ambit2.ui.jmol

Class CdkJmolAdapter

java.lang.Object

org.jmol.api.JmolAdapter

ambit2.ui.jmol.CdkJmolAdapter

public class CdkJmolAdapter
extends org.jmol.api.JmolAdapter

Provides an interface to CDK IO and CDK data classes. The openBufferedReader uses the ReaderFactory to get an CDK Reader. The getAtomIterator and other methods that act on a clientFile accept AtomContainers and ChemFiles.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	CdkJmolAdapter.StructureIterator

Field Summary

Fields inherited from class org.jmol.api.JmolAdapter

ORDER_AROMATIC, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_STEREO_FAR, ORDER_STEREO_NEAR, ORDER_UNSPECIFIED

Constructor Summary

Constructors

Constructor and Description
CdkJmolAdapter(String s)

Method Summary

Modifier and Type	Method and Description
org.jmol.api.JmolAdapter.AtomIterator	getAtomIterator(Object clientFile)
String	getAtomSetCollectionName(Object clientFile)
int	getAtomSetCount(Object clientFile)
org.jmol.api.JmolAdapter.BondIterator	getBondIterator(Object clientFile)
String	getClientAtomStringProperty(Object clientAtom, String propertyName)
int	getEstimatedAtomCount(Object clientFile)
String	getFileTypeName(Object clientFile)
float[]	getNotionalUnitcell(Object clientFile)
org.jmol.api.JmolAdapter.StructureIterator	getStructureIterator(Object clientFile)
Object	openBufferedReader(String name, BufferedReader bufferedReader)
Object	openBufferedReader(String name, String type, BufferedReader bufferedReader, Hashtable htParams)

Methods inherited from class org.jmol.api.JmolAdapter

canonizeAlphaDigit, canonizeAlternateLocationID, canonizeChainID, canonizeInsertionCode, coordinatesAreFractional, finish, getAdapterName, getAtomSetAuxiliaryInfo, getAtomSetCollectionAuxiliaryInfo, getAtomSetCollectionProperties, getAtomSetName, getAtomSetNumber, getAtomSetProperties, getPdbScaleMatrix, getPdbScaleTranslate, openBufferedReader, openBufferedReader, openBufferedReaders, openBufferedReaders, openDOMReader

Methods inherited from class java.lang.Object

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

Constructor Detail

CdkJmolAdapter

public CdkJmolAdapter(String s)

Method Detail

openBufferedReader

public Object openBufferedReader(String name,
                                 BufferedReader bufferedReader)

Overrides:

openBufferedReader in class org.jmol.api.JmolAdapter

openBufferedReader

public Object openBufferedReader(String name,
                                 String type,
                                 BufferedReader bufferedReader,
                                 Hashtable htParams)

Overrides:

openBufferedReader in class org.jmol.api.JmolAdapter

getFileTypeName

public String getFileTypeName(Object clientFile)

Overrides:

getFileTypeName in class org.jmol.api.JmolAdapter

getAtomSetCollectionName

public String getAtomSetCollectionName(Object clientFile)

Overrides:

getAtomSetCollectionName in class org.jmol.api.JmolAdapter

getAtomSetCount

public int getAtomSetCount(Object clientFile)

Overrides:

getAtomSetCount in class org.jmol.api.JmolAdapter

getEstimatedAtomCount

public int getEstimatedAtomCount(Object clientFile)

Specified by:

getEstimatedAtomCount in class org.jmol.api.JmolAdapter

getNotionalUnitcell

public float[] getNotionalUnitcell(Object clientFile)

Overrides:

getNotionalUnitcell in class org.jmol.api.JmolAdapter

getClientAtomStringProperty

public String getClientAtomStringProperty(Object clientAtom,
                                          String propertyName)

Overrides:

getClientAtomStringProperty in class org.jmol.api.JmolAdapter

getAtomIterator

public org.jmol.api.JmolAdapter.AtomIterator getAtomIterator(Object clientFile)

Specified by:

getAtomIterator in class org.jmol.api.JmolAdapter

getBondIterator

public org.jmol.api.JmolAdapter.BondIterator getBondIterator(Object clientFile)

Overrides:

getBondIterator in class org.jmol.api.JmolAdapter

getStructureIterator

public org.jmol.api.JmolAdapter.StructureIterator getStructureIterator(Object clientFile)

Overrides:

getStructureIterator in class org.jmol.api.JmolAdapter