toxTree.data

Class MoleculesFile

java.lang.Object

org.openscience.cdk.ChemObject

toxTree.data.MoleculesFile

All Implemented Interfaces:

Serializable, Cloneable, org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IChemObjectListener

public class MoleculesFile
extends org.openscience.cdk.ChemObject
implements org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.IChemObjectListener

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	bufferProperties
protected int	foundIndex
protected org.openscience.cdk.fingerprint.Fingerprinter	fp
protected static Logger	logger
protected static String	NA
protected PropertyChangeSupport	propertyChangeSupport
static String	propertyFingerprint
protected org.openscience.cdk.io.random.RandomAccessReader	reader
protected int	selectedIndex
protected org.openscience.cdk.smiles.SmilesGenerator	smigen
protected SortedPropertyList	sortedProperties
protected Map[]	updatedProperties

Constructor Summary

Constructors

Constructor and Description
MoleculesFile(File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
MoleculesFile(File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)
MoleculesFile(String resource, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)

Method Summary

Modifier and Type	Method and Description
void	add(org.openscience.cdk.interfaces.IAtomContainerSet arg0)
void	addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer a)
void	addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0, double arg1)
void	addPropertyChangeListener(PropertyChangeListener listener)
void	addPropertyChangeListener(String propertyName, PropertyChangeListener listener)
Iterable<org.openscience.cdk.interfaces.IAtomContainer>	atomContainers()
void	close()
org.openscience.cdk.io.random.RandomAccessReader	createReader(File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)
boolean	equals(Object obj)
protected void	finalize()
int	find(org.openscience.cdk.interfaces.IAtomContainer mol) TODO introduce isomorphism check to handle nonunique fingerprints
void	firePropertyChange(PropertyChangeEvent event)
void	firePropertyChange(String propertyName, Object oldValue, Object newValue)
Object	first()
org.openscience.cdk.interfaces.IAtomContainer	getAtomContainer(int index)
int	getAtomContainerCount()
BitSet	getFingerprint(org.openscience.cdk.interfaces.IAtomContainer mol)
Double	getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
Double	getMultiplier(int arg0)
Double[]	getMultipliers()
Object	getProperty(int index, Object key)
org.openscience.cdk.io.random.RandomAccessReader	getReader()
int	getSelectedIndex()
Collection<Comparable>	getValuesPerField(Object field, int limit)
boolean	hasNext()
boolean	hasPrevious()
int	indexOf(Object property, Object value)
boolean	isBuffered(int index, Object key)
boolean	isBufferProperties()
boolean	isEmpty()
Object	last()
Object	next()
int	nextIndex()
protected void	prepareProperty(Object property)
Object	previous()
int	previousIndex()
void	removeAllAtomContainers()
void	removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0)
void	removeAtomContainer(int arg0)
void	removePropertyChangeListener(PropertyChangeListener listener)
void	removePropertyChangeListener(String propertyName, PropertyChangeListener listener)
void	replaceAtomContainer(int arg0, org.openscience.cdk.interfaces.IAtomContainer arg1)
void	setAtomContainers(org.openscience.cdk.interfaces.IAtomContainer[] molecules)
void	setBufferProperties(boolean bufferProperties)
boolean	setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0, Double arg1)
void	setMultiplier(int arg0, Double arg1)
boolean	setMultipliers(Double[] arg0)
void	setProperty(int index, Object key, Object value)
Object	setSelectedIndex(int index)
void	sortAtomContainers(Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)
void	sortBy(Object property, boolean ascending)
void	stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
String	toString()

Methods inherited from class org.openscience.cdk.ChemObject

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

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

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

addListener, addProperties, clone, 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

propertyFingerprint

public static String propertyFingerprint

smigen

protected org.openscience.cdk.smiles.SmilesGenerator smigen

fp

protected org.openscience.cdk.fingerprint.Fingerprinter fp

NA

protected static String NA

reader

protected org.openscience.cdk.io.random.RandomAccessReader reader

updatedProperties

protected final Map[] updatedProperties

selectedIndex

protected int selectedIndex

bufferProperties

protected boolean bufferProperties

propertyChangeSupport

protected PropertyChangeSupport propertyChangeSupport

foundIndex

protected int foundIndex

logger

protected static transient Logger logger

sortedProperties

protected SortedPropertyList sortedProperties

Constructor Detail

MoleculesFile

public MoleculesFile(String resource,
                     org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                     org.openscience.cdk.io.listener.IReaderListener listener)
              throws Exception

Throws:

Exception

MoleculesFile

public MoleculesFile(File file,
                     org.openscience.cdk.interfaces.IChemObjectBuilder builder)
              throws Exception

