ambit2.smarts

Class SmartsManager

java.lang.Object

ambit2.smarts.SmartsManager

public class SmartsManager
extends Object

Implements utilities needed for handling searching with SMARTS utilizing JDK library. Some complex manipulations are encapsulated here (such as recursive smarts)

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IChemObjectBuilder	builder
boolean	mGenerateSubQueries
protected org.openscience.cdk.isomorphism.UniversalIsomorphismTester	uit

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	calcSmartsDataForTarget(org.openscience.cdk.interfaces.IAtomContainer mol)
protected boolean	checkComponentInCombination(int n, int[] a)
List<org.openscience.cdk.interfaces.IAtom>	generateFullAtomMapping(List bondMapList, org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.interfaces.IAtomContainer queryStr) This function generates full Atom Mapping from a Bond mapping (result from the CDK isomorphism
org.openscience.cdk.interfaces.IAtomContainer	generateFullIsomorphismMapping(List bondMapList, org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.interfaces.IAtomContainer queryStr)
org.openscience.cdk.interfaces.IAtomContainerSet	getAllIsomorphismMappings(org.openscience.cdk.interfaces.IAtomContainer target)
List	getBondMappings(org.openscience.cdk.interfaces.IAtomContainer target)
String	getErrors()
List<org.openscience.cdk.interfaces.IAtom>	getFirstPosAtomMappings(org.openscience.cdk.interfaces.IAtomContainer target)
boolean	getIsomorphismTesterFlagCheckStereoElements()
List<List<org.openscience.cdk.interfaces.IAtom>>	getMappingsForGroup(org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer groupQuery, SmartsConst.SSM_MODE FlagSSMode)
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	getQueryContaner()
boolean	getSupportDoubleBondAromaticityNotSpecified()
boolean	getSupportMOEExtension()
boolean	getSupportOpenBabelExtension()
boolean	getSupportOpenEyeExtension()
boolean	getUseMOEvPrimitive()
void	handleGroupRecursiveAtoms(org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer groupQuery)
boolean	isFlagUseCDKIsomorphismTester()
void	markAtomGroups(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> groupQueries) Calculates for each atom a bit set which describes the participation of this atom in each of the predefined groups.
void	markAtomGroups(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> groupQueries, SmartsConst.SSM_MODE FlagSSMode)
String	matchesToString(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> atomMaps)
boolean	searchIn(org.openscience.cdk.interfaces.IAtomContainer target)
void	setIsomorphismTesterFlagCheckStereoElements(boolean checkStereoElements)
void	setQuery(String smQuery)
void	setSmartsDataForTarget(boolean flag)
void	setUseCDKIsomorphismTester(boolean flag)
void	supportDoubleBondAromaticityNotSpecified(boolean support)
void	supportMOEExtension(boolean support)
void	supportOpenBabelExtension(boolean support)
void	supportOpenEyeExtension(boolean support)
void	testCombinations()
void	testSubQueries()
void	testTopLayers()
void	useMOEvPrimitive(boolean support)

Methods inherited from class java.lang.Object

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

Field Detail

uit

protected org.openscience.cdk.isomorphism.UniversalIsomorphismTester uit

mGenerateSubQueries

public boolean mGenerateSubQueries

builder

protected org.openscience.cdk.interfaces.IChemObjectBuilder builder

Constructor Detail

SmartsManager

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

Method Detail

isFlagUseCDKIsomorphismTester

public boolean isFlagUseCDKIsomorphismTester()

setQuery

public void setQuery(String smQuery)

getErrors

public String getErrors()

getQueryContaner

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer getQueryContaner()

setSmartsDataForTarget

public void setSmartsDataForTarget(boolean flag)

calcSmartsDataForTarget

public void calcSmartsDataForTarget(org.openscience.cdk.interfaces.IAtomContainer mol)
                             throws Exception

Throws:

