org.jmol.adapter.readers.more
Class GromacsReader

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

public class GromacsReader
extends AtomSetCollectionReader


Field Summary
 
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
GromacsReader()
           
 
Method Summary
protected  boolean checkLine()
           
(package private)  java.lang.String deduceElementSymbol(java.lang.String group3, java.lang.String atomName)
           
protected  void initializeReader()
           
private  void readAtoms()
           
private  void readUnitCell()
           
 
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, finalizeReader, 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
 

Constructor Detail

GromacsReader

public GromacsReader()
Method Detail

initializeReader

protected void initializeReader()
Overrides:
initializeReader in class AtomSetCollectionReader

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

readAtoms

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

deduceElementSymbol

java.lang.String deduceElementSymbol(java.lang.String group3,
                                     java.lang.String atomName)

readUnitCell

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