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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class CgdReader
extends AtomSetCollectionReader
```
A reader for TOPOS systre file Crystal Graph Data format. http://www.topos.samsu.ru/manuals.html http://gavrog.org/Systre-Help.html#file_formats H-M aliases from gavrov distribution geometry/sgtable.data

Field Summary

Fields
Modifier and Type	Field	Description
`private javajs.util.Lst<java.lang.String>`	`edgeData`
`private java.util.Map<Atom,javajs.util.V3[]>`	`htEdges`
`private java.lang.String`	`lastName`
`private boolean`	`noBondSym`
`private static java.lang.String`	`SG_ALIASES`
`private java.lang.String[]`	`tokens`
`private static javajs.util.V3[]`	`vecs`

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

CgdReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`atom()`
`protected boolean`	`checkLine()`
`private void`	`finalizeEdges()`	Now that we have all the edge data we can add edges to atoms
`private void`	`finalizeNet()`	Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
`void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private Atom`	`findAtom(javajs.util.P3 pt)`
`private javajs.util.P3`	`getCoord(int i)`
`private java.lang.String`	`getName(java.lang.String name)`
`private java.lang.String`	`group(java.lang.String name)`
`void`	`initializeReader()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, 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

noBondSym
```
private boolean noBondSym
```

tokens
```
private java.lang.String[] tokens
```

htEdges

private java.util.Map<Atom,javajs.util.V3[]> htEdges

lastName
```
private java.lang.String lastName
```

edgeData

private javajs.util.Lst<java.lang.String> edgeData

SG_ALIASES

private static final java.lang.String SG_ALIASES

See Also:: Constant Field Values

vecs

private static final javajs.util.V3[] vecs

Constructor Detail
- CgdReader
```
public CgdReader()
```

Method Detail
- initializeReader
```
public void initializeReader()
```
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
- 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
- group
```
private java.lang.String group(java.lang.String name)
```
- atom
```
private void atom()
```
- getName
```
private java.lang.String getName(java.lang.String name)
```
- finalizeSubclassReader
```
public 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
- finalizeEdges
```
private void finalizeEdges()
```
  Now that we have all the edge data we can add edges to atoms
- getCoord
```
private javajs.util.P3 getCoord(int i)
```
- finalizeNet
```
private void finalizeNet()
```
  Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
- findAtom
```
private Atom findAtom(javajs.util.P3 pt)
```

Class CgdReader

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

noBondSym

tokens

htEdges

lastName

edgeData

SG_ALIASES

vecs

Constructor Detail

CgdReader

Method Detail

initializeReader

checkLine

group

atom

getName

finalizeSubclassReader

finalizeEdges

getCoord

finalizeNet

findAtom