public class JcampdxReader extends MolReader
Modifier and Type | Field and Description |
---|---|
private java.lang.String |
allTypes |
private java.lang.String |
lastModel |
private java.lang.String |
modelID |
private java.lang.String |
modelIdList |
private AtomSetCollection |
models |
private java.util.List<java.lang.String> |
peakData |
private java.lang.String |
peakFilePath |
private int[] |
peakIndex |
private int |
selectedModel |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
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JcampdxReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addType(int imodel,
java.lang.String type)
sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
|
private java.lang.String |
addType(java.lang.String types,
java.lang.String type) |
boolean |
checkLine() |
void |
finalizeReader() |
private int |
findModelById(java.lang.String modelID) |
private static java.lang.String |
getAttribute(java.lang.String line,
java.lang.String tag) |
private AtomSetCollection |
getModelAtomSetCollection() |
void |
initializeReader() |
private void |
processPeakData()
integrate the
|
private boolean |
readModels() |
private boolean |
readPeaks() |
private void |
setBonding(AtomSetCollection a,
int ibase)
add bonding to a set of ModelData based on a MOL file
only if the this set has no bonding already
|
private void |
updateModelIDs(int model0,
boolean isFirst)
The first model set is allowed to be a single model and given no extension.
|
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private java.lang.String modelID
private AtomSetCollection models
private java.lang.String modelIdList
private java.util.List<java.lang.String> peakData
private java.lang.String lastModel
private int selectedModel
private int[] peakIndex
private java.lang.String peakFilePath
private java.lang.String allTypes
public void initializeReader() throws java.lang.Exception
initializeReader
in class MolReader
java.lang.Exception
public boolean checkLine() throws java.lang.Exception
public void finalizeReader() throws java.lang.Exception
finalizeReader
in class MolReader
java.lang.Exception
private int findModelById(java.lang.String modelID)
private boolean readModels() throws java.lang.Exception
java.lang.Exception
private void updateModelIDs(int model0, boolean isFirst)
model0
- isFirst
- private static java.lang.String getAttribute(java.lang.String line, java.lang.String tag)
private AtomSetCollection getModelAtomSetCollection() throws java.lang.Exception
java.lang.Exception
private void setBonding(AtomSetCollection a, int ibase)
a
- ibase
- private boolean readPeaks() throws java.lang.Exception
java.lang.Exception
private void processPeakData()
private void addType(int imodel, java.lang.String type)
imodel
- type
- private java.lang.String addType(java.lang.String types, java.lang.String type)