ambit2.db.search.structure

Class QueryExactStructure

java.lang.Object

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

ambit2.db.search.structure.AbstractStructureQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition>

ambit2.db.search.structure.QueryExactStructure

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.IParameterizedQuery<String,org.openscience.cdk.interfaces.IAtomContainer,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

Deprecated.

Convert to InChI and use QueryStructure

public class QueryExactStructure
extends AbstractStructureQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition>

This is a hack to cope with the failure of SmilesGenerator to produce canonical SMILES.

Author:

nina

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 SMARTSPropertiesReader	bondPropertiesReader Deprecated.
protected AtomConfigurator	configurator Deprecated.
protected static String	EXACT Deprecated.
protected FingerprintGenerator	fpGenerator Deprecated.
protected MoleculeReader	reader Deprecated.
protected QueryPrescreenBitSet	screening Deprecated.
protected StructureKeysBitSetGenerator	skGenerator Deprecated.
protected Property	smartsProperty Deprecated.
protected org.openscience.cdk.isomorphism.UniversalIsomorphismTester	uit Deprecated.

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
QueryExactStructure() Deprecated.

Method Summary

Modifier and Type	Method and Description
double	calculateMetric(IStructureRecord object) Deprecated.
String	getCategory() Deprecated.
String	getKey() Deprecated.
List<net.idea.modbcum.i.query.QueryParam>	getParameters() Deprecated.
String	getSQL() Deprecated.
boolean	isPrescreen() Deprecated.
void	prepareScreening() Deprecated.
void	setChemicalsOnly(boolean chemicalsOnly) Deprecated.
void	setId(Integer id) Deprecated.
void	setValue(org.openscience.cdk.interfaces.IAtomContainer value) Deprecated.
String	toString() Deprecated.

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, supportsPaging, 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, supportsPaging

Field Detail

skGenerator

protected transient StructureKeysBitSetGenerator skGenerator

Deprecated.

fpGenerator

protected transient FingerprintGenerator fpGenerator

Deprecated.

screening

protected QueryPrescreenBitSet screening

Deprecated.

reader

protected transient MoleculeReader reader

Deprecated.

configurator

protected transient AtomConfigurator configurator

Deprecated.

bondPropertiesReader

protected transient SMARTSPropertiesReader bondPropertiesReader

Deprecated.

smartsProperty

protected Property smartsProperty

Deprecated.

EXACT

protected static final String EXACT

Deprecated.

See Also:

Constant Field Values

uit

protected transient org.openscience.cdk.isomorphism.UniversalIsomorphismTester uit

Deprecated.

Constructor Detail

QueryExactStructure

public QueryExactStructure()
                    throws Exception

Deprecated.

Throws:

Exception

Method Detail

getSQL

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

Deprecated.

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setChemicalsOnly

public void setChemicalsOnly(boolean chemicalsOnly)

Deprecated.

Overrides:

setChemicalsOnly in class AbstractStructureQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition>

setId

public void setId(Integer id)

Deprecated.

Specified by:

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

Overrides:

setId in class AbstractQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

getParameters

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

Deprecated.

Throws:

net.idea.modbcum.i.exceptions.AmbitException

prepareScreening

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

Deprecated.

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setValue

public void setValue(org.openscience.cdk.interfaces.IAtomContainer value)

Deprecated.

Specified by:

setValue in interface net.idea.modbcum.i.IParameterizedQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition>

Overrides:

setValue in class AbstractQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

getKey

public String getKey()

Deprecated.

Specified by:

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

Overrides:

getKey in class AbstractQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

getCategory

public String getCategory()

Deprecated.

Specified by:

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

Overrides:

getCategory in class AbstractQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>

isPrescreen

public boolean isPrescreen()

Deprecated.

Specified by:

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

Overrides:

isPrescreen in class AbstractStructureQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition>

calculateMetric

public double calculateMetric(IStructureRecord object)

Deprecated.

Specified by:

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

Overrides:

calculateMetric in class AbstractStructureQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition>

toString

public String toString()

Deprecated.

Overrides:

toString in class AbstractQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord>