Uses of Class
javajs.util.Lst
Packages that use Lst
Package
Description
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
-
Uses of Lst in com.sparshui.server
Methods in com.sparshui.server that return LstModifier and TypeMethodDescriptionServerToClientProtocol.getGestures(int groupID) Retrieve a list of allowed gestures for the provided group id.Methods in com.sparshui.server with parameters of type LstModifier and TypeMethodDescriptionvoidServerToClientProtocol.processEvents(int groupID, Lst<Event> events) Instruct the client to process the events that have been generated by a group.Constructors in com.sparshui.server with parameters of type LstModifierConstructorDescriptionGroup(int id, Lst<GestureType> gestureTypes, ServerToClientProtocol clientProtocol) Construct a new group with the given gesture IDs and the given connection to the client. -
Uses of Lst in javajs.util
Methods in javajs.util that return LstModifier and TypeMethodDescriptionstatic <type> Lst<type>[]AU.createArrayOfArrayList(int size) Helper method for creating a List[] without warnings. Lst<javajs.util.CompoundDocDirEntry> CompoundDocument.getDirectory()Measure.getIntersectionPP(P4 plane1, P4 plane2) Calculate the line that is the intersection of two planes.Measure.getLatticePoints(Lst<P3> cpts, int h, int k, int l) Based on a set of centering points, creates a list of lattice points in place.Measure.getPointsOnPlane(P3[] pts, P4 plane) Based on a set of centering points, returns the list of points on a given plane.Measure.transformPoints(Lst<P3> vPts, M4 m4, P3 center) Methods in javajs.util with parameters of type LstModifier and TypeMethodDescriptionstatic P3[]Measure.getCenterAndPoints(Lst<P3> vPts) from a list of points, create an array that includes the center point as the first point.Measure.getLatticePoints(Lst<P3> cpts, int h, int k, int l) Based on a set of centering points, creates a list of lattice points in place.static floatFills a 4x4 matrix with rotation-translation of mapped points A to B.static Stringstatic Stringstatic StringAU.sortedItem(Lst<String> v, int n) Measure.transformPoints(Lst<P3> vPts, M4 m4, P3 center) -
Uses of Lst in jspecview.api
Methods in jspecview.api that return LstMethods in jspecview.api with parameters of type LstModifier and TypeMethodDescriptionvoidJSVTree.deleteNodes(Lst<JSVTreeNode> toDelete) AppletFrame.getJSVPanel(JSViewer viewer, Lst<Spectrum> specs) voidJSVMainPanel.setSelectedPanel(JSViewer viewer, JSVPanel jsvp, Lst<PanelNode> panelNodes) ScriptInterface.siGetNewJSVPanel2(Lst<Spectrum> specs) voidScriptInterface.siOpenDataOrFile(Object data, String name, Lst<Spectrum> specs, String url, int firstSpec, int lastSpec, boolean isAppend, String script, String id) from EXPORT command -
Uses of Lst in jspecview.app
Methods in jspecview.app that return LstMethods in jspecview.app with parameters of type Lst -
Uses of Lst in jspecview.appletjs
Methods in jspecview.appletjs with parameters of type Lst -
Uses of Lst in jspecview.application
Methods in jspecview.application with parameters of type LstModifier and TypeMethodDescriptionvoidAwtTree.deleteNodes(Lst<JSVTreeNode> toDelete) voidApplicationMenu.setRecentMenu(Lst<String> recentFilePaths) JSpecView.siGetNewJSVPanel2(Lst<Spectrum> specs) voidJSpecView.siOpenDataOrFile(Object data, String name, Lst<Spectrum> specs, String url, int firstSpec, int lastSpec, boolean isAppend, String script, String id) voidApplicationMenu.updateRecentMenus(Lst<String> recentFilePaths) -
Uses of Lst in jspecview.common
Subclasses of Lst in jspecview.commonModifier and TypeClassDescriptionclassfrom IntegralGraph a data structure for integration settingsclassclassa data structure for peak listsFields in jspecview.common declared as LstModifier and TypeFieldDescriptionLst<jspecview.common.GraphSet> PanelData.graphSetsJSViewer.panelNodesJSViewer.scriptQueueMethods in jspecview.common that return LstModifier and TypeMethodDescriptionstatic Lst<Annotation> IntegralData.getIntegrationRatiosFromString(Spectrum spec, String key_values) Parses x-coordinates and values from a string and returns them asIntegrationRatioobjectsSpectrum.getPeakList()static Lst<ScriptToken> ScriptToken.getScriptTokenList(String name, boolean isExact) Spectrum.getSubSpectra()read a string for possibly quoted tokens separated by space until // or # is reached.Methods in jspecview.common with parameters of type LstModifier and TypeMethodDescriptionvoidPanelData.addAnnotation(Lst<String> tokens) voidstatic PanelNodeReturns the tree node that is associated with a panelstatic PanelNodePanelNode.findNodeById(String id, Lst<PanelNode> panelNodes) static JDXSourcePanelNode.findSourceByNameOrId(String id, Lst<PanelNode> panelNodes) static AnnotationAnnotation.getColoredAnnotation(GenericGraphics g2d, Spectrum spec, Lst<String> args, Annotation lastAnnotation) static JSVPanelPanelNode.getLastFileFirstNode(Lst<PanelNode> panelNodes) static doubleReturns the maximum x value value from an array of arrays ofCoordinates.static doubleCoordinate.getMaxYUser(Lst<Spectrum> spectra, ViewData vd) Returns the maximum y value value from an array of arrays ofCoordinates.static doubleReturns the minimum x value value from an array of arrays ofCoordinates.static doubleCoordinate.getMinYUser(Lst<Spectrum> spectra, ViewData vd) Returns the minimum y value value from an array of arrays ofCoordinates.static StringScriptToken.getNameList(Lst<ScriptToken> list) static StringPanelNode.getSpectrumListAsString(Lst<PanelNode> panelNodes) voidstatic intvoidViewData.newSpectrum(Lst<Spectrum> spectra) intJSViewer.openDataOrFile(Object data, String name, Lst<Spectrum> specs, String strUrl, int firstSpec, int lastSpec, boolean isAppend, String id) static booleanSpectrum.process(Lst<Spectrum> specs, Spectrum.IRMode irMode) intJSViewer.selectPanel(JSVPanel jsvp, Lst<PanelNode> panelNodes) From (AwtMainPanel or JsMainPanel).setSelectedPanelintSpectrum.setPeakList(Lst<PeakInfo> list, String peakXLabel, String peakYLabel) Constructors in jspecview.common with parameters of type Lst -
Uses of Lst in jspecview.export
Fields in jspecview.export declared as LstModifier and TypeFieldDescriptionprotected Lst<Coordinate> XMLExporter.newXYCoordsprotected Lst<Coordinate> XMLExporter.newXYCoordsMethods in jspecview.export with parameters of type Lst -
Uses of Lst in jspecview.java
Methods in jspecview.java with parameters of type LstModifier and TypeMethodDescriptionstatic AwtPanelAwtPanel.getPanelMany(JSViewer viewer, Lst<Spectrum> spectra) Constructs aJSVPanelwith List of spectra and corresponding start and end indices of data points that should be displayedvoidAwtMainPanel.setSelectedPanel(JSViewer viewer, JSVPanel jsvp, Lst<PanelNode> panelNodes) -
Uses of Lst in jspecview.js2d
Methods in jspecview.js2d with parameters of type LstModifier and TypeMethodDescriptionstatic JsPanelJsPanel.getPanelMany(JSViewer viewer, Lst<Spectrum> spectra) Constructs aJSVPanelwith List of spectra and corresponding start and end indices of data points that should be displayedvoidJsMainPanel.setSelectedPanel(JSViewer viewer, JSVPanel jsvp, Lst<PanelNode> panelNodes) -
