org.jmol.adapter.readers.more
Class OdysseyXMLReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.OdysseyXMLReader

public class OdysseyXMLReader
extends AtomSetCollectionReader


Field Summary
(package private)  int atomCount
           
(package private)  int bondCount
           
(package private)  java.lang.String modelName
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
OdysseyXMLReader()
           
 
Method Summary
(package private)  void readAtoms()
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readBonds()
           
(package private)  void readDescription()
           
(package private)  java.util.Hashtable readXML(java.lang.String name)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

modelName

java.lang.String modelName

atomCount

int atomCount

bondCount

int bondCount
Constructor Detail

OdysseyXMLReader

public OdysseyXMLReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

readDescription

void readDescription()
               throws java.lang.Exception
Throws:
java.lang.Exception

readAtoms

void readAtoms()
         throws java.lang.Exception
Throws:
java.lang.Exception

readXML

java.util.Hashtable readXML(java.lang.String name)
                      throws java.lang.Exception
Throws:
java.lang.Exception

readBonds

void readBonds()
         throws java.lang.Exception
Throws:
java.lang.Exception