EspressoReader

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

All Implemented Interfaces:: javajs.api.GenericLineReader

public class EspressoReader
extends AtomSetCollectionReader

Field Summary

Fields
Modifier and Type Field Description

private float aPar

private float[] cellParams

private boolean endFlag

private java.lang.Double totEnergy
- 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

Fields
Modifier and Type	Field	Description
`private float`	`aPar`
`private float[]`	`cellParams`
`private boolean`	`endFlag`
`private java.lang.Double`	`totEnergy`

Constructor Summary

Constructors
Constructor Description

EspressoReader()

Constructors
Constructor	Description
`EspressoReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`protected void`	`initializeReader()`
`private void`	`newAtomSet()`
`private void`	`readAparam()`
`private void`	`readAtoms()`
`private void`	`readCellParam(boolean andAPar)`
`private void`	`readEnergy()`
`private void`	`setCellParams()`
`private void`	`setEnergy()`

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, 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

cellParams
```
private float[] cellParams
```

totEnergy
```
private java.lang.Double totEnergy
```

endFlag
```
private boolean endFlag
```

aPar
```
private float aPar
```

Constructor Detail
- EspressoReader
```
public EspressoReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
```
Overrides:

initializeReader in class AtomSetCollectionReader

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

readAparam

private void readAparam()
                 throws java.lang.Exception

Throws:: java.lang.Exception

readCellParam

private void readCellParam(boolean andAPar)
                    throws java.lang.Exception

Throws:: java.lang.Exception

newAtomSet

private void newAtomSet()
                 throws java.lang.Exception

Throws:: java.lang.Exception

setCellParams

private void setCellParams()
                    throws java.lang.Exception

Throws:: java.lang.Exception

readAtoms

private void readAtoms()
                throws java.lang.Exception

Throws:: java.lang.Exception

readEnergy

private void readEnergy()
                 throws java.lang.Exception

Throws:: java.lang.Exception

setEnergy
```
private void setEnergy()
```

Class EspressoReader

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

cellParams

totEnergy

endFlag

aPar

Constructor Detail

EspressoReader

Method Detail

initializeReader

checkLine

readAparam

readCellParam

newAtomSet

setCellParams

readAtoms

readEnergy

setEnergy