Class NMR_Viewer
- java.lang.Object
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- org.jmol.api.JmolViewer
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- org.jmol.viewer.Viewer
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- org.openscience.jmol.app.janocchio.NMR_Viewer
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- All Implemented Interfaces:
PlatformViewer
,AtomDataServer
public class NMR_Viewer extends Viewer
Implements some lost interfaces. It was a way to streamline the JavaScript; Not an especially good idea, I know.
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.viewer.Viewer
Viewer.ACCESS
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Field Summary
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Fields inherited from class org.jmol.viewer.Viewer
acm, allowArrayDotNotation, am, antialiased, appConsole, appletCodeBase, appletDocumentBase, appletIdiomaBase, appletName, async, atomHighlighted, autoExit, captureParams, chainMap, cm, compiler, creatingImage, currentCursor, definedAtomSets, display, displayLoadErrors, eval, executor, fm, frankOn, fullName, g, gdata, haveDisplay, headless, html5Applet, htmlName, imageFontScaling, isApplet, isJNLP, isJS, isJSNoAWT, isPreviewOnly, isPrintOnly, isSignedApplet, isSingleThreaded, isSwingJS, isSyntaxAndFileCheck, isSyntaxCheck, isWebGL, jmolObject, jsDocumentBase, listCommands, MIN_ADDH, MIN_HAVE_FIXED, MIN_NO_RANGE, MIN_QUICK, MIN_SILENT, mm, movableBitSet, ms, noFrankEcho, noGraphicsAllowed, nProcessors, nullDeletedAtoms, queueOnHold, rd, REFRESH_REPAINT, REFRESH_REPAINT_NO_MOTION_ONLY, REFRESH_SEND_WEBGL_NEW_ORIENTATION, REFRESH_SYNC, REFRESH_SYNC_MASK, scriptEditorVisible, shm, slm, sm, stateScriptVersionInt, stm, strJavaVendor, strJavaVersion, strOSName, SYNC_GRAPHICS_MESSAGE, SYNC_NO_GRAPHICS_MESSAGE, testAsync, timeouts, tm, tryPt, vwrOptions
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Fields inherited from class org.jmol.api.JmolViewer
apiPlatform, menuStructure
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Constructor Summary
Constructors Constructor Description NMR_Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Atom
getAtomAt(int i)
int
getAtomCount()
java.lang.String
getAtomName(int atomIndex)
int
getAtomNumber(int atomIndex)
int
getBondCount()
int
getCurrentModelIndex()
int
getDisplayModelIndex()
int
getFrameAtomIndex(int i)
int
getFrameBase(int i)
java.lang.Object
getFrameModelInfo(java.lang.String key)
int
getModelCount()
java.awt.Image
getScreenImage()
int
indexInFrame(Atom atom)
void
setFrameModelInfo(java.lang.String key, java.lang.Object value)
void
setSelectionHalos(boolean b)
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Methods inherited from class org.jmol.viewer.Viewer
addCommand, addFunction, addHydrogens, addHydrogensInline, addSelectionListener, addStateScript, addUnitCellOffset, alert, allocateViewer, allocTempEnum, allocTempPoints, allocTempScreens, allowCapture, allowEmbeddedScripts, areAxesTainted, autoCalculate, autoHbond, bindAction, bsA, cacheClear, cacheFileByName, cachePut, calcAtomsMinMax, calcBoundBoxDimensions, calculateChirality, calculateChiralityForSmiles, calculateFormalCharges, calculateMolecularDipole, calculatePartialCharges, calculateStraightness, calculateStructures, calculateStruts, calculateSurface, cd, checkCoordinatesChanged, checkHalt, checkInMotion, checkMenuUpdate, checkMotionRendering, checkObjectHovered, checkPrivateKey, checkPropertyParameter, checkSelect, clearAllMeasurements, clearFunctions, clearMeasurements, clearModelDependentObjects, clearScriptQueue, clearSelection, clearShapeRenderers, clearThreads, clearTimeout, clearTimeouts, clipImageOrPasteText, compileExpr, confirm, connectNBO, createZip, defineAtomSets, deleteAtoms, deleteBonds, deleteMeasurement, deleteModelAtoms, deleteModels, dialogAsk, displayAtoms, dispose, evalFile, evalFunctionFloat, evalParallel, evalString, evalStringQuiet, evalStringQuietSync, evalStringWaitStatusQueued, evaluateExpression, evaluateExpressionAsVariable, exitJmol, extractMolData, extractProperty, fillAtomData, finalize, finalizeTransformParameters, findNearestAtomIndex, findNearestAtomIndexMovable, fixInlineString, frankClicked, frankClickedModelKit, freeTempEnum, freeTempPoints, freeTempScreens, functionXY, functionXYZ, generateOutputForExport, getAdditionalHydrogens, getAllAtoms, getAllSettings, getAnnotationInfo, getAnnotationParser, getAsciiFileOrNull, getAtomBitSet, getAtomDefs, getAtomGroupQuaternions, getAtomInfo, getAtomsNearPt, getAtomValidation, getAuxiliaryInfoForAtoms, getBackgroundArgb, getBaseModelBitSet, getBindingInfo, getBioSmiles, getBondsForSelectedAtoms, getBoolean, getBooleanProperty, getBoundBoxCenter, getBoundBoxCenterX, getBoundBoxCenterY, getBoundBoxCornerVector, getBranchBitSet, getBufferedInputStream, getCenterAndPoints, getChainID, getChainIDStr, getChemicalInfo, getChimeInfo, getChimeMessenger, getCifData, getClipboardText, getColorPointForPropertyValue, getCommands, getConsole, getConsoleFontScale, getCoordinateState, getCurrentColorRange, getCurrentFileAsString, getCurrentModelAuxInfo, getCurrentUnitCell, getCursorX, getCursorY, getData, getDataObj, getDefaultDirectory, getDefaultLattice, getDefaultMeasurementLabel, getDefaultPropertyParam, getDefaultVdwNameOrData, getDefinedAtomSet, getDelayMaximumMs, getDistanceUnits, getDrawHover, getElementsPresentBitSet, getErrorMessage, getErrorMessageUn, getEvalContextAndHoldQueue, getExportDriverList, getFileAsString, getFileAsString3, getFileAsString4, getFloat, getFont3D, getFrameAtoms, getFrameTitle, getFullPathNameOrError, getFunction, getFunctionCalls, getFunctions, getGLmolView, getGroupsWithin, getHelp, getHermiteLevel, getHoverDelay, getHybridizationAndAxes, getImageAsBytes, getInchi, getInlineChar, getInMotion, getInsertedCommand, getInt, getIsosurfacePropertySmoothing, getJBR, getJDXBaseModelIndex, getJmolVersion, getJspecViewProperties, getJzt, getLigandModel, getLightingState, getLocalUrl, getLogFileName, getMacro, getMadBond, getMeasurementCount, getMeasurementCountPlusIndices, getMeasurementInfoAsString, getMeasurementStringValue, getMenu, getMinimizationInfo, getMinimizer, getModelAdapter, getModelCml, getModelDipole, getModelExtract, getModelFileData, getModelFileInfo, getModelFileInfoAll, getModelFileNumber, getModelForAtomIndex, getModelIndexFromId, getModelInfo, getModelkit, getModelkitProperty, getModelName, getModelNumber, getModelNumberDotted, getModelProperties, getModelSetAuxiliaryInfo, getModelSetFileName, getModelSetPathName, getModelSetProperties, getModelUndeletedAtomsBitSet, getModelUndeletedAtomsBitSetBs, getMotionEventNumber, getMotionFixedAtoms, getMouseEnabled, getNBOAtomLabel, getNMRCalculation, getNMRPredict, getObjectColix, getObjectMad10, getObjectMap, getOpenSmiles, getOrCalcPartialCharges, getOrientationText, getOutputChannel, getP, getParameter, getPdbAtomData, getPdbData, getPdbID, getPendingMeasurement, getPickingMode, getPolymerPointsAndVectors, getPOrNull, getPreserveState, getProperty, getPropertyNumber, getQuaternionFrame, getRefreshing, getRubberBandSelection, getScalePixelsPerAngstrom, getScreenDim, getScreenHeight, getScreenImageBuffer, getScreenWidth, getScriptContext, getScriptQueueInfo, getSelectedAtomIterator, getSelectionHalosEnabled, getSetHistory, getShapeErrorState, getShapeProperty, getShowAxes, getShowBbcage, getShowFrank, getShowNavigationPoint, getShowSelectedOnce, getShowUnitCell, getSmartsMap, getSmartsMatch, getSmartsMatchForNodes, getSmiles, getSmilesAtoms, getSmilesMatcher, getSmilesOpt, getSpinState, getStandardLabelFormat, getStateCreator, getStateInfo, getStateInfo3, getStatusChanged, getStrandCount, getStructureList, getStructureState, getSubstructureSetArray, getSubstructureSetArrayForNodes, getSymmetryInfo, getSymTemp, getTrajectoryState, getTriangulator, getUnitCellInfo, getUnitCellInfoText, getV0abc, getVanderwaalsMar, getVanderwaalsMarType, getVisibleFramesBitSet, getWrappedStateScript, getZapName, getZipDirectoryAsString, haltScriptExecution, handleError, hasDatabasePrefix, hasFocus, haveAccess, haveFileSet, highlight, highlightBond, historyFind, homePosition, hoverOnPt, initialize, initializeExporter, invertAtomCoordPlane, invertAtomCoordPt, invertRingAt, invertSelected, isBound, isDatabaseCode, isFunction, isJmolDataFrame, isModelPDB, isParallel, isRepaintPending, isScriptExecuting, jsEval, jsEvalSV, loadImageData, loadInline, loadInline, loadInline, loadInline, loadInline, loadInlineAppend, loadModelFromFile, log, makeConnections, menuEnabled, minimize, modelHasVibrationVectors, move, moveAtoms, moveAtomWithHydrogens, moveSelected, moveTo, moveUpdate, navigateAxis, navigatePt, navTranslatePercent, newMeasurementData, notifyError, notifyMinimizationStatus, notifyMouseClicked, notifyScriptEditor, notifyStatusReady, notifyViewerRepaintDone, openDOM, openExportChannel, openFile, openFileAsyncSpecial, openFileDropped, openFiles, openReader, openStringInline, openStringInlineParamsAppend, outputToFile, parseJSON, parseJSONArray, parseJSONMap, pauseScriptExecution, popHoldRepaint, popState, processMouseEvent, processTwoPointGesture, processWriteOrCapture, prompt, pushHoldRepaint, pushHoldRepaintWhy, pushState, readCifData, readCifData, readFileAsMap, rebond, rebondState, refresh, refreshMeasures, releaseScreenImage, removeCommand, removeFunction, removeSelectionListener, removeUserVariable, renderScreenImage, renderScreenImageStereo, requestRepaintAndWait, reset, resetShapes, resizeInnerPanel, rotateAboutPointsInternal, rotateAxisAngleAtCenter, rotateFront, rotateZBy, runScript, runScriptCautiously, script, scriptCheck, scriptEcho, scriptStatus, scriptStatusMsg, scriptWait, scriptWaitStatus, select, selectAll, selectBonds, sendConsoleMessage, setAnimation, setAnimationFps, setAnimationOn, setAnimationRange, setAnimDisplay, setAtomCoords, setAtomCoordsRelative, setAtomData, setAtomProperty, setAutoBond, setAxesOrientationRasmol, setBackgroundImage, setBackgroundModelIndex, setBondTolerance, setBooleanProperty, setCenterBitSet, setCenterSelected, setCGO, setColorBackground, setConsoleFontScale, setCurrentCage, setCurrentColorRange, setCurrentModelID, setCurrentModelIndex, setCurrentModelIndexClear, setCursor, setData, setDebugScript, setDefaultLattice, setDihedrals, setDisplay, setElementArgb, setErrorMessage, setFloatProperty, setFocus, setFrameDelayMs, setFrameOffsets, setFrameTitle, setFrameTitleObj, setFrankOn, setHistory, setHoverLabel, setInMotion, setInsertedCommand, setIntProperty, setIteratorForAtom, setIteratorForPoint, setJmolCallbackListener, setJmolDefaults, setJmolStatusListener, setLigandModel, setLoadFormat, setLoadParameters, setMarBond, setMenu, setMeshCreator, setMinBondDistance, setModelkitProperty, setModelKitRotateBondIndex, setModelSet, setModelVisibility, setModulation, setMotionFixedAtoms, setNavigationDepthPercent, setNavigationMode, setNewRotationCenter, setObjectArgb, setObjectMad10, setObjectProp, setObjectVisibility, setOptions, setParallel, setPercentVdwAtom, setPerspectiveDepth, setPicked, setPropertyColorScheme, setProteinType, setRasmolDefaults, setRotationRadius, setScreenDimension, setScriptStatus, setSelectionHalosEnabled, setSelectionSet, setShapeErrorState, setShapeProperty, setShapeSize, setShowAxes, setShowBbcage, setShowHydrogens, setShowMeasurements, setShowUnitCell, setSmilesString, setSpin, setStatusAtomPicked, setStatusDragDropped, setStatusMeasuring, setStatusResized, setStereo, setStereoMode, setStringProperty, setStructureList, setSyncDriver, setTainted, setTimeout, setUnits, setVectorScale, setVibrationPeriod, setVibrationScale, setWidthHeightVar, setWindowDimensions, showConsole, showEditor, showParameter, showString, showTimeout, showUrl, spinXYBy, startHoverWatcher, startNBO, startPlugin, startSpinningAxis, syncScript, toCartesian, toFractional, toUnitCell, translate, translateXYBy, triggerTimeout, unBindAction, undoMoveAction, undoMoveActionClear, unsetProperty, updateJS, useMinimizationThread, writeFileData, writeTextFile, zap
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Methods inherited from class org.jmol.api.JmolViewer
allocateViewer, allocateViewer, openFileAsync, openReader, renderScreenImage, setConsole
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Method Detail
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getDisplayModelIndex
public int getDisplayModelIndex()
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getAtomNumber
public int getAtomNumber(int atomIndex)
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getAtomName
public java.lang.String getAtomName(int atomIndex)
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getModelCount
public int getModelCount()
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getAtomCount
public int getAtomCount()
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getBondCount
public int getBondCount()
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setSelectionHalos
public void setSelectionHalos(boolean b)
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getScreenImage
public java.awt.Image getScreenImage()
- Overrides:
getScreenImage
in classViewer
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getAtomAt
public Atom getAtomAt(int i)
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getCurrentModelIndex
public int getCurrentModelIndex()
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indexInFrame
public int indexInFrame(Atom atom)
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setFrameModelInfo
public void setFrameModelInfo(java.lang.String key, java.lang.Object value)
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getFrameModelInfo
public java.lang.Object getFrameModelInfo(java.lang.String key)
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getFrameAtomIndex
public int getFrameAtomIndex(int i)
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getFrameBase
public int getFrameBase(int i)
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