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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class PWmatReader
extends AtomSetCollectionReader
```
crude PWmat atom.config reader http://pwmatus.com/manual

Author:

hansonr

Field Summary

Fields
Modifier and Type Field Description

private boolean haveLattice

private boolean haveMagnetic

private boolean havePositions

private int nAtoms
- 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, filterCased, 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, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

PWmatReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`applySymmetryAndSetTrajectory()`
`protected boolean`	`checkLine()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private java.lang.String`	`getLine()`
`protected void`	`initializeReader()`
`private void`	`readCoordinates()`
`private void`	`readDataBlock(java.lang.String name)`
`private void`	`readItems(java.lang.String name, int offset, float[] values)`
`private void`	`readUnitCell()`
`private void`	`readVectors(java.lang.String name, int offset, boolean haveLine)`
`private java.lang.String`	`removeComments()`
`private void`	`setProperties(java.lang.String name, float[] values, int iSet, int n)`
`private void`	`setVectors(java.lang.String name, float[] valuesX, float[] valuesY, float[] valuesZ, int n)`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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, getFilterWithCase, 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

nAtoms
```
private int nAtoms
```

haveLattice
```
private boolean haveLattice
```

havePositions
```
private boolean havePositions
```

haveMagnetic
```
private boolean haveMagnetic
```

Constructor Detail
- PWmatReader
```
public PWmatReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
                         throws java.lang.Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

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

readUnitCell

private void readUnitCell()
                   throws java.lang.Exception

Throws:: java.lang.Exception

readCoordinates

private void readCoordinates()
                      throws java.lang.Exception

Throws:: java.lang.Exception

readDataBlock

private void readDataBlock(java.lang.String name)
                    throws java.lang.Exception

Throws:: java.lang.Exception

readItems

private void readItems(java.lang.String name,
                       int offset,
                       float[] values)
                throws java.lang.Exception

Throws:: java.lang.Exception

setProperties

private void setProperties(java.lang.String name,
                           float[] values,
                           int iSet,
                           int n)

readVectors

private void readVectors(java.lang.String name,
                         int offset,
                         boolean haveLine)
                  throws java.lang.Exception

Throws:: java.lang.Exception

getLine

private java.lang.String getLine()
                          throws java.lang.Exception

Throws:: java.lang.Exception

removeComments

private java.lang.String removeComments()

setVectors

private void setVectors(java.lang.String name,
                        float[] valuesX,
                        float[] valuesY,
                        float[] valuesZ,
                        int n)

applySymmetryAndSetTrajectory
```
public void applySymmetryAndSetTrajectory()
                                   throws java.lang.Exception
```
Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

Throws:

java.lang.Exception

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

Modifier and Type	Field	Description
`private boolean`	`haveLattice`
`private boolean`	`haveMagnetic`
`private boolean`	`havePositions`
`private int`	`nAtoms`

Class PWmatReader

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

nAtoms

haveLattice

havePositions

haveMagnetic

Constructor Detail

PWmatReader

Method Detail

initializeReader

checkLine

readUnitCell

readCoordinates

readDataBlock

readItems

setProperties

readVectors

getLine

removeComments

setVectors

applySymmetryAndSetTrajectory

finalizeSubclassReader