public class JcampdxReader extends MolReader implements JmolJDXMOLReader
Modifier and Type | Field and Description |
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private javajs.util.Lst<String[]> |
acdAssignments |
private String |
acdMolFile |
private String |
allTypes |
private JmolJDXMOLParser |
mpr |
private int |
nPeaks |
private String |
nucleus |
private javajs.util.Lst<String> |
peakData |
private int |
selectedModel |
private String |
title |
private 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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JcampdxReader() |
Modifier and Type | Method and Description |
---|---|
void |
addPeakData(String info) |
private void |
addType(int imodel,
String type)
sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
|
private String |
addTypeStr(String types,
String type) |
boolean |
checkLine() |
void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private int |
findModelById(String modelID) |
void |
initializeReader() |
void |
processModelData(String data,
String id,
String type,
String base,
String last,
float modelScale,
float vibScale,
boolean isFirst) |
private void |
processPeakData()
integrate the
|
private void |
processPeakSelectAtom(int i,
String key,
String data) |
private boolean |
processPeakSelectModel(int i,
String title) |
private void |
removeAtomSet(int imodel)
note that sets must be iterated from LAST to FIRST
not a general method -- would mess up if we had unit cells
|
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,
String piUnitsX,
String piUnitsY) |
private void |
updateModelIDs(String id,
int model0,
boolean isFirst)
The first model set is allowed to be a single model and given no extension.
|
addMolAtom, addMolBond, finalizeReaderMR, fixOrder
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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, setupASCR
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, rd
private int selectedModel
private JmolJDXMOLParser mpr
private String acdMolFile
private int nPeaks
private javajs.util.Lst<String[]> acdAssignments
private String title
private String nucleus
private String type
private javajs.util.Lst<String> peakData
private String allTypes
public void initializeReader() throws Exception
initializeReader
in class MolReader
Exception
public boolean checkLine() throws Exception
public void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class MolReader
Exception
public void processModelData(String data, String id, String type, String base, String last, float modelScale, float vibScale, boolean isFirst) throws Exception
processModelData
in interface JmolJDXMOLReader
Exception
private void setBonding(AtomSetCollection a, int ibase)
a
- ibase
- private void updateModelIDs(String id, int model0, boolean isFirst)
id
- model0
- isFirst
- public void addPeakData(String info)
addPeakData
in interface JmolJDXMOLReader
private void processPeakData()
private int findModelById(String modelID)
private void addType(int imodel, String type)
imodel
- type
- private boolean processPeakSelectModel(int i, String title)
public void setSpectrumPeaks(int nH, String piUnitsX, String piUnitsY)
setSpectrumPeaks
in interface JmolJDXMOLReader
private void removeAtomSet(int imodel)
imodel
-