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 and 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, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor and Description

BilbaoReader()

Constructors
Constructor and Description
`BilbaoReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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

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 Detail

getHigh

getSym

normDispl

doDisplace

kvec

i0

nAtoms

isBCSfile

Constructor Detail

BilbaoReader

Method Detail

initializeReader

checkLine

readBilbaoDataFile

checkComment

readBilbaoFormat

readDisplacements

setTitle

rdLine

readVirtual

getAttr

getLinesUntil