public class SiestaReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private static double |
ACF_ANG |
private static double |
ACF_BOHR |
private static double |
ACF_M |
private static double |
ACF_NM |
private float |
acfFactor |
private java.lang.String |
acfUnits |
(package private) java.util.Map<java.lang.String,java.lang.String[]> |
htSpecies |
private float |
latticeConstant |
private java.lang.String |
latticeUnits |
private int |
noAtoms |
private int |
state |
private int |
STATE_INPUT |
private int |
STATE_OUTPUT |
private int |
STATE_UNKNOWN |
private java.lang.String[] |
tokens |
private float[] |
unitCellParamsS |
private float[] |
unitCellVectors |
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 |
---|
SiestaReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private java.lang.String |
fixToken(int i) |
private float |
getACFValue(float v) |
protected void |
initializeReader() |
private void |
newAtomSet() |
java.lang.String |
rdSiesta() |
private void |
readAtomicCoordinatesFormat() |
private boolean |
readAtoms() |
private void |
readAtomsCartGeomThenCell() |
private boolean |
readBlock(java.lang.String key) |
private boolean |
readSpecies() |
private void |
readValue(java.lang.String key) |
void |
setAtomCoordXYZ(Atom atom,
float x,
float y,
float z) |
private boolean |
setCell(java.lang.String key) |
private void |
skipModel() |
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, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
private int noAtoms
private java.lang.String acfUnits
private java.lang.String[] tokens
private final int STATE_UNKNOWN
private final int STATE_INPUT
private final int STATE_OUTPUT
private int state
private float acfFactor
java.util.Map<java.lang.String,java.lang.String[]> htSpecies
private float[] unitCellVectors
private float[] unitCellParamsS
private float latticeConstant
private java.lang.String latticeUnits
private static final double ACF_M
private static final double ACF_NM
private static final double ACF_ANG
private static final double ACF_BOHR
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readValue(java.lang.String key) throws java.lang.Exception
java.lang.Exception
private boolean readBlock(java.lang.String key) throws java.lang.Exception
java.lang.Exception
private boolean readSpecies() throws java.lang.Exception
java.lang.Exception
private java.lang.String fixToken(int i)
public java.lang.String rdSiesta() throws java.lang.Exception
java.lang.Exception
private float getACFValue(float v)
private void readAtomicCoordinatesFormat()
private void skipModel() throws java.lang.Exception
java.lang.Exception
private boolean setCell(java.lang.String key) throws java.lang.Exception
java.lang.Exception
private boolean readAtoms() throws java.lang.Exception
java.lang.Exception
public void setAtomCoordXYZ(Atom atom, float x, float y, float z)
setAtomCoordXYZ
in class AtomSetCollectionReader
private void newAtomSet() throws java.lang.Exception
java.lang.Exception
private void readAtomsCartGeomThenCell() throws java.lang.Exception
java.lang.Exception