Package org.jmol.adapter.readers.xtal
Class BilbaoReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.BilbaoReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
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
FieldsModifier and TypeFieldDescriptionprivate boolean
private boolean
private boolean
private int
private boolean
private String
private int
private boolean
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, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate boolean
protected boolean
private String
private String
getLinesUntil
(String key) void
private String
rdLine()
private void
private void
readBilbaoFormat
(String title, float fAmp) private void
readDisplacements
(float fAmp) private void
private void
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, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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 Details
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getHigh
private boolean getHigh -
getSym
private boolean getSym -
normDispl
private boolean normDispl -
doDisplace
private boolean doDisplace -
kvec
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i0
private int i0 -
nAtoms
private int nAtoms -
isBCSfile
private boolean isBCSfile
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Constructor Details
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BilbaoReader
public BilbaoReader()
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Method Details
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initializeReader
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
Exception
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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readBilbaoDataFile
- Throws:
Exception
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checkComment
private boolean checkComment() -
readBilbaoFormat
- Throws:
Exception
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readDisplacements
- Throws:
Exception
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setTitle
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rdLine
- Throws:
Exception
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readVirtual
- Throws:
Exception
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getAttr
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getLinesUntil
- Throws:
Exception
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