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 java.lang.String`	`global3`
`private boolean`	`haveLattice`
`private boolean`	`haveMagnetic`
`private boolean`	`havePositions`
`private int`	`nAtoms`	The format of pwmat config file specification is now clear, would like to adjust PWmatReader accordingly.

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, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, 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, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, 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`	`readComments()`
`private void`	`readCoordinates()`
`private boolean`	`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 n)`
`private void`	`setVectors(java.lang.String name, float[] valuesX, float[] valuesY, float[] valuesZ, int n)`
`private java.lang.String`	`trimPWPropertyNameTo(java.lang.String name, java.lang.String chars)`

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
```
    The format of pwmat config file specification is now clear, would like to adjust PWmatReader accordingly. The pwmat config file format accommodates conversion from other vendors and their formats. The first line always has number of atoms, before the number, could be spaces. after the number, there could be comments such as "generated from pwmat". Please ignore those comments, only gets the number from the first line. After the first line, there could be comments please ignore till reading of letter lattice or lattice vector. The letters are case non-sensitive. The lattice section consists of 3 lines representing lattice vector. For each line, there could be extra 3 numbers followed, please ignore. Following lattice section, there comes position section. As long as there is "position" case-insensitive leading the line, that is our position section. The position section consists of total lines of total atom number which is the from the first line. The lattice section, following by position section, then there are optional sections. The cue is always the words case-insensitive. After the keywords, following by the total lines of total atom number.
  - haveLattice
```
private boolean haveLattice
```
  - havePositions
```
private boolean havePositions
```
  - haveMagnetic
```
private boolean haveMagnetic
```
  - global3
```
private java.lang.String global3
```
- 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
  - readComments
```
private void readComments()
```
  - 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 boolean readDataBlock(java.lang.String name)
                       throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - trimPWPropertyNameTo
```
private java.lang.String trimPWPropertyNameTo(java.lang.String name,
                                              java.lang.String chars)
```
  - 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 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

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

global3

Constructor Detail

PWmatReader

Method Detail

initializeReader

checkLine

readComments

readUnitCell

readCoordinates

readDataBlock

trimPWPropertyNameTo

readItems

setProperties

readVectors

getLine

removeComments

setVectors

applySymmetryAndSetTrajectory

finalizeSubclassReader