org.jmol.adapter.readers.more
Class SpartanInputReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.SpartanInputReader
Direct Known Subclasses:
OdysseyReader, SpartanSmolReader

abstract class SpartanInputReader
extends AtomSetCollectionReader


Field Summary
protected  int atomCount
           
(package private)  int atomCount0
           
protected  int bondCount
           
protected  java.lang.String bondData
           
(package private)  int modelAtomCount
           
protected  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
SpartanInputReader()
           
 
Method Summary
private  void readAtomNames()
           
private  void readBonds(int atomCount0)
           
private  void readInputAtoms()
           
private  void readInputHeader()
           
protected  void readInputRecords()
           
private  void readTransform()
           
 
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, readAtomSetCollection, 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

protected java.lang.String modelName

atomCount

protected int atomCount

bondCount

protected int bondCount

bondData

protected java.lang.String bondData

modelAtomCount

int modelAtomCount

atomCount0

int atomCount0
Constructor Detail

SpartanInputReader

SpartanInputReader()
Method Detail

readInputRecords

protected void readInputRecords()

readTransform

private void readTransform()
                    throws java.lang.Exception
Throws:
java.lang.Exception

readInputHeader

private void readInputHeader()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readInputAtoms

private void readInputAtoms()
                     throws java.lang.Exception
Throws:
java.lang.Exception

readAtomNames

private void readAtomNames()
                    throws java.lang.Exception
Throws:
java.lang.Exception

readBonds

private void readBonds(int atomCount0)
                throws java.lang.Exception
Throws:
java.lang.Exception