toxTree.data
Class MoleculesFile
java.lang.Object
org.openscience.cdk.ChemObject
toxTree.data.MoleculesFile
- All Implemented Interfaces:
- java.io.Serializable, java.lang.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
Constructor Summary |
MoleculesFile(java.io.File file,
org.openscience.cdk.interfaces.IChemObjectBuilder builder)
|
MoleculesFile(java.io.File file,
org.openscience.cdk.interfaces.IChemObjectBuilder builder,
org.openscience.cdk.io.listener.IReaderListener listener)
|
MoleculesFile(java.lang.String resource,
org.openscience.cdk.interfaces.IChemObjectBuilder builder,
org.openscience.cdk.io.listener.IReaderListener listener)
|
Method Summary |
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(java.beans.PropertyChangeListener listener)
|
void |
addPropertyChangeListener(java.lang.String propertyName,
java.beans.PropertyChangeListener listener)
|
java.lang.Iterable<org.openscience.cdk.interfaces.IAtomContainer> |
atomContainers()
|
void |
close()
|
org.openscience.cdk.io.random.RandomAccessReader |
createReader(java.io.File file,
org.openscience.cdk.interfaces.IChemObjectBuilder builder,
org.openscience.cdk.io.listener.IReaderListener listener)
|
boolean |
equals(java.lang.Object obj)
|
protected void |
finalize()
|
int |
find(org.openscience.cdk.interfaces.IAtomContainer mol)
TODO introduce isomorphism check to handle nonunique fingerprints |
void |
firePropertyChange(java.beans.PropertyChangeEvent event)
|
void |
firePropertyChange(java.lang.String propertyName,
java.lang.Object oldValue,
java.lang.Object newValue)
|
java.lang.Object |
first()
|
org.openscience.cdk.interfaces.IAtomContainer |
getAtomContainer(int index)
|
int |
getAtomContainerCount()
|
java.util.BitSet |
getFingerprint(org.openscience.cdk.interfaces.IAtomContainer mol)
|
java.lang.Double |
getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
|
java.lang.Double |
getMultiplier(int arg0)
|
java.lang.Double[] |
getMultipliers()
|
java.util.Map |
getProperties(int index)
|
java.lang.Object |
getProperty(int index,
java.lang.Object key)
|
org.openscience.cdk.io.random.RandomAccessReader |
getReader()
|
int |
getSelectedIndex()
|
java.util.Collection<java.lang.Comparable> |
getValuesPerField(java.lang.Object field,
int limit)
|
boolean |
hasNext()
|
boolean |
hasPrevious()
|
int |
indexOf(java.lang.Object property,
java.lang.Object value)
|
boolean |
isBuffered(int index,
java.lang.Object key)
|
boolean |
isBufferProperties()
|
java.lang.Object |
last()
|
java.lang.Object |
next()
|
int |
nextIndex()
|
protected void |
prepareProperty(java.lang.Object property)
|
java.lang.Object |
previous()
|
int |
previousIndex()
|
void |
removeAllAtomContainers()
|
void |
removeAtomContainer(org.openscience.cdk.interfaces.IAtomContainer arg0)
|
void |
removeAtomContainer(int arg0)
|
void |
removePropertyChangeListener(java.beans.PropertyChangeListener listener)
|
void |
removePropertyChangeListener(java.lang.String propertyName,
java.beans.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,
java.lang.Double arg1)
|
void |
setMultiplier(int arg0,
java.lang.Double arg1)
|
boolean |
setMultipliers(java.lang.Double[] arg0)
|
void |
setProperty(int index,
java.lang.Object key,
java.lang.Object value)
|
java.lang.Object |
setSelectedIndex(int index)
|
void |
sortAtomContainers(java.util.Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)
|
void |
sortBy(java.lang.Object property,
boolean ascending)
|
void |
stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
|
java.lang.String |
toString()
|
Methods inherited from class org.openscience.cdk.ChemObject |
addListener, clone, compare, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, 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, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty |
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject |
getBuilder |
propertyFingerprint
public static java.lang.String propertyFingerprint
smigen
protected org.openscience.cdk.smiles.SmilesGenerator smigen
fp
protected org.openscience.cdk.fingerprint.Fingerprinter fp
NA
protected static java.lang.String NA
reader
protected org.openscience.cdk.io.random.RandomAccessReader reader
updatedProperties
protected final java.util.Hashtable[] updatedProperties
selectedIndex
protected int selectedIndex
bufferProperties
protected boolean bufferProperties
propertyChangeSupport
protected java.beans.PropertyChangeSupport propertyChangeSupport
foundIndex
protected int foundIndex
logger
protected TTLogger logger
sortedProperties
protected SortedPropertyList sortedProperties
MoleculesFile
public MoleculesFile(java.lang.String resource,
org.openscience.cdk.interfaces.IChemObjectBuilder builder,
org.openscience.cdk.io.listener.IReaderListener listener)
throws java.lang.Exception
- Throws:
java.lang.Exception
MoleculesFile
public MoleculesFile(java.io.File file,
org.openscience.cdk.interfaces.IChemObjectBuilder builder)
throws java.lang.Exception
- Throws:
java.lang.Exception
MoleculesFile
public MoleculesFile(java.io.File file,
