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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class FAHReader
extends AtomSetCollectionReader
```
FoldingAtHome json reader. Both the top and the coord files are necessary. But the coord files can be loaded as trajectories if the top has already been loaded for a given model.

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) float`	`factor`
`(package private) static java.lang.String`	`note`
`(package private) int[]`	`pt`
`private java.io.BufferedReader`	`readerSave`
`private java.lang.String`	`units`

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

FAHReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private boolean`	`checkBondlengths()`
`protected boolean`	`checkLine()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private void`	`getTopData()`
`protected void`	`initializeReader()`
`(package private) boolean`	`readTopAtomsAndBonds()`
`private boolean`	`readVnnCoords()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, 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
  - factor
```
float factor
```
  - pt
```
int[] pt
```
  - readerSave
```
private java.io.BufferedReader readerSave
```
  - units
```
private java.lang.String units
```
  - note
```
static final java.lang.String note
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - FAHReader
```
public FAHReader()
```
- Method Detail
  - initializeReader
```
protected void initializeReader()
```
    Overrides:
    
    initializeReader in class AtomSetCollectionReader
  - 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
  - checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
    Overrides:
    
    checkLine in class AtomSetCollectionReader
    
    Returns:
    
    true if next line needs to be read. Note that just a single token on line 1 is NOT possible. If that were the case, the xyz reader would have captured this.
    
    Throws:
    
    java.lang.Exception
  - readTopAtomsAndBonds
```
boolean readTopAtomsAndBonds()
                      throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readVnnCoords
```
private boolean readVnnCoords()
                       throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - checkBondlengths
```
private boolean checkBondlengths()
```
  - getTopData
```
private void getTopData()
```

Class FAHReader

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

factor

pt

readerSave

units

note

Constructor Detail

FAHReader

Method Detail

initializeReader

finalizeSubclassReader

checkLine

readTopAtomsAndBonds

readVnnCoords

checkBondlengths

getTopData