org.jmol.adapter.readers.xml.XmlArgusReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class XmlArgusReader extends XmlReader

A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.

Field Summary

Fields

Modifier and Type

Field

Description

private static final int

ATOM

private String

atomName1

private String

atomName2

private static final int

BOND

private int

bondOrder

private int

elementContext

private static String[]

keepCharsList

private static final int

MOLECULE

private int

ptTrans

private float[]

trans

private static final int

TRANSFORMMAT

private static final int

UNSET

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, bond, chars, keepChars, parent

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

XmlArgusReader()
Method Summary

Modifier and Type

Method

Description

private int

parseBondToken(String str)

(package private) void

processEndElement(String localName)

void

processStartElement(String localName, String nodeName)

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, finalizeSubclassReader, initializeReader, processDOM, processXml, processXml2, setKeepChars

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, 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, 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
- keepCharsList
  
  private static String[] keepCharsList
- atomName1
  
  private String atomName1
- atomName2
  
  private String atomName2
- bondOrder
  
  private int bondOrder
- elementContext
  
  private int elementContext
- UNSET
  
  private static final int UNSET
  See Also:
  
  Constant Field Values
- MOLECULE
  
  private static final int MOLECULE
  See Also:
  
  Constant Field Values
- ATOM
  
  private static final int ATOM
  See Also:
  
  Constant Field Values
- BOND
  
  private static final int BOND
  See Also:
  
  Constant Field Values
- TRANSFORMMAT
  
  private static final int TRANSFORMMAT
  See Also:
  
  Constant Field Values
- trans
  
  private float[] trans
- ptTrans
  
  private int ptTrans
Constructor Details
- XmlArgusReader
  
  public XmlArgusReader()
Method Details
- processStartElement
  
  public void processStartElement(String localName, String nodeName)
  
  Overrides:
  
  processStartElement in class XmlReader
  
  nodeName - TODO
- parseBondToken
  
  private int parseBondToken(String str)
- processEndElement
  
  void processEndElement(String localName)
  
  Overrides:
  
  processEndElement in class XmlReader

Class XmlArgusReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

keepCharsList

atomName1

atomName2

bondOrder

elementContext

UNSET

MOLECULE

ATOM

BOND

TRANSFORMMAT

trans

ptTrans

Constructor Details

XmlArgusReader

Method Details

processStartElement

parseBondToken

processEndElement