org.openscience.cdk.interfaces.IChemObjectBuilder builder,
org.openscience.cdk.io.listener.IReaderListener listener)
throws java.lang.Exception
- Throws:
java.lang.Exception
createReader
public org.openscience.cdk.io.random.RandomAccessReader createReader(java.io.File file,
org.openscience.cdk.interfaces.IChemObjectBuilder builder,
org.openscience.cdk.io.listener.IReaderListener listener)
throws java.lang.Exception
- Throws:
java.lang.Exception
close
public void close()
finalize
protected void finalize()
throws java.lang.Throwable
- Overrides:
finalize
in class java.lang.Object
- Throws:
java.lang.Throwable
first
public java.lang.Object first()
last
public java.lang.Object last()
setSelectedIndex
public java.lang.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
getAtomContainerCount
public int getAtomContainerCount()
- Specified by:
getAtomContainerCount
in interface org.openscience.cdk.interfaces.IAtomContainerSet
hasNext
public boolean hasNext()
next
public java.lang.Object next()
hasPrevious
public boolean hasPrevious()
previous
public java.lang.Object previous()
nextIndex
public int nextIndex()
previousIndex
public int previousIndex()
getProperties
public java.util.Map getProperties(int index)
isBuffered
public boolean isBuffered(int index,
java.lang.Object key)
getProperty
public java.lang.Object getProperty(int index,
java.lang.Object key)
setProperty
public final void setProperty(int index,
java.lang.Object key,
java.lang.Object value)
stateChanged
public void stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
- Specified by:
stateChanged
in interface org.openscience.cdk.interfaces.IChemObjectListener
toString
public java.lang.String toString()
- Specified by:
toString
in interface org.openscience.cdk.interfaces.IChemObject
- Overrides:
toString
in class java.lang.Object
isBufferProperties
public boolean isBufferProperties()
setBufferProperties
public void setBufferProperties(boolean bufferProperties)
equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in class java.lang.Object
getReader
public org.openscience.cdk.io.random.RandomAccessReader getReader()
addPropertyChangeListener
public void addPropertyChangeListener(java.beans.PropertyChangeListener listener)
removePropertyChangeListener
public void removePropertyChangeListener(java.beans.PropertyChangeListener listener)
addPropertyChangeListener
public void addPropertyChangeListener(java.lang.String propertyName,
java.beans.PropertyChangeListener listener)
removePropertyChangeListener
public void removePropertyChangeListener(java.lang.String propertyName,
java.beans.PropertyChangeListener listener)
firePropertyChange
public void firePropertyChange(java.lang.String propertyName,
java.lang.Object oldValue,
java.lang.Object newValue)
firePropertyChange
public void firePropertyChange(java.beans.PropertyChangeEvent event)
prepareProperty
protected void prepareProperty(java.lang.Object property)
throws java.lang.Exception
- Throws:
java.lang.Exception
indexOf
public int indexOf(java.lang.Object property,
java.lang.Object value)
throws java.lang.Exception
- Throws:
java.lang.Exception
sortBy
public void sortBy(java.lang.Object property,
boolean ascending)
throws java.lang.Exception
- Throws:
java.lang.Exception
getValuesPerField
public java.util.Collection<java.lang.Comparable> getValuesPerField(java.lang.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 java.lang.Iterable<org.openscience.cdk.interfaces.IAtomContainer> atomContainers()
- Specified by:
atomContainers
in interface org.openscience.cdk.interfaces.IAtomContainerSet
getMultiplier
public java.lang.Double getMultiplier(int arg0)
- Specified by:
getMultiplier
in interface org.openscience.cdk.interfaces.IAtomContainerSet
getMultiplier
public java.lang.Double getMultiplier(org.openscience.cdk.interfaces.IAtomContainer arg0)
- Specified by:
getMultiplier
in interface org.openscience.cdk.interfaces.IAtomContainerSet
getMultipliers
public java.lang.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,
java.lang.Double arg1)
- Specified by:
setMultiplier
in interface org.openscience.cdk.interfaces.IAtomContainerSet
setMultiplier
public void setMultiplier(int arg0,
java.lang.Double arg1)
- Specified by:
setMultiplier
in interface org.openscience.cdk.interfaces.IAtomContainerSet
setMultipliers
public boolean setMultipliers(java.lang.Double[] arg0)
- Specified by:
setMultipliers
in interface org.openscience.cdk.interfaces.IAtomContainerSet
find
public int find(org.openscience.cdk.interfaces.IAtomContainer mol)
throws java.lang.Exception
- TODO introduce isomorphism check to handle nonunique fingerprints
- Throws:
java.lang.Exception
getFingerprint
public java.util.BitSet getFingerprint(org.openscience.cdk.interfaces.IAtomContainer mol)
throws java.lang.Exception
- Throws:
java.lang.Exception
sortAtomContainers
public void sortAtomContainers(java.util.Comparator<org.openscience.cdk.interfaces.IAtomContainer> comparator)
- Specified by:
sortAtomContainers
in interface org.openscience.cdk.interfaces.IAtomContainerSet
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