Exception

setUseCDKIsomorphismTester

public void setUseCDKIsomorphismTester(boolean flag)

supportMOEExtension

public void supportMOEExtension(boolean support)

supportOpenEyeExtension

public void supportOpenEyeExtension(boolean support)

supportOpenBabelExtension

public void supportOpenBabelExtension(boolean support)

supportDoubleBondAromaticityNotSpecified

public void supportDoubleBondAromaticityNotSpecified(boolean support)

useMOEvPrimitive

public void useMOEvPrimitive(boolean support)

getSupportMOEExtension

public boolean getSupportMOEExtension()

getSupportOpenEyeExtension

public boolean getSupportOpenEyeExtension()

getSupportOpenBabelExtension

public boolean getSupportOpenBabelExtension()

getSupportDoubleBondAromaticityNotSpecified

public boolean getSupportDoubleBondAromaticityNotSpecified()

getUseMOEvPrimitive

public boolean getUseMOEvPrimitive()

searchIn

public boolean searchIn(org.openscience.cdk.interfaces.IAtomContainer target)
                 throws Exception

Throws:

Exception

checkComponentInCombination

protected boolean checkComponentInCombination(int n,
                                              int[] a)

getAllIsomorphismMappings

public org.openscience.cdk.interfaces.IAtomContainerSet getAllIsomorphismMappings(org.openscience.cdk.interfaces.IAtomContainer target)
                                                                           throws Exception

Throws:

Exception

getFirstPosAtomMappings

public List<org.openscience.cdk.interfaces.IAtom> getFirstPosAtomMappings(org.openscience.cdk.interfaces.IAtomContainer target)
                                                                   throws Exception

Throws:

Exception

getBondMappings

public List getBondMappings(org.openscience.cdk.interfaces.IAtomContainer target)
                     throws Exception

Throws:

Exception

matchesToString

public String matchesToString(org.openscience.cdk.interfaces.IAtomContainer target,
                              List<org.openscience.cdk.interfaces.IAtom> atomMaps)

generateFullAtomMapping

public List<org.openscience.cdk.interfaces.IAtom> generateFullAtomMapping(List bondMapList,
                                                                          org.openscience.cdk.interfaces.IAtomContainer target,
                                                                          org.openscience.cdk.interfaces.IAtomContainer queryStr)

This function generates full Atom Mapping from a Bond mapping (result from the CDK isomorphism

generateFullIsomorphismMapping

public org.openscience.cdk.interfaces.IAtomContainer generateFullIsomorphismMapping(List bondMapList,
                                                                                    org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                    org.openscience.cdk.interfaces.IAtomContainer queryStr)

markAtomGroups

public void markAtomGroups(org.openscience.cdk.interfaces.IAtomContainer target,
                           List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> groupQueries)
                    throws EmptyMoleculeException

Calculates for each atom a bit set which describes the participation of this atom in each of the predefined groups. This function uses IsomorphismTest for substructure searching. All possible groups mappings are found (FlagSSMode = SmartsConst.SSM_ALL)

Parameters:

target -

groupQueries -

Throws:

EmptyMoleculeException

markAtomGroups

public void markAtomGroups(org.openscience.cdk.interfaces.IAtomContainer target,
                           List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> groupQueries,
                           SmartsConst.SSM_MODE FlagSSMode)
                    throws EmptyMoleculeException

Throws:

EmptyMoleculeException

handleGroupRecursiveAtoms

public void handleGroupRecursiveAtoms(org.openscience.cdk.interfaces.IAtomContainer target,
                                      org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer groupQuery)
                               throws EmptyMoleculeException

Throws:

EmptyMoleculeException

getMappingsForGroup

public List<List<org.openscience.cdk.interfaces.IAtom>> getMappingsForGroup(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                            org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer groupQuery,
                                                                            SmartsConst.SSM_MODE FlagSSMode)

testCombinations

public void testCombinations()

testTopLayers

public void testTopLayers()

testSubQueries

public void testSubQueries()

getIsomorphismTesterFlagCheckStereoElements

public boolean getIsomorphismTesterFlagCheckStereoElements()

setIsomorphismTesterFlagCheckStereoElements

public void setIsomorphismTesterFlagCheckStereoElements(boolean checkStereoElements)