public class JanaReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
(package private) static int |
CELL |
(package private) static int |
END |
private float[] |
floats |
private java.lang.String |
LABELS |
(package private) static int |
LATT |
private javajs.util.List<float[]> |
lattvecs |
private boolean |
modAverage |
private java.lang.String |
modAxes |
private int |
modDim |
(package private) static int |
NDIM |
(package private) static int |
QI |
private int |
qicount |
(package private) static java.lang.String |
records |
(package private) static int |
SPG |
(package private) static int |
SYM |
private int |
thisSub |
(package private) static int |
TITLE |
static java.lang.String |
U_LIST |
(package private) static int |
WMATRIX |
addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr
Constructor and Description |
---|
JanaReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addSinCos(int j,
java.lang.String key,
java.lang.String label,
java.io.BufferedReader r) |
private void |
adjustM40Occupancies()
M40 occupancies are divided by the site multiplicity;
here we factor that back in.
|
private void |
cell() |
private void |
checkFourier(int j)
presumption here is that there is only one model
(that atModel is "@0") and that there is just one dimension?
|
protected boolean |
checkLine() |
void |
doPreSymmetry() |
void |
finalizeReader()
optional reader-specific method run first.
|
private int |
getInt(int col1,
int col2) |
private BS |
getSubSystemList() |
void |
initializeReader() |
private void |
ndim() |
private void |
qi() |
private void |
readM40Data()
read the M40 file
|
private float[][] |
readM40FloatLines(int nLines,
int nFloats,
java.io.BufferedReader r) |
private java.lang.String |
readM40Floats(java.io.BufferedReader r) |
private void |
readM40WaveVectors(java.io.BufferedReader r) |
private void |
symmetry() |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
private javajs.util.List<float[]> lattvecs
private int thisSub
private boolean modAverage
private java.lang.String modAxes
private int modDim
static final java.lang.String records
static final int TITLE
static final int CELL
static final int NDIM
static final int QI
static final int LATT
static final int SYM
static final int SPG
static final int END
static final int WMATRIX
private int qicount
private final java.lang.String LABELS
public static final java.lang.String U_LIST
private float[] floats
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
public void finalizeReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
private void cell() throws java.lang.Exception
java.lang.Exception
private void ndim() throws java.lang.Exception
java.lang.Exception
private void qi()
private void symmetry() throws java.lang.Exception
java.lang.Exception
private void readM40Data() throws java.lang.Exception
java.lang.Exception
private BS getSubSystemList()
private void readM40WaveVectors(java.io.BufferedReader r) throws java.lang.Exception
java.lang.Exception
private void addSinCos(int j, java.lang.String key, java.lang.String label, java.io.BufferedReader r) throws java.lang.Exception
java.lang.Exception
private void checkFourier(int j)
j
- private int getInt(int col1, int col2)
private java.lang.String readM40Floats(java.io.BufferedReader r) throws java.lang.Exception
java.lang.Exception
private float[][] readM40FloatLines(int nLines, int nFloats, java.io.BufferedReader r) throws java.lang.Exception
java.lang.Exception
private void adjustM40Occupancies()
public void doPreSymmetry()
doPreSymmetry
in class AtomSetCollectionReader