Class NMR_Viewer
java.lang.Object
org.jmol.api.JmolViewer
org.jmol.viewer.Viewer
org.openscience.jmol.app.janocchio.NMR_Viewer
- All Implemented Interfaces:
PlatformViewer
,AtomDataServer
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
Nested classes/interfaces inherited from class org.jmol.viewer.Viewer
Viewer.ACCESS
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Field Summary
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, hasSelected, 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, MIN_XX, mm, MODIFY_DELETE_ATOM, MODIFY_DELETE_ATOMS, MODIFY_DELETE_BONDS, MODIFY_DELETE_MODEL, MODIFY_MAKE_BOND, MODIFY_SET_COORD, 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
Fields inherited from class org.jmol.api.JmolViewer
apiPlatform, menuStructure
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAtomAt
(int i) int
getAtomName
(int atomIndex) int
getAtomNumber
(int atomIndex) int
int
int
int
getFrameAtomIndex
(int i) int
getFrameBase
(int i) getFrameModelInfo
(String key) int
int
indexInFrame
(Atom atom) void
setFrameModelInfo
(String key, Object value) void
setSelectionHalos
(boolean b) Methods inherited from class org.jmol.viewer.Viewer
addCommand, addFunction, addHydrogens, addHydrogensInline, addSelectionListener, addStateScript, addUnitCellOffset, alert, allocateViewer, allocTempEnum, allocTempPoints, allocTempScreens, allowCapture, allowEmbeddedScripts, areAxesTainted, assignSpaceGroup, 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, evalStringGUI, evalStringQuiet, evalStringQuietSync, evalStringWaitStatusQueued, evaluateExpression, evaluateExpressionAsVariable, exitJmol, extractMolData, extractProperty, fillAtomData, finalize, finalizeTransformParameters, findNearestAtomIndex, findNearestAtomIndexMovable, findSpaceGroup, fixInlineString, formatText, 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, getOperativeSymmetry, getOrCalcPartialCharges, getOrientation, getOutputChannel, getP, getParameter, getPdbAtomData, getPdbData, getPdbID, getPendingMeasurement, getPickingMode, getPolymerPointsAndVectors, getPOrNull, getPreserveState, getProperty, getPropertyNumber, getQuaternionFrame, getRefreshing, getRubberBandSelection, getScalePixelsPerAngstrom, getScaleText, 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, getSymmetryEquivPointList, getSymmetryEquivPoints, getSymmetryInfo, getSymTemp, getThisModelAtoms, getTrajectoryState, getTriangulator, getUnitCellInfo, getUnitCellInfoText, getV0abc, getVanderwaalsMar, getVanderwaalsMarType, getVisibleFramesBitSet, getWrappedStateScript, getZapName, getZipDirectoryAsString, haltScriptExecution, handleError, hasDatabasePrefix, hasFocus, haveAccess, haveFileSet, highlight, highlightBond, historyFind, homePosition, hoverOnPt, initialize, initializeExporter, invertAtomCoord, invertSelected, isBound, isDatabaseCode, isFunction, isJmolDataFrame, isModelKitPickingRotateBond, 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, openFileAsyncSpecialType, 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, restrictToModel, rotateAboutPointsInternal, rotateAxisAngleAtCenter, rotateFront, rotateZBy, runScript, runScriptCautiously, script, scriptCheck, scriptEcho, scriptStatus, scriptStatusMsg, scriptWait, scriptWaitStatus, select, selectAll, selectBonds, selectStatus, 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, setMotionFixed, setMotionFixedAtoms, setNavigationDepthPercent, setNavigationMode, setNewRotationCenter, setObjectArgb, setObjectMad10, setObjectProp, setObjectVisibility, setOptions, setParallel, setPercentVdwAtom, setPerspectiveDepth, setPicked, setPickingMode, setPropertyColorScheme, setProteinType, setRasmolDefaults, setRotationRadius, setScreenDimension, setScriptStatus, setSelectionHalosEnabled, setSelectionSet, setShapeErrorState, setShapeProperty, setShapeSize, setShowAxes, setShowBbcage, setShowHydrogens, setShowMeasurements, setShowUnitCell, setSmilesString, setSpin, setStatusAtomMoved, setStatusAtomPicked, setStatusDragDropped, setStatusMeasuring, setStatusResized, setStatusSelect, 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, toCartesianUC, toFractional, toFractionalUC, toUnitCell, translate, translateXYBy, triggerTimeout, unBindAction, undoMoveAction, undoMoveActionClear, unsetProperty, updateJS, useMinimizationThread, wasmInchiHack, writeFileData, writeTextFile, zap
Methods inherited from class org.jmol.api.JmolViewer
allocateViewer, allocateViewer, openFileAsync, openReader, renderScreenImage, setConsole
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Constructor Details
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NMR_Viewer
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Method Details
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getDisplayModelIndex
public int getDisplayModelIndex() -
getAtomNumber
public int getAtomNumber(int atomIndex) -
getAtomName
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getModelCount
public int getModelCount() -
getAtomCount
public int getAtomCount() -
getBondCount
public int getBondCount() -
setSelectionHalos
public void setSelectionHalos(boolean b) -
getScreenImage
- Overrides:
getScreenImage
in classViewer
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getAtomAt
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getCurrentModelIndex
public int getCurrentModelIndex() -
indexInFrame
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setFrameModelInfo
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getFrameModelInfo
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getFrameAtomIndex
public int getFrameAtomIndex(int i) -
getFrameBase
public int getFrameBase(int i)
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