ambit2.db.search.structure

Class QuerySMARTS

java.lang.Object

ambit2.db.search.AbstractQuery<F,T,C,IStructureRecord>

ambit2.db.search.structure.AbstractStructureQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>

ambit2.db.search.structure.QuerySMARTS

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.IParameterizedQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>, net.idea.modbcum.i.IQueryObject<IStructureRecord>, net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>, net.idea.modbcum.i.IRetrieval<IStructureRecord>, net.idea.modbcum.i.IStatement

public class QuerySMARTS
extends AbstractStructureQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>

Select structures by querying fungroups table by smarts

Author:

Nina Jeliazkova nina@acad.bg

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ambit2.db.search.structure.AbstractStructureQuery

AbstractStructureQuery.FIELD_NAMES

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IChemObjectBuilder	builder
protected AtomConfigurator	configurator
protected boolean	fp1024_screening
protected FingerprintGenerator	fpGenerator
protected org.openscience.cdk.tools.CDKHydrogenAdder	hAdder
protected MoleculeReader	reader
protected QueryPrescreenBitSet	screening
protected boolean	sk1024_screening
protected StructureKeysBitSetGenerator	skGenerator
protected static String	SMARTS
protected Property	smartsProperty
protected SmartsToChemObject	smartsToChemObject
protected boolean	usePrecalculatedAtomProperties

Fields inherited from class ambit2.db.search.structure.AbstractStructureQuery

chemicalsOnly, group, nanomaterial, order_descendant, where_group

Fields inherited from class ambit2.db.search.AbstractQuery

condition, fieldname, id, logger, maxRecords, name, page, selected, value

Fields inherited from interface net.idea.modbcum.i.IQueryRetrieval

NaN

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
double	calculateMetric(IStructureRecord object)
String	getCategory()
String	getKey()
List<net.idea.modbcum.i.query.QueryParam>	getParameters()
String	getSQL()
boolean	isFp1024_screening()
boolean	isPrescreen()
boolean	isSk1024_screening()
boolean	isUsePrecalculatedAtomProperties()
void	prepareScreening()
void	setChemicalsOnly(boolean chemicalsOnly)
void	setFp1024_screening(boolean fp1024_screening)
void	setId(Integer id)
void	setSk1024_screening(boolean sk1024_screening)
void	setUsePrecalculatedAtomProperties(boolean usePrecalculatedAtomProperties)
void	setValue(FunctionalGroup value)
boolean	supportsPaging()
String	toString()

Methods inherited from class ambit2.db.search.structure.AbstractStructureQuery

getObject, isChemicalsOnly, isNanomaterial, isOrder_descendant, isPreferredStructure, retrieveMetric, retrieveStrucType, retrieveValue, setNanomaterial, setOrder_descendant

Methods inherited from class ambit2.db.search.AbstractQuery

getCondition, getFieldname, getId, getName, getPage, getPageSize, getValue, isSelected, setCondition, setFieldname, setName, setPage, setPageSize, setSelected, stringify, test

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.idea.modbcum.i.IQueryObject

getId, getPage, getPageSize, setPage, setPageSize

Field Detail

smartsToChemObject

protected SmartsToChemObject smartsToChemObject

skGenerator

protected final transient StructureKeysBitSetGenerator skGenerator

fpGenerator

protected final transient FingerprintGenerator fpGenerator

screening

protected QueryPrescreenBitSet screening

reader

protected transient MoleculeReader reader

configurator

protected transient AtomConfigurator configurator

hAdder

protected transient org.openscience.cdk.tools.CDKHydrogenAdder hAdder

smartsProperty

protected Property smartsProperty

SMARTS

protected static final String SMARTS

See Also:

Constant Field Values

fp1024_screening

protected boolean fp1024_screening

sk1024_screening

protected boolean sk1024_screening

usePrecalculatedAtomProperties

protected boolean usePrecalculatedAtomProperties

builder

protected org.openscience.cdk.interfaces.IChemObjectBuilder builder

Constructor Detail

QuerySMARTS

public QuerySMARTS()
            throws Exception

Throws:

Exception

QuerySMARTS

public QuerySMARTS(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
            throws Exception

Throws:

Exception

Method Detail

isFp1024_screening

public boolean isFp1024_screening()

setFp1024_screening

public void setFp1024_screening(boolean fp1024_screening)

isSk1024_screening

public boolean isSk1024_screening()

setSk1024_screening

public void setSk1024_screening(boolean sk1024_screening)

isUsePrecalculatedAtomProperties

public boolean isUsePrecalculatedAtomProperties()

setUsePrecalculatedAtomProperties

public void setUsePrecalculatedAtomProperties(boolean usePrecalculatedAtomProperties)

getSQL

public String getSQL()
              throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setChemicalsOnly

public void setChemicalsOnly(boolean chemicalsOnly)

Overrides:

setChemicalsOnly in class AbstractStructureQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>

setId

public void setId(Integer id)

Specified by:

setId in interface net.idea.modbcum.i.IQueryObject<IStructureRecord>

Overrides:

setId in class AbstractQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

getParameters

public List<net.idea.modbcum.i.query.QueryParam> getParameters()
                                                        throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

prepareScreening

public void prepareScreening()
                      throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setValue

public void setValue(FunctionalGroup value)

Specified by:

setValue in interface net.idea.modbcum.i.IParameterizedQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>

Overrides:

setValue in class AbstractQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

getKey

public String getKey()

Specified by:

getKey in interface net.idea.modbcum.i.IQueryObject<IStructureRecord>

Overrides:

getKey in class AbstractQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

getCategory

public String getCategory()

Specified by:

getCategory in interface net.idea.modbcum.i.IQueryObject<IStructureRecord>

Overrides:

getCategory in class AbstractQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

isPrescreen

public boolean isPrescreen()

Specified by:

isPrescreen in interface net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>

Overrides:

isPrescreen in class AbstractStructureQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>

calculateMetric

public double calculateMetric(IStructureRecord object)

Specified by:

calculateMetric in interface net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>

Overrides:

calculateMetric in class AbstractStructureQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition>

toString

public String toString()

Overrides:

toString in class AbstractQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

supportsPaging

public boolean supportsPaging()

Specified by:

supportsPaging in interface net.idea.modbcum.i.IQueryObject<IStructureRecord>

Overrides:

supportsPaging in class AbstractQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>