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  java.util.Vector trajectorySteps
           
 
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
MdCrdReader()
           
 
Method Summary
private  float getFloat()
           
private  javax.vecmath.Point3f getPoint()
           
private  boolean getTrajectoryStep(javax.vecmath.Point3f[] trajectoryStep, boolean isPeriodic)
           
 void readAtomSetCollection(java.io.BufferedReader br)
           
(package private)  void readCoordinates()
           
private  boolean skipFloats(int n)
           
 
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

trajectorySteps

private java.util.Vector trajectorySteps

ptFloat

private int ptFloat

lenLine

private int lenLine
Constructor Detail

MdCrdReader

public MdCrdReader()
Method Detail

readAtomSetCollection

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

readCoordinates

void readCoordinates()
               throws java.lang.Exception
Throws:
java.lang.Exception

getFloat

private float getFloat()
                throws java.lang.Exception
Throws:
java.lang.Exception

getPoint

private javax.vecmath.Point3f getPoint()
                                throws java.lang.Exception
Throws:
java.lang.Exception

getTrajectoryStep

private boolean getTrajectoryStep(javax.vecmath.Point3f[] trajectoryStep,
                                  boolean isPeriodic)
                           throws java.lang.Exception
Throws:
java.lang.Exception

skipFloats

private boolean skipFloats(int n)
                    throws java.lang.Exception
Throws:
java.lang.Exception