ambit2.reactions.reactor

Class ReactorStrategy

java.lang.Object

ambit2.reactions.reactor.ReactorStrategy

public class ReactorStrategy
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
List<StructureRecord>	allowedProducts
protected boolean	FlagCalcProductInchiKey
boolean	FlagCheckNodeDuplicationOnPush
boolean	FlagCheckReactionConditions
boolean	FlagFailedNodeOnOneForbiddenProduct
boolean	FlagLogExplicitHToImplicit
boolean	FlagLogMainReactionFlow
boolean	FlagLogNameInReactionPath
boolean	FlagLogNumberOfProcessedNodes
boolean	FlagLogReactionPath
boolean	FlagProcessRemainingStackNodes
boolean	FlagProcessSingleReagentInNode
boolean	FlagReactOneReagentOnly
boolean	FlagRemoveReagentIfAllowedProduct
boolean	FlagRemoveReagentIfForbiddenProduct
boolean	FlagStopOnMaxLevel
boolean	FlagStoreFailedNodes
boolean	FlagStoreProducts
boolean	FlagStoreSuccessNodes
boolean	FlagSuccessNodeOnReachingAllowedProducts
boolean	FlagSuccessNodeOnZeroForbiddenProducts
boolean	FlagTraceParentNodes
boolean	FlagTraceReactionPath
List<StructureRecord>	forbiddenProducts
int	maxLevel
int	maxNumOfFailedNodes
int	maxNumOfNodes
int	maxNumOfReactions
int	maxNumOfSuccessNodes
int	NodeLogingFrequency

Constructor Summary

Constructors

Constructor and Description
ReactorStrategy()
ReactorStrategy(File jsonFile)

Method Summary

Modifier and Type	Method and Description
static void	configureStructureRecord(StructureRecord strRecord, org.openscience.cdk.inchi.InChIGeneratorFactory igf, List<net.sf.jniinchi.INCHI_OPTION> options)
static ReactorStrategy	readReactorStrategyFromJSON(File jsonFile)
static ReactorStrategy	readReactorStrategyFromJSONFile(File jsonFile, ReactorStrategy reactorStrategy)
static ReactorStrategy	readReactorStrategyFromJsonNode(com.fasterxml.jackson.databind.JsonNode node)
static ReactorStrategy	readReactorStrategyFromJsonNode(com.fasterxml.jackson.databind.JsonNode node, ReactorStrategy reactorStrategy)
String	toJSONString(String offset)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

maxNumOfReactions

public int maxNumOfReactions

maxLevel

public int maxLevel

FlagStopOnMaxLevel

public boolean FlagStopOnMaxLevel

maxNumOfNodes

public int maxNumOfNodes

maxNumOfFailedNodes

public int maxNumOfFailedNodes

maxNumOfSuccessNodes

public int maxNumOfSuccessNodes

FlagCalcProductInchiKey

protected boolean FlagCalcProductInchiKey

FlagCheckReactionConditions

public boolean FlagCheckReactionConditions

FlagStoreSuccessNodes

public boolean FlagStoreSuccessNodes

FlagStoreFailedNodes

public boolean FlagStoreFailedNodes

FlagTraceParentNodes

public boolean FlagTraceParentNodes

FlagStoreProducts

public boolean FlagStoreProducts

FlagTraceReactionPath

public boolean FlagTraceReactionPath

FlagCheckNodeDuplicationOnPush

public boolean FlagCheckNodeDuplicationOnPush

allowedProducts

public List<StructureRecord> allowedProducts

forbiddenProducts

public List<StructureRecord> forbiddenProducts

FlagSuccessNodeOnReachingAllowedProducts

public boolean FlagSuccessNodeOnReachingAllowedProducts

FlagSuccessNodeOnZeroForbiddenProducts

public boolean FlagSuccessNodeOnZeroForbiddenProducts

FlagFailedNodeOnOneForbiddenProduct

public boolean FlagFailedNodeOnOneForbiddenProduct

FlagReactOneReagentOnly

public boolean FlagReactOneReagentOnly

FlagProcessRemainingStackNodes

public boolean FlagProcessRemainingStackNodes

FlagProcessSingleReagentInNode

public boolean FlagProcessSingleReagentInNode

FlagRemoveReagentIfAllowedProduct

public boolean FlagRemoveReagentIfAllowedProduct

FlagRemoveReagentIfForbiddenProduct

public boolean FlagRemoveReagentIfForbiddenProduct

FlagLogMainReactionFlow

public boolean FlagLogMainReactionFlow

FlagLogReactionPath

public boolean FlagLogReactionPath

FlagLogNameInReactionPath

public boolean FlagLogNameInReactionPath

FlagLogExplicitHToImplicit

public boolean FlagLogExplicitHToImplicit

FlagLogNumberOfProcessedNodes

public boolean FlagLogNumberOfProcessedNodes

NodeLogingFrequency

public int NodeLogingFrequency

Constructor Detail

ReactorStrategy

public ReactorStrategy()

ReactorStrategy

public ReactorStrategy(File jsonFile)
                throws Exception

Throws:

Exception

Method Detail

readReactorStrategyFromJSON

public static ReactorStrategy readReactorStrategyFromJSON(File jsonFile)
                                                   throws Exception

Throws:

Exception

readReactorStrategyFromJSONFile

public static ReactorStrategy readReactorStrategyFromJSONFile(File jsonFile,
                                                              ReactorStrategy reactorStrategy)
                                                       throws Exception

Throws:

Exception

readReactorStrategyFromJsonNode

public static ReactorStrategy readReactorStrategyFromJsonNode(com.fasterxml.jackson.databind.JsonNode node)
                                                       throws Exception

Throws:

Exception

readReactorStrategyFromJsonNode

public static ReactorStrategy readReactorStrategyFromJsonNode(com.fasterxml.jackson.databind.JsonNode node,
                                                              ReactorStrategy reactorStrategy)
                                                       throws Exception

Throws:

Exception

configureStructureRecord

public static void configureStructureRecord(StructureRecord strRecord,
                                            org.openscience.cdk.inchi.InChIGeneratorFactory igf,
                                            List<net.sf.jniinchi.INCHI_OPTION> options)
                                     throws Exception

Throws:

Exception

toJSONString

public String toJSONString(String offset)

toString

public String toString()

Overrides:

toString in class Object