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 |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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.List<javax.vecmath.Point3f[]> trajectorySteps
ptFloat
private int ptFloat
lenLine
private int lenLine
MdCrdReader
public MdCrdReader()
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
readCoordinates
private 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