ambit2.smarts

Class SmartsParser

java.lang.Object

ambit2.smarts.SmartsParser

public class SmartsParser
extends Object

Implements SMARTS parser

Author:

Nikolay Kochev nick@uni-plovdiv.bg

Field Summary

Fields

Modifier and Type	Field and Description
List<Integer>	fragmentComponents
List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer>	fragments
boolean	hasRecursiveSmarts
int	maxCompNumber
boolean	mSupportDoubleBondAromaticityNotSpecified
boolean	mSupportMOEExtension
boolean	mSupportOpenBabelExtension
boolean	mSupportOpenEyeExtension
boolean	mSupportSingleBondAromaticityNotSpecified
boolean	mSupportSmirksSyntax
boolean	mUseMOEvPrimitive
int	numFragments

Constructor Summary

Constructors

Constructor and Description
SmartsParser()

Method Summary

Modifier and Type	Method and Description
int[]	getAtomNeighbourCode(org.openscience.cdk.interfaces.IAtom center, org.openscience.cdk.interfaces.IAtom neighAtom)
String	getErrorMessages()
List<SmartsParserError>	getErrors()
static int[]	getExplicitHAtomData(org.openscience.cdk.interfaces.IAtomContainer container)
int	getLastAtomToken()
static List<int[]>	getRindData(org.openscience.cdk.interfaces.IAtomContainer container, org.openscience.cdk.interfaces.IRingSet ringSet)
static List<int[]>	getRindData2(org.openscience.cdk.interfaces.IAtomContainer container, org.openscience.cdk.interfaces.IRingSet ringSet)
static int	getRingNumberInRingSet(org.openscience.cdk.interfaces.IAtomContainer ring, org.openscience.cdk.interfaces.IRingSet rs)
boolean	needExplicitHData()
boolean	needNeighbourData()
boolean	needParentMoleculeData()
boolean	needRingData()
boolean	needRingData2()
boolean	needValencyData()
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	parse(String sm)
void	parseAP_RecursiveSmarts()
static void	prepareTargetForSMARTSSearch(boolean neighbourData, boolean valenceData, boolean ringData, boolean ringData2, boolean explicitHData, boolean parentMoleculeData, org.openscience.cdk.interfaces.IAtomContainer container)
static void	prepareTargetForSMARTSSearch(SmartsFlags flags, org.openscience.cdk.interfaces.IAtomContainer container)
static void	prepareTargetForSMARTSSearchFull(org.openscience.cdk.interfaces.IAtomContainer container)
void	setComponentLevelGrouping(boolean flag)
static void	setExplicitHAtomData(org.openscience.cdk.interfaces.IAtomContainer container)
void	setNeededDataFlags()
static void	setNeighbourData(org.openscience.cdk.interfaces.IAtomContainer container)
static void	setParentMoleculeData(org.openscience.cdk.interfaces.IAtomContainer container)
static void	setRingData(org.openscience.cdk.interfaces.IAtomContainer container, boolean rData, boolean rData2)
void	setSMARTSData(org.openscience.cdk.interfaces.IAtomContainer container)
static void	setValenceData(org.openscience.cdk.interfaces.IAtomContainer container)
int	testFor2CharElement()
void	testForDefaultAND()

Methods inherited from class java.lang.Object

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

Field Detail

hasRecursiveSmarts

public boolean hasRecursiveSmarts

mSupportMOEExtension

public boolean mSupportMOEExtension

mUseMOEvPrimitive

public boolean mUseMOEvPrimitive

mSupportOpenEyeExtension

public boolean mSupportOpenEyeExtension

mSupportOpenBabelExtension

public boolean mSupportOpenBabelExtension

mSupportSmirksSyntax

public boolean mSupportSmirksSyntax

mSupportDoubleBondAromaticityNotSpecified

public boolean mSupportDoubleBondAromaticityNotSpecified

mSupportSingleBondAromaticityNotSpecified

public boolean mSupportSingleBondAromaticityNotSpecified

numFragments

public int numFragments

maxCompNumber

public int maxCompNumber

fragments

public List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> fragments

fragmentComponents

public List<Integer> fragmentComponents

Constructor Detail

SmartsParser

public SmartsParser()

Method Detail

parse

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer parse(String sm)

setComponentLevelGrouping

public void setComponentLevelGrouping(boolean flag)

needNeighbourData

public boolean needNeighbourData()

needExplicitHData

public boolean needExplicitHData()

needValencyData

public boolean needValencyData()

needRingData

public boolean needRingData()

needRingData2

public boolean needRingData2()

needParentMoleculeData

public boolean needParentMoleculeData()

setNeededDataFlags

public void setNeededDataFlags()

getErrorMessages

public String getErrorMessages()

getErrors

public List<SmartsParserError> getErrors()

testForDefaultAND

public void testForDefaultAND()

testFor2CharElement

public int testFor2CharElement()

getLastAtomToken

public int getLastAtomToken()

parseAP_RecursiveSmarts

public void parseAP_RecursiveSmarts()

getAtomNeighbourCode

public int[] getAtomNeighbourCode(org.openscience.cdk.interfaces.IAtom center,
                                  org.openscience.cdk.interfaces.IAtom neighAtom)

setSMARTSData

public void setSMARTSData(org.openscience.cdk.interfaces.IAtomContainer container)
                   throws Exception

Throws:

Exception

prepareTargetForSMARTSSearch

public static void prepareTargetForSMARTSSearch(boolean neighbourData,
                                                boolean valenceData,
                                                boolean ringData,
                                                boolean ringData2,
                                                boolean explicitHData,
                                                boolean parentMoleculeData,
                                                org.openscience.cdk.interfaces.IAtomContainer container)
                                         throws Exception

Throws:

Exception

prepareTargetForSMARTSSearchFull

public static void prepareTargetForSMARTSSearchFull(org.openscience.cdk.interfaces.IAtomContainer container)

prepareTargetForSMARTSSearch

public static void prepareTargetForSMARTSSearch(SmartsFlags flags,
                                                org.openscience.cdk.interfaces.IAtomContainer container)

setNeighbourData

public static void setNeighbourData(org.openscience.cdk.interfaces.IAtomContainer container)

setValenceData

public static void setValenceData(org.openscience.cdk.interfaces.IAtomContainer container)

setExplicitHAtomData

public static void setExplicitHAtomData(org.openscience.cdk.interfaces.IAtomContainer container)

getExplicitHAtomData

public static int[] getExplicitHAtomData(org.openscience.cdk.interfaces.IAtomContainer container)

setRingData

public static void setRingData(org.openscience.cdk.interfaces.IAtomContainer container,
                               boolean rData,
                               boolean rData2)

getRindData

public static List<int[]> getRindData(org.openscience.cdk.interfaces.IAtomContainer container,
                                      org.openscience.cdk.interfaces.IRingSet ringSet)

getRindData2

public static List<int[]> getRindData2(org.openscience.cdk.interfaces.IAtomContainer container,
                                       org.openscience.cdk.interfaces.IRingSet ringSet)

getRingNumberInRingSet

public static int getRingNumberInRingSet(org.openscience.cdk.interfaces.IAtomContainer ring,
                                         org.openscience.cdk.interfaces.IRingSet rs)

setParentMoleculeData

public static void setParentMoleculeData(org.openscience.cdk.interfaces.IAtomContainer container)