public class JcampdxReader extends MolReader implements JmolJDXMOLReader
| Modifier and Type | Field and Description |
|---|---|
private javajs.util.Lst<java.lang.String[]> |
acdAssignments |
private java.lang.String |
acdMolFile |
private java.lang.String |
allTypes |
private JmolJDXMOLParser |
mpr |
private int |
nPeaks |
private java.lang.String |
nucleus |
private javajs.util.Lst<java.lang.String> |
peakData |
private int |
selectedModel |
private java.lang.String |
title |
private java.lang.String |
type |
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 |
|---|
JcampdxReader() |
| Modifier and Type | Method and Description |
|---|---|
void |
addPeakData(java.lang.String info) |
private void |
addType(int imodel,
java.lang.String type)
sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
|
private java.lang.String |
addTypeStr(java.lang.String types,
java.lang.String type) |
boolean |
checkLine() |
void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private int |
findModelById(java.lang.String modelID) |
void |
initializeReader() |
void |
processModelData(java.lang.String data,
java.lang.String id,
java.lang.String type,
java.lang.String base,
java.lang.String last,
float modelScale,
float vibScale,
boolean isFirst) |
private void |
processPeakData()
integrate the
|
private void |
processPeakSelectAtom(int i,
java.lang.String key,
java.lang.String data) |
private boolean |
processPeakSelectModel(int i,
java.lang.String title) |
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
|
void |
setSpectrumPeaks(int nH,
java.lang.String piUnitsX,
java.lang.String piUnitsY) |
private void |
updateModelIDs(java.lang.String id,
int model0,
boolean isFirst)
The first model set is allowed to be a single model and given no extension.
|
addMolAtom, addMolBond, finalizeReaderMRaddAtomXYZSymName, 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, 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, setupASCRclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitdiscardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, rdprivate int selectedModel
private JmolJDXMOLParser mpr
private java.lang.String acdMolFile
private int nPeaks
private javajs.util.Lst<java.lang.String[]> acdAssignments
private java.lang.String title
private java.lang.String nucleus
private java.lang.String type
private javajs.util.Lst<java.lang.String> peakData
private java.lang.String allTypes
public void initializeReader()
throws java.lang.Exception
initializeReader in class MolReaderjava.lang.Exceptionpublic boolean checkLine()
throws java.lang.Exception
public void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class MolReaderjava.lang.Exceptionpublic void processModelData(java.lang.String data,
java.lang.String id,
java.lang.String type,
java.lang.String base,
java.lang.String last,
float modelScale,
float vibScale,
boolean isFirst)
throws java.lang.Exception
processModelData in interface JmolJDXMOLReaderjava.lang.Exceptionprivate void setBonding(AtomSetCollection a, int ibase)
a - ibase - private void updateModelIDs(java.lang.String id,
int model0,
boolean isFirst)
id - model0 - isFirst - public void addPeakData(java.lang.String info)
addPeakData in interface JmolJDXMOLReaderprivate void processPeakData()
private int findModelById(java.lang.String modelID)
private void addType(int imodel,
java.lang.String type)
imodel - type - private java.lang.String addTypeStr(java.lang.String types,
java.lang.String type)
private void processPeakSelectAtom(int i,
java.lang.String key,
java.lang.String data)
private boolean processPeakSelectModel(int i,
java.lang.String title)
public void setSpectrumPeaks(int nH,
java.lang.String piUnitsX,
java.lang.String piUnitsY)
setSpectrumPeaks in interface JmolJDXMOLReader