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 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, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, 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

Modifier and Type

Method

Description

void

applySymmetryAndSetTrajectory()

protected boolean

checkLine()

protected void

finalizeSubclassReader()

optional reader-specific method run first.

private String

getLine()

protected void

initializeReader()

private void

readComments()

private void

readCoordinates()

private boolean

readDataBlock(String name)

private void

readItems(String name, int offset, float[] values)

private void

readUnitCell()

private void

readVectors(String name, int offset, boolean haveLine)

private String

removeComments()

private void

setProperties(String name, float[] values, int n)

private void

setVectors(String name, float[] valuesX, float[] valuesY, float[] valuesZ, int n)

private String

trimPWPropertyNameTo(String name, 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 Details
- 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 String global3
Constructor Details
- PWmatReader
  
  public PWmatReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readComments
  
  private void readComments()
- readUnitCell
  
  private void readUnitCell() throws Exception
  
  Throws:
  
  Exception
- readCoordinates
  
  private void readCoordinates() throws Exception
  
  Throws:
  
  Exception
- readDataBlock
  
  private boolean readDataBlock(String name) throws Exception
  
  Throws:
  
  Exception
- trimPWPropertyNameTo
  
  private String trimPWPropertyNameTo(String name, String chars)
- readItems
  
  private void readItems(String name, int offset, float[] values) throws Exception
  
  Throws:
  
  Exception
- setProperties
  
  private void setProperties(String name, float[] values, int n)
- readVectors
  
  private void readVectors(String name, int offset, boolean haveLine) throws Exception
  
  Throws:
  
  Exception
- getLine
  
  private String getLine() throws Exception
  
  Throws:
  
  Exception
- removeComments
  
  private String removeComments()
- setVectors
  
  private void setVectors(String name, float[] valuesX, float[] valuesY, float[] valuesZ, int n)
- applySymmetryAndSetTrajectory
  
  public void applySymmetryAndSetTrajectory() throws Exception
  
  Overrides:
  
  applySymmetryAndSetTrajectory in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  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 Details

nAtoms

haveLattice

havePositions

haveMagnetic

global3

Constructor Details

PWmatReader

Method Details

initializeReader

checkLine

readComments

readUnitCell

readCoordinates

readDataBlock

trimPWPropertyNameTo

readItems

setProperties

readVectors

getLine

removeComments

setVectors

applySymmetryAndSetTrajectory

finalizeSubclassReader