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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class AmpacReader
extends AtomSetCollectionReader
```
A reader for AMPAC output. http://www.semichem.com/ampac/

Author:

Bob Hanson (hansonr@stolaf.edu)

Field Summary

Fields
Modifier and Type Field Description

private int ac

private javajs.util.P3[] atomPositions

private int freqAtom0

private float[] partialCharges
- Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
  addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

AmpacReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ac
```
private int ac
```

freqAtom0
```
private int freqAtom0
```

partialCharges
```
private float[] partialCharges
```

atomPositions
```
private javajs.util.P3[] 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

Modifier and Type	Field	Description
`private int`	`ac`
`private javajs.util.P3[]`	`atomPositions`
`private int`	`freqAtom0`
`private float[]`	`partialCharges`

Class AmpacReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

ac

freqAtom0

partialCharges

atomPositions

Constructor Detail

AmpacReader

Method Detail

checkLine

readCoordinates

setPositions

readPartialCharges

readFrequencies