org.jmol.adapter.readers.quantum
Class SpartanSmolReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.SpartanInputReader
org.jmol.adapter.readers.quantum.SpartanSmolReader
public class SpartanSmolReader
- extends SpartanInputReader
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 |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, 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 |
iHaveModelStatement
private boolean iHaveModelStatement
espCharges
private boolean espCharges
isCompoundDocument
boolean isCompoundDocument
endCheck
private String endCheck
moData
private Hashtable moData
title
private String title
spartanArchive
SpartanArchive spartanArchive
titles
Hashtable titles
haveCharges
private boolean haveCharges
SpartanSmolReader
public SpartanSmolReader()
initializeReader
protected void initializeReader()
throws Exception
- Overrides:
initializeReader
in class AtomSetCollectionReader
- Throws:
Exception
checkLine
protected boolean checkLine()
throws Exception
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
finalizeReader
protected void finalizeReader()
throws Exception
- Overrides:
finalizeReader
in class AtomSetCollectionReader
- Throws:
Exception
readTransform
private void readTransform()
throws Exception
- Throws:
Exception
bytesToDoubleToFloat
private float bytesToDoubleToFloat(byte[] bytes,
int j)
readOutput
private void readOutput()
throws Exception
- Throws:
Exception
readArchive
private void readArchive()
throws Exception
- Throws:
Exception
setCharges
private void setCharges()
readProperties
private void readProperties()
throws Exception
- Throws:
Exception
getModelNumber
private int getModelNumber()
readArchiveHeader
private boolean readArchiveHeader()
throws Exception
- Throws:
Exception