Throws:

Exception

MoleculesFile

public MoleculesFile(File file,
                     org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                     org.openscience.cdk.io.listener.IReaderListener listener)
              throws Exception

Throws:

Exception

Method Detail

createReader

public org.openscience.cdk.io.random.RandomAccessReader createReader(File file,
                                                                     org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                     org.openscience.cdk.io.listener.IReaderListener listener)
                                                              throws Exception

Throws:

Exception

close

public void close()

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

first

public Object first()

last

public Object last()

setSelectedIndex

public Object setSelectedIndex(int index)

getSelectedIndex

public int getSelectedIndex()

setAtomContainers

public void setAtomContainers(org.openscience.cdk.interfaces.IAtomContainer[] molecules)

getAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(int index)

Specified by:

getAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAllAtomContainers

public void removeAllAtomContainers()

Specified by:

removeAllAtomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface org.openscience.cdk.interfaces.IAtomContainerSet

getAtomContainerCount

public int getAtomContainerCount()

Specified by:

getAtomContainerCount in interface org.openscience.cdk.interfaces.IAtomContainerSet

hasNext

public boolean hasNext()

next

public Object next()

hasPrevious

public boolean hasPrevious()

previous

public Object previous()

nextIndex

public int nextIndex()

previousIndex

public int previousIndex()

isBuffered

public boolean isBuffered(int index,
                          Object key)

getProperty

public Object getProperty(int index,
                          Object key)

setProperty

public final void setProperty(int index,
                              Object key,
                              Object value)

stateChanged

public void stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)

Specified by:

stateChanged in interface org.openscience.cdk.interfaces.IChemObjectListener

toString

public String toString()

Specified by:

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

Overrides:

toString in class Object

isBufferProperties

public boolean isBufferProperties()

setBufferProperties

public void setBufferProperties(boolean bufferProperties)

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getReader

public org.openscience.cdk.io.random.RandomAccessReader getReader()

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener listener)

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener listener)

addPropertyChangeListener

public void addPropertyChangeListener(String propertyName,
                                      PropertyChangeListener listener)

removePropertyChangeListener

public void removePropertyChangeListener(String propertyName,
                                         PropertyChangeListener listener)

firePropertyChange

public void firePropertyChange(String propertyName,
                               Object oldValue,
                               Object newValue)

firePropertyChange

public void firePropertyChange(PropertyChangeEvent event)

prepareProperty

protected void prepareProperty(Object property)
                        throws Exception

Throws:

Exception

indexOf

public int indexOf(Object property,
                   Object value)
            throws Exception

Throws:

Exception

sortBy

public void sortBy(Object property,
                   boolean ascending)
            throws Exception

Throws:

Exception

getValuesPerField

public Collection<Comparable> getValuesPerField(Object field,
                                                int limit)

add

public void add(org.openscience.cdk.interfaces.IAtomContainerSet arg0)

Specified by:

add in interface org.openscience.cdk.interfaces.IAtomContainerSet

addAtomContainer

public void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer a)

Specified by:

addAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

addAtomContainer

public void addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0,
                             double arg1)

Specified by:

addAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

atomContainers

public Iterable<org.openscience.cdk.interfaces.IAtomContainer> atomContainers()

Specified by:

atomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public Double getMultiplier(int arg0)

Specified by:

getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultiplier

public Double getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)

Specified by:

getMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

getMultipliers

public Double[] getMultipliers()

Specified by:

getMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0)

Specified by:

removeAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(int arg0)

Specified by:

removeAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

replaceAtomContainer

public void replaceAtomContainer(int arg0,
                                 org.openscience.cdk.interfaces.IAtomContainer arg1)

Specified by:

replaceAtomContainer in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultiplier

public boolean setMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0,
                             Double arg1)

Specified by:

setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultiplier

public void setMultiplier(int arg0,
                          Double arg1)

Specified by:

setMultiplier in interface org.openscience.cdk.interfaces.IAtomContainerSet

setMultipliers

public boolean setMultipliers(Double[] arg0)

Specified by:

setMultipliers in interface org.openscience.cdk.interfaces.IAtomContainerSet

find

public int find(org.openscience.cdk.interfaces.IAtomContainer mol)
         throws Exception

TODO introduce isomorphism check to handle nonunique fingerprints

Throws:

Exception

getFingerprint

public BitSet getFingerprint(org.openscience.cdk.interfaces.IAtomContainer mol)
                      throws Exception

Throws:

Exception

sortAtomContainers

public void sortAtomContainers(Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)

Specified by:

sortAtomContainers in interface org.openscience.cdk.interfaces.IAtomContainerSet