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<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
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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, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, 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 String
getName(String name)
private String
group(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, 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 String[] tokens
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lastName
private String lastName
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edgeData
private javajs.util.Lst<String> edgeData
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SG_ALIASES
private static final 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 Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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atom
private void atom()
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finalizeSubclassReader
public void finalizeSubclassReader() throws Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
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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