public class JcampdxReader extends MolReader
Modifier and Type | Field and Description |
---|---|
private String |
allTypes |
private String |
lastModel |
private String |
modelIdList |
private AtomSetCollection |
models |
private javajs.util.List<String> |
peakData |
private String |
peakFilePath |
private int[] |
peakIndex |
(package private) String |
piUnitsX |
(package private) String |
piUnitsY |
private int |
selectedModel |
private String |
thisModelID |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, 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, viewer
Constructor and Description |
---|
JcampdxReader() |
Modifier and Type | Method and Description |
---|---|
private void |
add(javajs.util.List<String> peakData,
String info) |
private void |
addType(int imodel,
String type)
sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
|
private String |
addType(String types,
String type) |
boolean |
checkLine() |
private String |
discardUntil(Object ignored,
String tag) |
private String |
escape(String s) |
void |
finalizeReader()
optional reader-specific method run first.
|
private int |
findModelById(String modelID) |
private static String |
getAttribute(String line,
String tag) |
private AtomSetCollection |
getModelAtomSetCollection() |
private String |
getPeakFilePath() |
private int |
getPeakIndex() |
private String |
getQuotedAttribute(String s,
String attr) |
private void |
info(String s) |
void |
initializeReader() |
private void |
processPeakData()
integrate the
|
private boolean |
readModels() |
private int |
readPeaks(boolean isSignals)
read a
|
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 |
setSpectrumPeaks(Object o1,
Object o2,
int nH) |
private String |
simpleReplace(String s,
String sfrom,
String sto) |
private BS |
unescapeBitSet(String s) |
private void |
updateModelIDs(int model0,
boolean isFirst)
The first model set is allowed to be a single model and given no extension.
|
finalizeReaderMR
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, 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, getElementSymbol, getFilter, getFortranFormatLengths, 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, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
private String thisModelID
private AtomSetCollection models
private String modelIdList
private javajs.util.List<String> peakData
private String lastModel
private int selectedModel
private int[] peakIndex
private String peakFilePath
String piUnitsX
String piUnitsY
private String allTypes
public void initializeReader() throws Exception
initializeReader
in class MolReader
Exception
public boolean checkLine() throws Exception
public void finalizeReader() throws Exception
AtomSetCollectionReader
finalizeReader
in class MolReader
Exception
private int findModelById(String modelID)
private void updateModelIDs(int model0, boolean isFirst)
model0
- isFirst
- private AtomSetCollection getModelAtomSetCollection() throws Exception
Exception
private void setBonding(AtomSetCollection a, int ibase)
a
- ibase
- private int readPeaks(boolean isSignals) throws Exception
isSignals
- Exception
private void info(String s)
private void setSpectrumPeaks(Object o1, Object o2, int nH)
o1
- o2
- nH
- private String getPeakFilePath()
private String discardUntil(Object ignored, String tag) throws Exception
ignored
- tag
- Exception
private int getPeakIndex()
private void processPeakData()
private void addType(int imodel, String type)
imodel
- type
-