org.jmol.adapter.smarter

Class SmarterJmolAdapter

public class SmarterJmolAdapter extends JmolAdapter

Nested Class Summary
classSmarterJmolAdapter.AtomIterator
classSmarterJmolAdapter.BondIterator
classSmarterJmolAdapter.StructureIterator
Field Summary
static StringPATH_KEY
static StringPATH_SEPARATOR
Constructor Summary
SmarterJmolAdapter()
Method Summary
booleancoordinatesAreFractional(Object clientFile)
voidfinish(Object clientFile)
JmolAdapter.AtomIteratorgetAtomIterator(Object clientFile)
HashtablegetAtomSetAuxiliaryInfo(Object clientFile, int atomSetIndex)
HashtablegetAtomSetCollectionAuxiliaryInfo(Object clientFile)
StringgetAtomSetCollectionName(Object clientFile)
PropertiesgetAtomSetCollectionProperties(Object clientFile)
intgetAtomSetCount(Object clientFile)
StringgetAtomSetName(Object clientFile, int atomSetIndex)
intgetAtomSetNumber(Object clientFile, int atomSetIndex)
PropertiesgetAtomSetProperties(Object clientFile, int atomSetIndex)
JmolAdapter.BondIteratorgetBondIterator(Object clientFile)
intgetEstimatedAtomCount(Object clientFile)
StringgetFileTypeName(Object clientFile)
float[]getNotionalUnitcell(Object clientFile)
float[]getPdbScaleMatrix(Object clientFile)
float[]getPdbScaleTranslate(Object clientFile)
JmolAdapter.StructureIteratorgetStructureIterator(Object clientFile)
ObjectopenBufferedReader(String name, String type, BufferedReader bufferedReader, Hashtable htParams)
ObjectopenBufferedReaders(JmolFileReaderInterface fileReader, String[] names, String[] types, Hashtable[] htParams)
ObjectopenDOMReader(Object DOMNode)
ObjectopenZipFiles(InputStream is, String fileName, String[] zipDirectory, Hashtable htParams, boolean asBufferedReader)
String[]specialLoad(String name, String type)
static StringstaticGetFileTypeName(Object clientFile)
static ObjectstaticOpenBufferedReader(String name, String type, BufferedReader bufferedReader, Hashtable htParams)
static ObjectstaticOpenBufferedReaders(JmolFileReaderInterface fileReader, String[] names, String[] types, Hashtable[] htParams)
static ObjectstaticOpenDOMReader(Object DOMNode)
static ObjectstaticOpenZipFiles(InputStream is, String fileName, String[] zipDirectory, Hashtable htParams, int subFilePtr, boolean asBufferedReader)

Field Detail

PATH_KEY

public static final String PATH_KEY

PATH_SEPARATOR

public static final String PATH_SEPARATOR

Constructor Detail

SmarterJmolAdapter

public SmarterJmolAdapter()

Method Detail

coordinatesAreFractional

public boolean coordinatesAreFractional(Object clientFile)

finish

public void finish(Object clientFile)

getAtomIterator

public JmolAdapter.AtomIterator getAtomIterator(Object clientFile)

getAtomSetAuxiliaryInfo

public Hashtable getAtomSetAuxiliaryInfo(Object clientFile, int atomSetIndex)

getAtomSetCollectionAuxiliaryInfo

public Hashtable getAtomSetCollectionAuxiliaryInfo(Object clientFile)

getAtomSetCollectionName

public String getAtomSetCollectionName(Object clientFile)

getAtomSetCollectionProperties

public Properties getAtomSetCollectionProperties(Object clientFile)

getAtomSetCount

public int getAtomSetCount(Object clientFile)

getAtomSetName

public String getAtomSetName(Object clientFile, int atomSetIndex)

getAtomSetNumber

public int getAtomSetNumber(Object clientFile, int atomSetIndex)

getAtomSetProperties

public Properties getAtomSetProperties(Object clientFile, int atomSetIndex)

getBondIterator

public JmolAdapter.BondIterator getBondIterator(Object clientFile)

getEstimatedAtomCount

public int getEstimatedAtomCount(Object clientFile)

getFileTypeName

public String getFileTypeName(Object clientFile)

getNotionalUnitcell

public float[] getNotionalUnitcell(Object clientFile)

getPdbScaleMatrix

public float[] getPdbScaleMatrix(Object clientFile)

getPdbScaleTranslate

public float[] getPdbScaleTranslate(Object clientFile)

getStructureIterator

public JmolAdapter.StructureIterator getStructureIterator(Object clientFile)

openBufferedReader

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

openBufferedReaders

public Object openBufferedReaders(JmolFileReaderInterface fileReader, String[] names, String[] types, Hashtable[] htParams)

openDOMReader

public Object openDOMReader(Object DOMNode)

openZipFiles

public Object openZipFiles(InputStream is, String fileName, String[] zipDirectory, Hashtable htParams, boolean asBufferedReader)

specialLoad

public String[] specialLoad(String name, String type)

staticGetFileTypeName

private static String staticGetFileTypeName(Object clientFile)

staticOpenBufferedReader

private static Object staticOpenBufferedReader(String name, String type, BufferedReader bufferedReader, Hashtable htParams)

staticOpenBufferedReaders

private static Object staticOpenBufferedReaders(JmolFileReaderInterface fileReader, String[] names, String[] types, Hashtable[] htParams)

staticOpenDOMReader

private static Object staticOpenDOMReader(Object DOMNode)

staticOpenZipFiles

private static Object staticOpenZipFiles(InputStream is, String fileName, String[] zipDirectory, Hashtable htParams, int subFilePtr, boolean asBufferedReader)