org.jmol.adapter.readers.simple
Class AmpacReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by 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, 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
 
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, 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, initializeReader, 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
 

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