ambit2.smarts

Class SmartsAtomExpression

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.QueryAtom

org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

ambit2.smarts.SmartsAtomExpression

All Implemented Interfaces:

Cloneable, org.openscience.cdk.interfaces.IAtom, org.openscience.cdk.interfaces.IAtomType, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IElement, org.openscience.cdk.interfaces.IIsotope, org.openscience.cdk.isomorphism.matchers.IQueryAtom

public class SmartsAtomExpression
extends org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

Author:

Nikolay Kochev nick@uni-plovdiv.bg

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType

org.openscience.cdk.interfaces.IAtomType.Hybridization

Field Summary

Fields

Modifier and Type	Field and Description
ExtendedChiralityInfo	extChirInfo
boolean	hasImplicitHStereoLigand
List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer>	recSmartsContainers
List<List<org.openscience.cdk.interfaces.IAtom>>	recSmartsMatches
List<String>	recSmartsStrings
List<org.openscience.cdk.interfaces.IAtom>	stereoLigands
List<SmartsExpressionToken>	stereoRemovedTokens
int[]	stereoTokenIndices
List<SmartsExpressionToken>	tokens

Fields inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtom

atomicNumber, charge, electronValency, exactMass, formalCharge, formalNeighbourCount, fractionalPoint3d, hybridization, hydrogenCount, naturalAbundance, point2d, point3d, stereoParity, symbol

Constructor Summary

Constructors

Constructor and Description
SmartsAtomExpression(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
SmartsExpressionToken	getLastToken()
void	getStereoRemovedTokens()
boolean	match_GMOE(int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_iMOE(int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_NMOE(org.openscience.cdk.interfaces.IAtom atom)
boolean	match_OB_Hybr(int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_r(int[] atomRings, int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_R(int[] atomRings, int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_vMOE(int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_x(int param, org.openscience.cdk.interfaces.IAtom atom)
boolean	match_XMOE(org.openscience.cdk.interfaces.IAtom atom)
boolean	matches(org.openscience.cdk.interfaces.IAtom atom)
boolean	stereoMatch(org.openscience.cdk.interfaces.IAtom atom, int targetStereo)
String	stereoRemovedToString()
String	toString()

Methods inherited from class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

chiralityMatches

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtom

bonds, clone, getAtomicNumber, getAtomTypeName, getBondCount, getBondOrderSum, getCharge, getContainer, getCovalentRadius, getExactMass, getFormalCharge, getFormalNeighbourCount, getFractionalPoint3d, getHybridization, getImplicitHydrogenCount, getIndex, getMassNumber, getMaxBondOrder, getNaturalAbundance, getPoint2d, getPoint3d, getStereoParity, getSymbol, getValency, isAromatic, isInRing, setAtomicNumber, setAtomTypeName, setBondOrderSum, setCharge, setCovalentRadius, setExactMass, setFormalCharge, setFormalNeighbourCount, setFractionalPoint3d, setHybridization, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMassNumber, setMaxBondOrder, setNaturalAbundance, setPoint2d, setPoint3d, setStereoParity, setSymbol, setValency

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.IAtom

bonds, clone, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setPoint2d, setPoint3d, setStereoParity

Methods inherited from interface org.openscience.cdk.interfaces.IAtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

Methods inherited from interface org.openscience.cdk.interfaces.IIsotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Methods inherited from interface org.openscience.cdk.interfaces.IElement

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Field Detail

tokens

public List<SmartsExpressionToken> tokens

recSmartsStrings

public List<String> recSmartsStrings

recSmartsContainers

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

recSmartsMatches

public List<List<org.openscience.cdk.interfaces.IAtom>> recSmartsMatches

stereoLigands

public List<org.openscience.cdk.interfaces.IAtom> stereoLigands

extChirInfo

public ExtendedChiralityInfo extChirInfo

stereoRemovedTokens

public List<SmartsExpressionToken> stereoRemovedTokens

stereoTokenIndices

public int[] stereoTokenIndices

hasImplicitHStereoLigand

public boolean hasImplicitHStereoLigand

Constructor Detail

SmartsAtomExpression

public SmartsAtomExpression(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

matches

public boolean matches(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

matches in interface org.openscience.cdk.isomorphism.matchers.IQueryAtom

Overrides:

matches in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

stereoMatch

public boolean stereoMatch(org.openscience.cdk.interfaces.IAtom atom,
                           int targetStereo)

getLastToken

public SmartsExpressionToken getLastToken()

match_R

public boolean match_R(int[] atomRings,
                       int param,
                       org.openscience.cdk.interfaces.IAtom atom)

match_r

public boolean match_r(int[] atomRings,
                       int param,
                       org.openscience.cdk.interfaces.IAtom atom)

match_x

public boolean match_x(int param,
                       org.openscience.cdk.interfaces.IAtom atom)

match_iMOE

public boolean match_iMOE(int param,
                          org.openscience.cdk.interfaces.IAtom atom)

match_GMOE

public boolean match_GMOE(int param,
                          org.openscience.cdk.interfaces.IAtom atom)

match_XMOE

public boolean match_XMOE(org.openscience.cdk.interfaces.IAtom atom)

match_NMOE

public boolean match_NMOE(org.openscience.cdk.interfaces.IAtom atom)

match_vMOE

public boolean match_vMOE(int param,
                          org.openscience.cdk.interfaces.IAtom atom)

match_OB_Hybr

public boolean match_OB_Hybr(int param,
                             org.openscience.cdk.interfaces.IAtom atom)

toString

public String toString()

Specified by:

toString in interface org.openscience.cdk.interfaces.IChemObject

Overrides:

toString in class Object

stereoRemovedToString

public String stereoRemovedToString()

getStereoRemovedTokens

public void getStereoRemovedTokens()