ambit2.tautomers

Class TautomerManager

java.lang.Object

ambit2.tautomers.TautomerManager

public class TautomerManager
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
boolean	FlagAddImplicitHAtomsOnTautomerProcess
boolean	FlagApplySimpleAromaticityRankCorrection
boolean	FlagCalculateCACTVSEnergyRank
boolean	FlagCheckDuplicationOnRegistering
boolean	FlagCheckNumOfRegistrationsForIncrementalAlgorithm
boolean	FlagCheckValencyOnRegistering
int	FlagEnergyRankingMethod
boolean	FlagExcludeWarnFiltersOnRegistering
boolean	FlagGenerateStereoBasedOn2D
boolean	FlagGenerateTautomerRelationGraph
boolean	FlagNewRuleInstanceSearchOnEnergyRanking
boolean	FlagPrintExtendedRuleInstances
boolean	FlagPrintIcrementalStepDebugInfo
boolean	FlagPrintTargetMoleculeInfo
boolean	FlagProcessRemainingStackIncSteps
boolean	FlagRecurseBackResultTautomers
boolean	FlagRegisterOnlyBestRankTautomers
boolean	FlagSetStereoElementsOnTautomerProcess
boolean	FlagStopGenerationOnReachingRuleSelectorLimit
boolean	FlagSwitchToCombinatorialOnReachingRuleLimit
protected static Logger	logger
int	maxNumOfBackTracks
int	maxNumOfSubCombinations
int	maxNumOfTautomerRegistrations
FilterTautomers	tautomerFilter
TautomerRegion	tautomerRegion

Constructor Summary

Constructors

Constructor and Description
TautomerManager()

Method Summary

Modifier and Type	Method and Description
static void	calcCACTVSEnergyRanks(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)
List<org.openscience.cdk.interfaces.IAtomContainer>	generateTautomers_ImprovedCombApproach()
List<org.openscience.cdk.interfaces.IAtomContainer>	generateTautomers() This is pure combinatorial approach It is the initial approach 00 based on binary combinations.
List<org.openscience.cdk.interfaces.IAtomContainer>	generateTautomersIncrementaly()
org.openscience.cdk.interfaces.IAtomContainer	getCanonicTautomer(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)
org.openscience.cdk.interfaces.IAtomContainer	getCanonicTautomer0(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)
TautomerConst.CanonicTautomerMethod	getCanonicTautomerMethod()
int[]	getCodeStrBondSequence()
EnergyRanking	getEnergyRanking()
int	getInitialRuleCount()
KnowledgeBase	getKnowledgeBase()
RuleSelector	getRuleSelector()
int	getStatus()
TautomerRelationGraph	getTautomerRelationGraph()
void	printDebugInfo() TODO: Rewrite with logger and proper logger levels
static void	processTautomer(org.openscience.cdk.interfaces.IAtomContainer tautomer, org.openscience.cdk.interfaces.IAtomContainer originalMol, boolean FlagSetStereo, boolean FlagGenerateStereoFrom2D, boolean FlagAddImplicitHAtoms)
void	registerBestRankTautomer(org.openscience.cdk.interfaces.IAtomContainer newTautomer)
boolean	registerTautomer(org.openscience.cdk.interfaces.IAtomContainer newTautomer)
void	setCanonicTautomerMethod(TautomerConst.CanonicTautomerMethod canonicTautomerMethod)
void	setCurIncrStep(TautomerIncrementStep cis)
void	setEnergyRanking(EnergyRanking energyRanking)
void	setRuleSelector(RuleSelector ruleSelector)
void	setStructure(org.openscience.cdk.interfaces.IAtomContainer str)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final Logger logger

