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

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, 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

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, 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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 Detail

BilbaoReader

public BilbaoReader()

Method Detail

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