ambit2.tautomers

Class FilterTautomers

java.lang.Object

ambit2.tautomers.FilterTautomers

public class FilterTautomers
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
List<List<Integer>>	excludeFilters
List<List<Integer>>	excludeFiltersOriginalPos
protected boolean	FlagApplyDuplicationCheckInChI
protected boolean	FlagApplyDuplicationCheckIsomorphism
protected boolean	FlagApplyDuplicationFilter
protected boolean	FlagApplyExcludeFilter
boolean	FlagApplySimpleAromaticityRankCorrection
protected boolean	FlagApplyWarningFilter
protected boolean	FlagExcludeWarningTautomers
protected boolean	FlagFilterIncorrectHAtomsStructures
protected boolean	FlagFilterIncorrectValencySumStructures
protected boolean	FlagStoreRemovedByFilterTautomers
protected boolean	FlagTreatAromaticBondsAsEquivalentFilter
List<org.openscience.cdk.interfaces.IAtomContainer>	removedTautomers
TautomerManager	tman
List<List<Integer>>	warnFilters
List<List<Integer>>	warnFiltersOriginalPos

Constructor Summary

Constructors

Constructor and Description
FilterTautomers(TautomerManager m)

Method Summary

Modifier and Type	Method and Description
boolean	checkMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
List<org.openscience.cdk.interfaces.IAtomContainer>	filter(List<org.openscience.cdk.interfaces.IAtomContainer> tautomers)
List<Integer>	getExcludeFilters(org.openscience.cdk.interfaces.IAtomContainer tautomer)
List<net.sf.jniinchi.INCHI_OPTION>	getInchiOptions()
void	getOriginalPositions()
static int	getValencySum(org.openscience.cdk.interfaces.IAtomContainer ac)
List<Integer>	getWarnFilters(org.openscience.cdk.interfaces.IAtomContainer tautomer)
boolean	isFlagApplyDuplicationCheckInChI()
boolean	isFlagApplyDuplicationCheckIsomorphism()
boolean	isFlagApplyDuplicationFilter()
boolean	isFlagApplyExcludeFilter()
boolean	isFlagApplyWarningFilter()
boolean	isFlagExcludeWarningTautomers()
boolean	isFlagFilterIncorrectHAtomsStructures()
boolean	isFlagFilterIncorrectValencySumStructures()
boolean	isFlagStoreRemovedByFilterTautomers()
void	setFlagApplyDuplicationCheckInChI(boolean flagApplyDuplicationCheckInChI)
void	setFlagApplyDuplicationCheckIsomorphism(boolean flagApplyDuplicationCheckIsomorphism)
void	setFlagApplyDuplicationFilter(boolean flagApplyDuplicationFilter)
void	setFlagApplyExcludeFilter(boolean flagApplyExcludeFilter)
void	setFlagApplyWarningFilter(boolean flagApplyWarningFilter)
void	setFlagExcludeWarningTautomers(boolean flagExcludeWarningTautomers)
void	setFlagFilterIncorrectHAtomsStructures(boolean flagFilterIncorrectHAtomsStructures)
void	setFlagFilterIncorrectValencySumStructures(boolean flagFilterIncorrectValencySumStructures)
void	setFlagStoreRemovedByFilterTautomers(boolean flagStoreRemovedByFilterTautomers)
void	setInchiOptions(List<net.sf.jniinchi.INCHI_OPTION> options)