tautomerFilter

public FilterTautomers tautomerFilter

tautomerRegion

public TautomerRegion tautomerRegion

FlagEnergyRankingMethod

public int FlagEnergyRankingMethod

FlagNewRuleInstanceSearchOnEnergyRanking

public boolean FlagNewRuleInstanceSearchOnEnergyRanking

FlagApplySimpleAromaticityRankCorrection

public boolean FlagApplySimpleAromaticityRankCorrection

FlagGenerateTautomerRelationGraph

public boolean FlagGenerateTautomerRelationGraph

FlagSwitchToCombinatorialOnReachingRuleLimit

public boolean FlagSwitchToCombinatorialOnReachingRuleLimit

FlagRecurseBackResultTautomers

public boolean FlagRecurseBackResultTautomers

FlagCalculateCACTVSEnergyRank

public boolean FlagCalculateCACTVSEnergyRank

FlagCheckDuplicationOnRegistering

public boolean FlagCheckDuplicationOnRegistering

FlagCheckValencyOnRegistering

public boolean FlagCheckValencyOnRegistering

FlagExcludeWarnFiltersOnRegistering

public boolean FlagExcludeWarnFiltersOnRegistering

FlagRegisterOnlyBestRankTautomers

public boolean FlagRegisterOnlyBestRankTautomers

FlagPrintTargetMoleculeInfo

public boolean FlagPrintTargetMoleculeInfo

FlagPrintExtendedRuleInstances

public boolean FlagPrintExtendedRuleInstances

FlagPrintIcrementalStepDebugInfo

public boolean FlagPrintIcrementalStepDebugInfo

maxNumOfBackTracks

public int maxNumOfBackTracks

maxNumOfTautomerRegistrations

public int maxNumOfTautomerRegistrations

maxNumOfSubCombinations

public int maxNumOfSubCombinations

FlagProcessRemainingStackIncSteps

public boolean FlagProcessRemainingStackIncSteps

FlagGenerateStereoBasedOn2D

public boolean FlagGenerateStereoBasedOn2D

FlagSetStereoElementsOnTautomerProcess

public boolean FlagSetStereoElementsOnTautomerProcess

FlagAddImplicitHAtomsOnTautomerProcess

public boolean FlagAddImplicitHAtomsOnTautomerProcess

FlagStopGenerationOnReachingRuleSelectorLimit

public boolean FlagStopGenerationOnReachingRuleSelectorLimit

FlagCheckNumOfRegistrationsForIncrementalAlgorithm

public boolean FlagCheckNumOfRegistrationsForIncrementalAlgorithm

Constructor Detail

TautomerManager

public TautomerManager()

Method Detail

setStructure

public void setStructure(org.openscience.cdk.interfaces.IAtomContainer str)
                  throws Exception

Throws:

Exception

getKnowledgeBase

public KnowledgeBase getKnowledgeBase()

getRuleSelector

public RuleSelector getRuleSelector()

setRuleSelector

public void setRuleSelector(RuleSelector ruleSelector)

getTautomerRelationGraph

public TautomerRelationGraph getTautomerRelationGraph()

generateTautomers

public List<org.openscience.cdk.interfaces.IAtomContainer> generateTautomers()
                                                                      throws Exception

This is pure combinatorial approach It is the initial approach 00 based on binary combinations. n rule instances define 2^n combinations (binary number with n digits)

Throws:

Exception

generateTautomers_ImprovedCombApproach

public List<org.openscience.cdk.interfaces.IAtomContainer> generateTautomers_ImprovedCombApproach()
                                                                                           throws Exception

Returns:

Throws:

Exception - Approach 01: improved combinatorial approach

generateTautomersIncrementaly

public List<org.openscience.cdk.interfaces.IAtomContainer> generateTautomersIncrementaly()
                                                                                  throws Exception

Returns:

Throws:

Exception - This is the basic approach Approach 02 (basic one) based on first depth search algorithm

registerBestRankTautomer

public void registerBestRankTautomer(org.openscience.cdk.interfaces.IAtomContainer newTautomer)
                              throws Exception

Throws:

Exception

registerTautomer

public boolean registerTautomer(org.openscience.cdk.interfaces.IAtomContainer newTautomer)
                         throws Exception

Throws:

Exception

printDebugInfo

public void printDebugInfo()

TODO: Rewrite with logger and proper logger levels

getCanonicTautomer0

public org.openscience.cdk.interfaces.IAtomContainer getCanonicTautomer0(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)

getCanonicTautomer

public org.openscience.cdk.interfaces.IAtomContainer getCanonicTautomer(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)

getInitialRuleCount

public int getInitialRuleCount()

getStatus

public int getStatus()

calcCACTVSEnergyRanks

public static void calcCACTVSEnergyRanks(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)

processTautomer

public static void processTautomer(org.openscience.cdk.interfaces.IAtomContainer tautomer,
                                   org.openscience.cdk.interfaces.IAtomContainer originalMol,
                                   boolean FlagSetStereo,
                                   boolean FlagGenerateStereoFrom2D,
                                   boolean FlagAddImplicitHAtoms)
                            throws Exception

Throws:

Exception

getEnergyRanking

public EnergyRanking getEnergyRanking()
                               throws Exception

Throws:

Exception

setEnergyRanking

public void setEnergyRanking(EnergyRanking energyRanking)

getCanonicTautomerMethod

public TautomerConst.CanonicTautomerMethod getCanonicTautomerMethod()

setCanonicTautomerMethod

public void setCanonicTautomerMethod(TautomerConst.CanonicTautomerMethod canonicTautomerMethod)

setCurIncrStep

public void setCurIncrStep(TautomerIncrementStep cis)

getCodeStrBondSequence

public int[] getCodeStrBondSequence()