cage.viewer.jmol
Class CaGeJmolAdapter

java.lang.Object
  org.jmol.api.JmolAdapter
      cage.viewer.jmol.CaGeJmolAdapter

public class CaGeJmolAdapter
extends org.jmol.api.JmolAdapter

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.api.JmolAdapter

org.jmol.api.JmolAdapter.AtomIterator, org.jmol.api.JmolAdapter.BondIterator, org.jmol.api.JmolAdapter.StructureIterator

Field Summary

Fields inherited from class org.jmol.api.JmolAdapter

ORDER_AROMATIC, ORDER_AROMATIC_DOUBLE, ORDER_AROMATIC_SINGLE, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_PARTIAL23, ORDER_PARTIAL32, ORDER_STEREO_FAR, ORDER_STEREO_NEAR, ORDER_UNSPECIFIED, SHELL_D_CARTESIAN, SHELL_D_SPHERICAL, SHELL_F_CARTESIAN, SHELL_F_SPHERICAL, SHELL_L, SHELL_P, SHELL_S, SHELL_SP

Constructor Summary

CaGeJmolAdapter()

Method Summary

org.jmol.api.JmolAdapter.AtomIterator	getAtomIterator(java.lang.Object clientFile)
org.jmol.api.JmolAdapter.BondIterator	getBondIterator(java.lang.Object clientFile)
int	getEstimatedAtomCount(java.lang.Object clientFile)
EmbeddableGraph	getGraph()
java.lang.Object	openBufferedReader(java.lang.String name, java.io.BufferedReader bufferedReader)
java.lang.Object	openBufferedReader(java.lang.String name, java.io.BufferedReader bufferedReader, java.util.Hashtable htParams)
java.lang.Object	openBufferedReader(java.lang.String name, java.lang.String type, java.io.BufferedReader bufferedReader)
java.lang.Object	openBufferedReader(java.lang.String name, java.lang.String type, java.io.BufferedReader bufferedReader, java.util.Hashtable htParams)
java.lang.Object	openBufferedReaders(org.jmol.api.JmolFileReaderInterface fileReader, java.lang.String[] names, java.lang.String[] types, java.util.Hashtable[] htParams)
java.lang.Object	openDOMReader(java.lang.Object DOMNode)
java.lang.Object	openZipFiles(java.io.InputStream is, java.lang.String fileName, java.lang.String[] zipDirectory, java.util.Hashtable htParams, boolean asBufferedReader)
void	setGeneratorInfo(GeneratorInfo generatorInfo)
void	setGraph(EmbeddableGraph graph)

Methods inherited from class org.jmol.api.JmolAdapter

canonicalizeQuantumSubshellTag, canonizeAlphaDigit, canonizeAlternateLocationID, canonizeChainID, canonizeInsertionCode, coordinatesAreFractional, finish, getAdapterName, getAtomSetAuxiliaryInfo, getAtomSetCollectionAuxiliaryInfo, getAtomSetCollectionName, getAtomSetCollectionProperties, getAtomSetCount, getAtomSetName, getAtomSetNumber, getAtomSetProperties, getClientAtomStringProperty, getElementNumber, getElementSymbol, getFileTypeName, getNotionalUnitcell, getPdbScaleMatrix, getPdbScaleTranslate, getQuantumShellTagID, getQuantumShellTagIDSpherical, getQuantumSubshellTag, getQuantumSubshellTagID, getStructureIterator, isHetero, specialLoad

Methods inherited from class java.lang.Object

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

Constructor Detail

CaGeJmolAdapter

public CaGeJmolAdapter()

Method Detail

openBufferedReader

public java.lang.Object openBufferedReader(java.lang.String name,
                                           java.lang.String type,
                                           java.io.BufferedReader bufferedReader,
                                           java.util.Hashtable htParams)

Overrides:

openBufferedReader in class org.jmol.api.JmolAdapter

openBufferedReader

public java.lang.Object openBufferedReader(java.lang.String name,
                                           java.io.BufferedReader bufferedReader)

Overrides:

openBufferedReader in class org.jmol.api.JmolAdapter

openBufferedReader

public java.lang.Object openBufferedReader(java.lang.String name,
                                           java.io.BufferedReader bufferedReader,
                                           java.util.Hashtable htParams)

Overrides:

openBufferedReader in class org.jmol.api.JmolAdapter

openBufferedReader

public java.lang.Object openBufferedReader(java.lang.String name,
                                           java.lang.String type,
                                           java.io.BufferedReader bufferedReader)

Overrides:

openBufferedReader in class org.jmol.api.JmolAdapter

openBufferedReaders

public java.lang.Object openBufferedReaders(org.jmol.api.JmolFileReaderInterface fileReader,
                                            java.lang.String[] names,
                                            java.lang.String[] types,
                                            java.util.Hashtable[] htParams)

Overrides:

openBufferedReaders in class org.jmol.api.JmolAdapter

openDOMReader

public java.lang.Object openDOMReader(java.lang.Object DOMNode)

Overrides:

openDOMReader in class org.jmol.api.JmolAdapter

openZipFiles

public java.lang.Object openZipFiles(java.io.InputStream is,
                                     java.lang.String fileName,
                                     java.lang.String[] zipDirectory,
                                     java.util.Hashtable htParams,
                                     boolean asBufferedReader)

Overrides:

openZipFiles in class org.jmol.api.JmolAdapter

getGraph

public EmbeddableGraph getGraph()

setGraph

public void setGraph(EmbeddableGraph graph)

setGeneratorInfo

public void setGeneratorInfo(GeneratorInfo generatorInfo)

getEstimatedAtomCount

public int getEstimatedAtomCount(java.lang.Object clientFile)

Specified by:

getEstimatedAtomCount in class org.jmol.api.JmolAdapter

getAtomIterator

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

Specified by:

getAtomIterator in class org.jmol.api.JmolAdapter

getBondIterator

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

Overrides:

getBondIterator in class org.jmol.api.JmolAdapter