public class BilbaoReader extends AtomSetCollectionReader
Modifier and Type | Field and 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 |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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BilbaoReader() |
Modifier and Type | Method and 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) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, 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, processDSSR, 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
private boolean getHigh
private boolean getSym
private boolean normDispl
private boolean doDisplace
private java.lang.String kvec
private int i0
private int nAtoms
private boolean isBCSfile
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readBilbaoDataFile() throws java.lang.Exception
java.lang.Exception
private boolean checkComment()
private void readBilbaoFormat(java.lang.String title, float fAmp) throws java.lang.Exception
java.lang.Exception
private void readDisplacements(float fAmp) throws java.lang.Exception
java.lang.Exception
private void setTitle(java.lang.String title)
private java.lang.String rdLine() throws java.lang.Exception
java.lang.Exception
private void readVirtual() throws java.lang.Exception
java.lang.Exception
private java.lang.String getAttr(java.lang.String s, java.lang.String key)
private java.lang.String getLinesUntil(java.lang.String key) throws java.lang.Exception
java.lang.Exception