ambit2.smarts.processors

Class StructureKeysBitSetGenerator

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,BitSet>

ambit2.smarts.processors.StructureKeysBitSetGenerator

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,BitSet>

public class StructureKeysBitSetGenerator
extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,BitSet>

Generates screening fingerprints / structural keys for smarts queries

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected CDKHueckelAromaticityDetector	aromaticDetector
protected AtomConfigurator	cfg
protected boolean	cleanKekuleBonds
protected IsomorphismTester	isoTester
protected static int	nKeys
protected static List<List<QuerySequenceElement>>	sequences
protected static List<String>	smartsKeys
protected static List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer>	smartsQueries

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
StructureKeysBitSetGenerator()
StructureKeysBitSetGenerator(List<String> externalSmartsKeys)

Method Summary

Modifier and Type	Method and Description
static String	getKey(int index)
protected BitSet	getStructureKeyBits(org.openscience.cdk.interfaces.IAtomContainer ac)
static int	indexOf(String key)
boolean	isCleanKekuleBonds()
protected void	prepareKeySequences(List<String> keys, int nKeys)
BitSet	process(org.openscience.cdk.interfaces.IAtomContainer target)
void	setCleanKekuleBonds(boolean cleanKekuleBonds)
void	setSmartsKeys(List<String> smartsKeys)

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

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

Field Detail

isoTester

protected IsomorphismTester isoTester

smartsQueries

protected static List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> smartsQueries

sequences

protected static List<List<QuerySequenceElement>> sequences

smartsKeys

protected static List<String> smartsKeys

nKeys

protected static int nKeys

cfg

protected AtomConfigurator cfg

aromaticDetector

protected CDKHueckelAromaticityDetector aromaticDetector

cleanKekuleBonds

protected boolean cleanKekuleBonds

Constructor Detail

StructureKeysBitSetGenerator

public StructureKeysBitSetGenerator()
                             throws Exception

Throws:

Exception

StructureKeysBitSetGenerator

public StructureKeysBitSetGenerator(List<String> externalSmartsKeys)
                             throws Exception

Throws:

Exception

Method Detail

isCleanKekuleBonds

public boolean isCleanKekuleBonds()

setCleanKekuleBonds

public void setCleanKekuleBonds(boolean cleanKekuleBonds)

setSmartsKeys

public void setSmartsKeys(List<String> smartsKeys)
                   throws EmptyMoleculeException

Throws:

EmptyMoleculeException

prepareKeySequences

protected void prepareKeySequences(List<String> keys,
                                   int nKeys)
                            throws EmptyMoleculeException

Throws:

EmptyMoleculeException

process

public BitSet process(org.openscience.cdk.interfaces.IAtomContainer target)
               throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getStructureKeyBits

protected BitSet getStructureKeyBits(org.openscience.cdk.interfaces.IAtomContainer ac)

getKey

public static String getKey(int index)

indexOf

public static int indexOf(String key)