java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.AimsReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class AimsReader
extends AtomSetCollectionReader
```
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).

Version:

1.3

Author:

Joerg Meyer, TU Muenchen 2011 (joerg.meyer@ch.tum.de)

Field Summary

Fields
Modifier and Type Field Description

private boolean globalDoApplySymmetry

private boolean isFractional

private int nLatticeVectors
- 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

AimsReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`protected void`	`initializeReader()`
`private void`	`readAtom(java.lang.String[] tokens, boolean isFractional)`
`private void`	`readLatticeVector(java.lang.String[] tokens)`
`private void`	`readMultipole(java.lang.String[] tokens)`

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, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, 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
  - globalDoApplySymmetry
```
private boolean globalDoApplySymmetry
```
  - isFractional
```
private boolean isFractional
```
  - nLatticeVectors
```
private int nLatticeVectors
```
- Constructor Detail
  - AimsReader
```
public AimsReader()
```
- Method Detail
  - initializeReader
```
protected void initializeReader()
```
    Overrides:
    
    initializeReader in class AtomSetCollectionReader
  - checkLine
```
protected boolean checkLine()
```
    Overrides:
    
    checkLine in class AtomSetCollectionReader
    
    Returns:
    
    true if need to read new line
  - finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
    Description copied from class: AtomSetCollectionReader
    
    optional reader-specific method run first.
    
    Overrides:
    
    finalizeSubclassReader in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception
  - readLatticeVector
```
private void readLatticeVector(java.lang.String[] tokens)
```
  - readAtom
```
private void readAtom(java.lang.String[] tokens,
                      boolean isFractional)
```
  - readMultipole
```
private void readMultipole(java.lang.String[] tokens)
```

Modifier and Type	Field	Description
`private boolean`	`globalDoApplySymmetry`
`private boolean`	`isFractional`
`private int`	`nLatticeVectors`

Class AimsReader

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

globalDoApplySymmetry

isFractional

nLatticeVectors

Constructor Detail

AimsReader

Method Detail

initializeReader

checkLine

finalizeSubclassReader

readLatticeVector

readAtom

readMultipole