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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr| Constructor and Description |
|---|
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, 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, setupASCRprivate 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 AtomSetCollectionReaderjava.lang.Exceptionprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readBilbaoDataFile()
throws java.lang.Exception
java.lang.Exceptionprivate boolean checkComment()
private void readBilbaoFormat(java.lang.String title,
float fAmp)
throws java.lang.Exception
java.lang.Exceptionprivate void readDisplacements(float fAmp)
throws java.lang.Exception
java.lang.Exceptionprivate void setTitle(java.lang.String title)
private java.lang.String rdLine()
throws java.lang.Exception
java.lang.Exceptionprivate void readVirtual()
throws java.lang.Exception
java.lang.Exceptionprivate 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