org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.BilbaoReader

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

Field Summary

Fields

Modifier and Type

Field

Description

private boolean

doDisplace

private boolean

getHigh

private boolean

getSym

private int

i0

private boolean

isBCSfile

private String

kvec

private int

nAtoms

private boolean

normDispl

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
Constructor Summary

Constructors

Constructor

Description

BilbaoReader()
Method Summary

Modifier and Type

Method

Description

private boolean

checkComment()

protected boolean

checkLine()

private String

getAttr(String s, String key)

private String

getLinesUntil(String key)

void

initializeReader()

private String

rdLine()

private void

readBilbaoDataFile()

private void

readBilbaoFormat(String title, float fAmp)

private void

readDisplacements(float fAmp)

private void

readVirtual()

private void

setTitle(String title)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- getHigh
  
  private boolean getHigh
- getSym
  
  private boolean getSym
- normDispl
  
  private boolean normDispl
- doDisplace
  
  private boolean doDisplace
- kvec
  
  private String kvec
- i0
  
  private int i0
- nAtoms
  
  private int nAtoms
- isBCSfile
  
  private boolean isBCSfile
Constructor Details
- BilbaoReader
  
  public BilbaoReader()
Method Details
- initializeReader
  
  public void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readBilbaoDataFile
  
  private void readBilbaoDataFile() throws Exception
  
  Throws:
  
  Exception
- checkComment
  
  private boolean checkComment()
- readBilbaoFormat
  
  private void readBilbaoFormat(String title, float fAmp) throws Exception
  
  Throws:
  
  Exception
- readDisplacements
  
  private void readDisplacements(float fAmp) throws Exception
  
  Throws:
  
  Exception
- setTitle
  
  private void setTitle(String title)
- rdLine
  
  private String rdLine() throws Exception
  
  Throws:
  
  Exception
- readVirtual
  
  private void readVirtual() throws Exception
  
  Throws:
  
  Exception
- getAttr
  
  private String getAttr(String s, String key)
- getLinesUntil
  
  private String getLinesUntil(String key) throws Exception
  
  Throws:
  
  Exception

Class BilbaoReader

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 Details

getHigh

getSym

normDispl

doDisplace

kvec

i0

nAtoms

isBCSfile

Constructor Details

BilbaoReader

Method Details

initializeReader

checkLine

readBilbaoDataFile

checkComment

readBilbaoFormat

readDisplacements

setTitle

rdLine

readVirtual

getAttr

getLinesUntil