org.jmol.adapter.readers.quantum
Class SpartanInputReader

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

public abstract class SpartanInputReader
extends BasisFunctionReader


Field Summary
protected  int atomCount
           
protected  java.lang.String bondData
           
(package private)  java.lang.String constraints
           
protected  int modelAtomCount
           
protected  java.lang.String modelName
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
 
Constructor Summary
SpartanInputReader()
           
 
Method Summary
private  void readAtomNames()
           
private  void readBonds(int atomCount0)
           
private  void readConstraints()
           
private  void readInputAtoms()
           
private  void readInputHeader()
           
protected  void readInputRecords()
           
private  void readTransform()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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

modelAtomCount

protected int modelAtomCount

atomCount

protected int atomCount

bondData

protected java.lang.String bondData

constraints

java.lang.String constraints
Constructor Detail

SpartanInputReader

public SpartanInputReader()
Method Detail

readInputRecords

protected void readInputRecords()
                         throws java.lang.Exception
Throws:
java.lang.Exception

readConstraints

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

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