org.jmol.adapter.readers.simple
Class AmpacReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.simple.AmpacReader

public class AmpacReader
extends AtomSetCollectionReader

A reader for AMPAC output. http://www.semichem.com/ampac/

Author:

Bob Hanson (hansonr@stolaf.edu)

Field Summary

private int	atomCount
private javax.vecmath.Point3f[]	atomPositions
private int	freqAtom0
private float[]	partialCharges

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

AmpacReader()

Method Summary

protected boolean	checkLine()
private void	readCoordinates() Reads a set of coordinates
private void	readFrequencies() Reads a set of vibrations.
private void	readPartialCharges()
private void	setPositions()

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, 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

atomCount

private int atomCount

freqAtom0

private int freqAtom0

partialCharges

private float[] partialCharges

atomPositions

private javax.vecmath.Point3f[] atomPositions

Constructor Detail

AmpacReader

public AmpacReader()

Method Detail

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

Reads a set of coordinates

Throws:

java.lang.Exception - if an I/O error occurs

setPositions

private void setPositions()

readPartialCharges

private void readPartialCharges()
                         throws java.lang.Exception

Throws:

java.lang.Exception

readFrequencies

private void readFrequencies()
                      throws java.lang.Exception

Reads a set of vibrations.

Throws:

java.lang.Exception - if an I/O error occurs