java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xml.XmlReader
  - - org.jmol.adapter.readers.xml.XmlChemDrawReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class XmlChemDrawReader
extends XmlReader
```
An chem3d c3xml reader

Field Summary

Fields
Modifier and Type	Field	Description
`private javajs.util.Lst<java.lang.Object[]>`	`bonds`
`private boolean`	`is3D`
`private float`	`maxX`
`private float`	`maxY`
`private float`	`maxZ`
`private float`	`minX`
`private float`	`minY`
`private float`	`minZ`
`(package private) boolean`	`optimize2D`
`private Atom`	`warningAtom`

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, 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

XmlChemDrawReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`center()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private void`	`fixConnections()`
`(package private) void`	`processEndElement(java.lang.String localName)`
`void`	`processStartElement(java.lang.String localName, java.lang.String nodeName)`
`protected void`	`processXml(XmlReader parent, java.lang.Object saxReader)`
`private void`	`setAtom(java.lang.String key)`

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, initCML, initializeReader, processDOM, 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 Detail

optimize2D
```
boolean optimize2D
```

minX
```
private float minX
```

minY
```
private float minY
```

minZ
```
private float minZ
```

maxZ
```
private float maxZ
```

maxY
```
private float maxY
```

maxX
```
private float maxX
```

is3D
```
private boolean is3D
```

bonds

private javajs.util.Lst<java.lang.Object[]> bonds

warningAtom
```
private Atom warningAtom
```

Constructor Detail
- XmlChemDrawReader
```
public XmlChemDrawReader()
```

Method Detail

processXml

protected void processXml(XmlReader parent,
                          java.lang.Object saxReader)
                   throws java.lang.Exception

Overrides:: processXml in class XmlReader
Throws:: java.lang.Exception

processStartElement

public void processStartElement(java.lang.String localName,
                                java.lang.String nodeName)

Overrides:: processStartElement in class XmlReader; nodeName - TODO

setAtom

private void setAtom(java.lang.String key)

processEndElement
```
void processEndElement(java.lang.String localName)
```
Overrides:

processEndElement in class XmlReader

finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class XmlReader

Throws:

java.lang.Exception

fixConnections
```
private void fixConnections()
```

center
```
private void center()
```

Class XmlChemDrawReader

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 Detail

optimize2D

minX

minY

minZ

maxZ

maxY

maxX

is3D

bonds

warningAtom

Constructor Detail

XmlChemDrawReader

Method Detail

processXml

processStartElement

setAtom

processEndElement

finalizeSubclassReader

fixConnections

center