org.jmol.adapter.readers.more
Class MdCrdReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
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
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 |
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 |
trajectorySteps
private java.util.Vector trajectorySteps
ptFloat
private int ptFloat
lenLine
private int lenLine
MdCrdReader
public MdCrdReader()
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