org.jmol.adapter.readers.more
Class MdCrdReader

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

public class MdCrdReader
extends AtomSetCollectionReader

Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command


Field Summary
private  int lenLine
           
private  int ptFloat
           
private  List trajectorySteps
           
 
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
MdCrdReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  float getFloat()
           
private  Point3f getPoint()
           
private  boolean getTrajectoryStep(Point3f[] trajectoryStep, boolean isPeriodic)
           
protected  void initializeReader()
           
private  void readCoordinates()
           
private  boolean skipFloats(int n)
           
 
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, 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
 

Field Detail

trajectorySteps

private List trajectorySteps

ptFloat

private int ptFloat

lenLine

private int lenLine
Constructor Detail

MdCrdReader

public MdCrdReader()
Method Detail

initializeReader

protected void initializeReader()
Overrides:
initializeReader in class AtomSetCollectionReader

checkLine

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

readCoordinates

private void readCoordinates()
                      throws Exception
Throws:
Exception

getFloat

private float getFloat()
                throws Exception
Throws:
Exception

getPoint

private Point3f getPoint()
                  throws Exception
Throws:
Exception

getTrajectoryStep

private boolean getTrajectoryStep(Point3f[] trajectoryStep,
                                  boolean isPeriodic)
                           throws Exception
Throws:
Exception

skipFloats

private boolean skipFloats(int n)
                    throws Exception
Throws:
Exception