Package org.jmol.adapter.readers.xtal
Class BilbaoReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.BilbaoReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class BilbaoReader extends AtomSetCollectionReader
Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML. Keys for Bilbao format data are a given bit of text such as "High symmetry structure". Any changes to that (including capitalization) will cause this reader to fail. The space group number is read immediately after the "pre" tag on that line. filter options include: HIGH include high-symmetry structure; preliminary only- Author:
- Bob Hanson
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Field Summary
Fields Modifier and Type Field Description private boolean
doDisplace
private boolean
getHigh
private boolean
getSym
private int
i0
private boolean
isBCSfile
private java.lang.String
kvec
private int
nAtoms
private boolean
normDispl
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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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description BilbaoReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private boolean
checkComment()
protected boolean
checkLine()
private java.lang.String
getAttr(java.lang.String s, java.lang.String key)
private java.lang.String
getLinesUntil(java.lang.String key)
void
initializeReader()
private java.lang.String
rdLine()
private void
readBilbaoDataFile()
private void
readBilbaoFormat(java.lang.String title, float fAmp)
private void
readDisplacements(float fAmp)
private void
readVirtual()
private void
setTitle(java.lang.String title)
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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, finalizeSubclassReader, 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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Method Detail
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initializeReader
public void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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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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readBilbaoDataFile
private void readBilbaoDataFile() throws java.lang.Exception
- Throws:
java.lang.Exception
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checkComment
private boolean checkComment()
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readBilbaoFormat
private void readBilbaoFormat(java.lang.String title, float fAmp) throws java.lang.Exception
- Throws:
java.lang.Exception
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readDisplacements
private void readDisplacements(float fAmp) throws java.lang.Exception
- Throws:
java.lang.Exception
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setTitle
private void setTitle(java.lang.String title)
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rdLine
private java.lang.String rdLine() throws java.lang.Exception
- Throws:
java.lang.Exception
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readVirtual
private void readVirtual() throws java.lang.Exception
- Throws:
java.lang.Exception
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getAttr
private java.lang.String getAttr(java.lang.String s, java.lang.String key)
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getLinesUntil
private java.lang.String getLinesUntil(java.lang.String key) throws java.lang.Exception
- Throws:
java.lang.Exception
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