org.jmol.adapter.readers.quantum
Class SpartanSmolReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.SpartanInputReader
          extended by org.jmol.adapter.readers.quantum.SpartanSmolReader

public class SpartanSmolReader
extends SpartanInputReader


Field Summary
private  java.lang.String endCheck
           
private  boolean espCharges
           
private  boolean haveCharges
           
private  boolean iHaveModelStatement
           
(package private)  boolean isCompoundDocument
           
private  java.util.Hashtable moData
           
(package private)  SpartanArchive spartanArchive
           
private  java.lang.String title
           
(package private)  java.util.Hashtable titles
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.SpartanInputReader
atomCount, bondData, constraints, modelAtomCount, modelName
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
SpartanSmolReader()
           
 
Method Summary
private  float bytesToDoubleToFloat(byte[] bytes, int j)
           
protected  boolean checkLine()
           
protected  void finalizeReader()
           
private  int getModelNumber()
           
protected  void initializeReader()
           
private  void readArchive()
           
private  boolean readArchiveHeader()
           
private  void readOutput()
           
private  void readProperties()
           
private  void readTransform()
           
private  void setCharges()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.SpartanInputReader
readInputRecords
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, 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

iHaveModelStatement

private boolean iHaveModelStatement

espCharges

private boolean espCharges

isCompoundDocument

boolean isCompoundDocument

endCheck

private java.lang.String endCheck

moData

private java.util.Hashtable moData

title

private java.lang.String title

spartanArchive

SpartanArchive spartanArchive

titles

java.util.Hashtable titles

haveCharges

private boolean haveCharges
Constructor Detail

SpartanSmolReader

public SpartanSmolReader()
Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception
Overrides:
initializeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

checkLine

protected boolean checkLine()
                     throws java.lang.Exception
Overrides:
checkLine in class AtomSetCollectionReader
Returns:
true if need to read new line
Throws:
java.lang.Exception

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception
Overrides:
finalizeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

readTransform

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

bytesToDoubleToFloat

private float bytesToDoubleToFloat(byte[] bytes,
                                   int j)

readOutput

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

readArchive

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

setCharges

private void setCharges()

readProperties

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

getModelNumber

private int getModelNumber()

readArchiveHeader

private boolean readArchiveHeader()
                           throws java.lang.Exception
Throws:
java.lang.Exception