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

Field Summary

Fields

Modifier and Type	Field and Description
private int	lenLine
private int	ptFloat

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
MdCrdReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
private float	getFloat()
private javax.vecmath.Point3f	getPoint()
private boolean	getTrajectoryStep(javax.vecmath.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, 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, initializeTrajectoryFile, 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, setElementAndIsotope, 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

Field Detail

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 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