Package org.jmol.adapter.readers.xtal
Class CgdReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.CgdReader
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- 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
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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
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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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description CgdReader()
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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 atomsprivate void
finalizeNet()
Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdgesvoid
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()
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, 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, 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
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Field Detail
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noBondSym
private boolean noBondSym
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tokens
private java.lang.String[] tokens
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htEdges
private java.util.Map<Atom,javajs.util.V3[]> htEdges
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lastName
private java.lang.String lastName
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edgeData
private javajs.util.Lst<java.lang.String> edgeData
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SG_ALIASES
private static final java.lang.String SG_ALIASES
- See Also:
- Constant Field Values
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vecs
private static final javajs.util.V3[] vecs
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Method Detail
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initializeReader
public void initializeReader()
- Overrides:
initializeReader
in classAtomSetCollectionReader
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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group
private java.lang.String group(java.lang.String name)
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atom
private void atom()
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getName
private java.lang.String getName(java.lang.String name)
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finalizeSubclassReader
public void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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finalizeEdges
private void finalizeEdges()
Now that we have all the edge data we can add edges to atoms
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getCoord
private javajs.util.P3 getCoord(int i)
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finalizeNet
private void finalizeNet()
Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
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findAtom
private Atom findAtom(javajs.util.P3 pt)
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