Methods inherited from class java.lang.Object

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

Field Detail

FlagApplyWarningFilter

protected boolean FlagApplyWarningFilter

FlagApplyExcludeFilter

protected boolean FlagApplyExcludeFilter

FlagApplyDuplicationFilter

protected boolean FlagApplyDuplicationFilter

FlagTreatAromaticBondsAsEquivalentFilter

protected boolean FlagTreatAromaticBondsAsEquivalentFilter

FlagApplyDuplicationCheckIsomorphism

protected boolean FlagApplyDuplicationCheckIsomorphism

FlagApplySimpleAromaticityRankCorrection

public boolean FlagApplySimpleAromaticityRankCorrection

FlagApplyDuplicationCheckInChI

protected boolean FlagApplyDuplicationCheckInChI

FlagFilterIncorrectValencySumStructures

protected boolean FlagFilterIncorrectValencySumStructures

FlagStoreRemovedByFilterTautomers

protected boolean FlagStoreRemovedByFilterTautomers

FlagFilterIncorrectHAtomsStructures

protected boolean FlagFilterIncorrectHAtomsStructures

tman

public TautomerManager tman

removedTautomers

public List<org.openscience.cdk.interfaces.IAtomContainer> removedTautomers

warnFilters

public List<List<Integer>> warnFilters

excludeFilters

public List<List<Integer>> excludeFilters

warnFiltersOriginalPos

public List<List<Integer>> warnFiltersOriginalPos

excludeFiltersOriginalPos

public List<List<Integer>> excludeFiltersOriginalPos

FlagExcludeWarningTautomers

protected boolean FlagExcludeWarningTautomers

Constructor Detail

FilterTautomers

public FilterTautomers(TautomerManager m)

Method Detail

getInchiOptions

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

setInchiOptions

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

isFlagApplyWarningFilter

public boolean isFlagApplyWarningFilter()

setFlagApplyWarningFilter

public void setFlagApplyWarningFilter(boolean flagApplyWarningFilter)

isFlagApplyExcludeFilter

public boolean isFlagApplyExcludeFilter()

setFlagApplyExcludeFilter

public void setFlagApplyExcludeFilter(boolean flagApplyExcludeFilter)

isFlagApplyDuplicationFilter

public boolean isFlagApplyDuplicationFilter()

setFlagApplyDuplicationFilter

public void setFlagApplyDuplicationFilter(boolean flagApplyDuplicationFilter)

isFlagApplyDuplicationCheckIsomorphism

public boolean isFlagApplyDuplicationCheckIsomorphism()

setFlagApplyDuplicationCheckIsomorphism

public void setFlagApplyDuplicationCheckIsomorphism(boolean flagApplyDuplicationCheckIsomorphism)

isFlagApplyDuplicationCheckInChI

public boolean isFlagApplyDuplicationCheckInChI()

setFlagApplyDuplicationCheckInChI

public void setFlagApplyDuplicationCheckInChI(boolean flagApplyDuplicationCheckInChI)

isFlagFilterIncorrectValencySumStructures

public boolean isFlagFilterIncorrectValencySumStructures()

setFlagFilterIncorrectValencySumStructures

public void setFlagFilterIncorrectValencySumStructures(boolean flagFilterIncorrectValencySumStructures)

isFlagStoreRemovedByFilterTautomers

public boolean isFlagStoreRemovedByFilterTautomers()

setFlagStoreRemovedByFilterTautomers

public void setFlagStoreRemovedByFilterTautomers(boolean flagStoreRemovedByFilterTautomers)

isFlagFilterIncorrectHAtomsStructures

public boolean isFlagFilterIncorrectHAtomsStructures()

setFlagFilterIncorrectHAtomsStructures

public void setFlagFilterIncorrectHAtomsStructures(boolean flagFilterIncorrectHAtomsStructures)

isFlagExcludeWarningTautomers

public boolean isFlagExcludeWarningTautomers()

setFlagExcludeWarningTautomers

public void setFlagExcludeWarningTautomers(boolean flagExcludeWarningTautomers)

filter

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

Throws:

Exception

getOriginalPositions

public void getOriginalPositions()
                          throws Exception

Throws:

Exception

getWarnFilters

public List<Integer> getWarnFilters(org.openscience.cdk.interfaces.IAtomContainer tautomer)
                             throws Exception

Throws:

Exception

getExcludeFilters

public List<Integer> getExcludeFilters(org.openscience.cdk.interfaces.IAtomContainer tautomer)
                                throws Exception

Throws:

Exception

getValencySum

public static int getValencySum(org.openscience.cdk.interfaces.IAtomContainer ac)

checkMolecule

public boolean checkMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
                      throws Exception

Throws:

Exception