()
int[]	getReactionCenterIndices()
String	getReactionClass()
static GenericReaction	getReactionFromJsonNode(com.fasterxml.jackson.databind.JsonNode node)
static GenericReaction	getReactionFromTokens(String[] tokens, Map<String,Integer> indices)
GenericReaction.ReactionType	getReactionType()
double	getReliabilityScore()
String	getSmirks()
Map<SmirksTransformationFlag,Boolean>	getSmirksFlag()
SMIRKSReaction	getSmirksReaction()
GenericReaction.TransformType	getTransformType()
double	getYieldHi()
double	getYieldLo()
boolean	isFlagUse()
void	setApplicationConditions(List<ICondition> applicationConditions)
void	setBasicScore(double basicScore)
void	setConditions(List<ICondition> conditions)
void	setConditionScores(List<Double> conditionScores)
void	setExperimentalConditionsInfo(String experimentalConditionsInfo)
void	setExperimentalConditionsScore(double experimentalConditionsScore)
void	setExternId(String externId)
void	setFlagUse(boolean flagUse)
void	setId(int id)
void	setInfo(String info)
void	setName(String name)
void	setPriorityScore(double priorityScore)
void	setReactionCenterIndices(int[] reactionCenterIndices)
void	setReactionClass(String reactionClass)
void	setReactionType(GenericReaction.ReactionType reactionType)
void	setReliabilityScore(double reliabilityScore)
void	setSmirks(String smirks)
void	setSmirksFlag(Map<SmirksTransformationFlag,Boolean> smirksFlag)
void	setSmirksReaction(SMIRKSReaction smirksReaction)
void	setTransformType(GenericReaction.TransformType transformType)
void	setYieldHi(double yieldHi)
void	setYieldLo(double yieldLo)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

FlagUse

protected boolean FlagUse

id

protected int id

externId

protected String externId

name

protected String name

smirks

protected String smirks

smirksFlag

protected Map<SmirksTransformationFlag,Boolean> smirksFlag

conditions

protected List<ICondition> conditions

conditionScores

protected List<Double> conditionScores

applicationConditions

protected List<ICondition> applicationConditions

reactionClass

protected String reactionClass

info

protected String info

experimentalConditionsInfo

protected String experimentalConditionsInfo

reactionCenterIndices

protected int[] reactionCenterIndices

reactionType

protected GenericReaction.ReactionType reactionType

transformType

protected GenericReaction.TransformType transformType

experimentalConditionsScore

protected double experimentalConditionsScore

basicScore

protected double basicScore

reliabilityScore

protected double reliabilityScore

yieldLo

protected double yieldLo

yieldHi

protected double yieldHi

priorityScore

protected double priorityScore

smirksReaction

protected SMIRKSReaction smirksReaction

configStatus

protected GenericReaction.ReactionConfigStatus configStatus

Constructor Detail

GenericReaction

public GenericReaction()

Method Detail

isFlagUse

public boolean isFlagUse()

setFlagUse

public void setFlagUse(boolean flagUse)

getId

public int getId()

setId

public void setId(int id)

getExternId

public String getExternId()

setExternId

public void setExternId(String externId)

getName

public String getName()

setName

public void setName(String name)

getSmirks

public String getSmirks()

setSmirks

public void setSmirks(String smirks)

getSmirksFlag

public Map<SmirksTransformationFlag,Boolean> getSmirksFlag()

setSmirksFlag

public void setSmirksFlag(Map<SmirksTransformationFlag,Boolean> smirksFlag)

getConditions

public List<ICondition> getConditions()

setConditions

public void setConditions(List<ICondition> conditions)

getConditionScores

public List<Double> getConditionScores()

setConditionScores

public void setConditionScores(List<Double> conditionScores)

getApplicationConditions

public List<ICondition> getApplicationConditions()

setApplicationConditions

public void setApplicationConditions(List<ICondition> applicationConditions)

