Package org.jmol.adapter.readers.more
Class JcampdxReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.molxyz.MolReader
org.jmol.adapter.readers.more.JcampdxReader
- All Implemented Interfaces:
GenericLineReader
,JmolJDXMOLReader
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS=
records
Designed by Robert Lancashire and Bob Hanson
specifications (by example here):
##$MODELS= acetophenone
DSViewer 3D 0
17 17 0 0 0 0 0 0 0 0999 V2000 ... 17 14 1 0 0 0 M END
17 1 Energy: -1454.38826 Freq: 3199.35852 C -1.693100
0.007800 0.000000 -0.000980 0.000120 0.000000 ...
-- All XML data should be line-oriented in the above fashion. Leading spaces
will be ignored. -- Any number of segments can be present -- The
first model is referred to as the "base" model -- The base model: -- will
generally be of type MOL, but any known type is acceptable -- will be used to
generate bonding for later models that have no bonding information -- will be
the only model for NMR -- Additional models can represent vibrations (XYZ
format) or MS fragmentation (MOL format, probably)
##$PEAKS= ...
-- peak record must be a single line of information because Jmol will use
line.trim() as a key to pass information to JSpecView.
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Field Summary
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addPeakData
(String info) boolean
void
optional reader-specific method run first.void
void
processModelData
(String data, String id, String type, String base, String last, float modelScale, float vibScale, boolean isFirst) void
setSpectrumPeaks
(int nH, String piUnitsX, String piUnitsY) Methods inherited from class org.jmol.adapter.readers.molxyz.MolReader
addMolAtom, addMolBond, deleteAtom, finalizeReaderMR
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, 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, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, rd
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Constructor Details
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JcampdxReader
public JcampdxReader()
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Method Details
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initializeReader
- Overrides:
initializeReader
in classMolReader
- Throws:
Exception
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checkLine
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classMolReader
- Throws:
Exception
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processModelData
public void processModelData(String data, String id, String type, String base, String last, float modelScale, float vibScale, boolean isFirst) throws Exception - Specified by:
processModelData
in interfaceJmolJDXMOLReader
- Throws:
Exception
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addPeakData
- Specified by:
addPeakData
in interfaceJmolJDXMOLReader
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setSpectrumPeaks
- Specified by:
setSpectrumPeaks
in interfaceJmolJDXMOLReader
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