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
protected  java.lang.String fileType
           
 
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
GromacsReader()
           
 
Method Summary
(package private)  java.lang.String deduceElementSymbol(java.lang.String group3, java.lang.String atomName)
           
private  int readAtomCount()
           
private  void readAtoms(int modelAtomCount)
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
private  void readHeader()
           
 
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, 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

fileType

protected java.lang.String fileType
Constructor Detail

GromacsReader

public GromacsReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

readAtomCount

private int readAtomCount()
                   throws java.lang.Exception
Throws:
java.lang.Exception

readHeader

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

readAtoms

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

deduceElementSymbol

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