getReactionClass

public String getReactionClass()

setReactionClass

public void setReactionClass(String reactionClass)

getInfo

public String getInfo()

setInfo

public void setInfo(String info)

getExperimentalConditionsInfo

public String getExperimentalConditionsInfo()

setExperimentalConditionsInfo

public void setExperimentalConditionsInfo(String experimentalConditionsInfo)

getReactionCenterIndices

public int[] getReactionCenterIndices()

setReactionCenterIndices

public void setReactionCenterIndices(int[] reactionCenterIndices)

getReactionType

public GenericReaction.ReactionType getReactionType()

setReactionType

public void setReactionType(GenericReaction.ReactionType reactionType)

getTransformType

public GenericReaction.TransformType getTransformType()

setTransformType

public void setTransformType(GenericReaction.TransformType transformType)

getExperimentalConditionsScore

public double getExperimentalConditionsScore()

setExperimentalConditionsScore

public void setExperimentalConditionsScore(double experimentalConditionsScore)

getBasicScore

public double getBasicScore()

setBasicScore

public void setBasicScore(double basicScore)

getReliabilityScore

public double getReliabilityScore()

setReliabilityScore

public void setReliabilityScore(double reliabilityScore)

getYieldLo

public double getYieldLo()

setYieldLo

public void setYieldLo(double yieldLo)

getYieldHi

public double getYieldHi()

setYieldHi

public void setYieldHi(double yieldHi)

getPriorityScore

public double getPriorityScore()

setPriorityScore

public void setPriorityScore(double priorityScore)

getSmirksReaction

public SMIRKSReaction getSmirksReaction()

setSmirksReaction

public void setSmirksReaction(SMIRKSReaction smirksReaction)

getConfigStatus

public GenericReaction.ReactionConfigStatus getConfigStatus()

checkConditionsForTarget

public boolean checkConditionsForTarget(Object target)

configure

public void configure(SMIRKSManager smrkMan)
               throws Exception

Throws:

Exception

getReactionFromJsonNode

public static GenericReaction getReactionFromJsonNode(com.fasterxml.jackson.databind.JsonNode node)
                                               throws Exception

Throws:

Exception

getReactionFromTokens

public static GenericReaction getReactionFromTokens(String[] tokens,
                                                    Map<String,Integer> indices)
                                             throws Exception

Throws:

Exception

findReactionInstances

public List<List<org.openscience.cdk.interfaces.IAtom>> findReactionInstances(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                              SMIRKSManager smrkMan)
                                                                       throws EmptyMoleculeException

Throws:

EmptyMoleculeException

findReactionInstances

public List<List<org.openscience.cdk.interfaces.IAtom>> findReactionInstances(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                              SMIRKSManager smrkMan,
                                                                              SmartsConst.SSM_MODE SSMode)
                                                                       throws EmptyMoleculeException

Throws:

EmptyMoleculeException

applyAtInstance

public org.openscience.cdk.interfaces.IAtomContainer applyAtInstance(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                     List<org.openscience.cdk.interfaces.IAtom> instance,
                                                                     SMIRKSManager smrkMan)
                                                              throws Exception

Throws:

Exception

applyAtInstance

public org.openscience.cdk.interfaces.IAtomContainer applyAtInstance(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                     List<org.openscience.cdk.interfaces.IAtom> instance,
                                                                     SMIRKSManager smrkMan,
                                                                     boolean FlagClone)
                                                              throws Exception

Throws:

Exception

applyAtInstancesSimultaneously

public org.openscience.cdk.interfaces.IAtomContainer applyAtInstancesSimultaneously(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                    List<List<org.openscience.cdk.interfaces.IAtom>> instances,
                                                                                    SMIRKSManager smrkMan,
                                                                                    boolean FlagClone)
                                                                             throws Exception

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Object

getInt

public static final Integer getInt(String s)

getDouble

public static final Double getDouble(String s)