CgdReader

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 and Description
`private javajs.util.Lst<String>`	`edgeData`
`private Map<Atom,javajs.util.V3[]>`	`htEdges`
`private String`	`lastName`
`private boolean`	`noBondSym`
`private static String`	`SG_ALIASES`
`private 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 and Description

CgdReader()

Constructors
Constructor and Description
`CgdReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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 String`	`getName(String name)`
`private String`	`group(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 String[] tokens
```
  - htEdges
```
private Map<Atom,javajs.util.V3[]> htEdges
```
  - lastName
```
private String lastName
```
  - edgeData
```
private javajs.util.Lst<String> edgeData
```
  - SG_ALIASES
```
private static final 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 Exception
```
    Overrides:
    
    checkLine in class AtomSetCollectionReader
    
    Returns:
    
    true if need to read new line
    
    Throws:
    
    Exception
  - group
```
private String group(String name)
```
  - atom
```
private void atom()
```
  - getName
```
private String getName(String name)
```
  - finalizeSubclassReader
```
public void finalizeSubclassReader()
                            throws Exception
```
    Description copied from class: AtomSetCollectionReader
    
    optional reader-specific method run first.
    
    Overrides:
    
    finalizeSubclassReader in class AtomSetCollectionReader
    
    Throws:
    
    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