Uses of Lst in jspecview.source
Fields in jspecview.source declared as LstMethods in jspecview.source that return LstModifier and TypeMethodDescriptionJDXHeader.getHeaderTable()Returns the table of headersJDXSource.getSpectra()Returns the Vector of SpectraMethods in jspecview.source with parameters of type LstModifier and TypeMethodDescriptionstatic JDXSourceJDXSource.createView(Lst<Spectrum> specs) voidJDXHeader.setHeaderTable(Lst<String[]> table) Sets the headerTable for this Source or spectrum -
Uses of Lst in jspecview.tree
Methods in jspecview.tree with parameters of type Lst -
Uses of Lst in org.jmol.adapter.readers.cif
Fields in org.jmol.adapter.readers.cif declared as LstMethods in org.jmol.adapter.readers.cif with parameters of type LstModifier and TypeMethodDescriptionbooleanMSRdr.addLatticeVector(Lst<float[]> lattvecs, String data) -
Uses of Lst in org.jmol.adapter.readers.pymol
Methods in org.jmol.adapter.readers.pymol that return LstModifier and TypeMethodDescriptionMethods in org.jmol.adapter.readers.pymol with parameters of type Lst -
Uses of Lst in org.jmol.adapter.readers.quantum
Fields in org.jmol.adapter.readers.quantum declared as LstModifier and TypeFieldDescriptionGamessReader.atomNamesMOReader.moTypesBasisFunctionReader.orbitalsLst<int[]> BasisFunctionReader.shellsprotected Lst<SlaterData> BasisFunctionReader.slatersprotected Lst<AdfReader.SymmetryData> AdfReader.vSymmetriesMethods in org.jmol.adapter.readers.quantum that return LstMethods in org.jmol.adapter.readers.quantum with parameters of type LstModifier and TypeMethodDescriptionprotected voidNBOParser.getAllStructures(String output, Lst<Object> list) NBOParser.getStructureMap(Lst<Object> structureList, String type, int index) Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structureintNBOParser.getStructures(String data, String nrtType, Lst<Object> list) Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.static voidNBOParser.getStructures46(String[] tokens, String type, Lst<Object> structures, int nAtoms) Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.static voidGenNBOReader.setNboLabels(String[] tokens, int nLabels, Lst<Map<String, Object>> orbitals, int nOrbitals0, String moType) -
Uses of Lst in org.jmol.adapter.readers.simple
Fields in org.jmol.adapter.readers.simple declared as Lst -
Uses of Lst in org.jmol.adapter.readers.xtal
Fields in org.jmol.adapter.readers.xtal declared as Lst -
Uses of Lst in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter declared as LstModifier and TypeFieldDescriptionAtomSetCollectionReader.lstNCSAtom.tensorsAtomSetCollectionReader.trajectoryStepsMethods in org.jmol.adapter.smarter that return LstModifier and TypeMethodDescriptionAtomSetCollectionReader.getFortranFormatLengths(String s) get all integers after letters negative entries are spaces (1Xn)XtalSymmetry.FileSymmetry.setSpinList(String configuration) Methods in org.jmol.adapter.smarter with parameters of type LstModifier and TypeMethodDescriptionbooleanMSInterface.addLatticeVector(Lst<float[]> lattvecs, String substring) booleanXtalSymmetry.FileSymmetry.addMagLatticeVectors(Lst<float[]> lattvecs) voidXtalSymmetry.FileSymmetry.addSpinLattice(Lst<String> lstSpinFrames, Map<String, String> mapSpinIdToUVW) voidAtomSetCollection.finalizeTrajectoryAs(Lst<P3[]> trajectorySteps, Lst<V3[]> vibrationSteps) Constructors in org.jmol.adapter.smarter with parameters of type LstModifierConstructorDescriptionAtomSetCollection(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, Lst<?> list) -
Uses of Lst in org.jmol.api
Methods in org.jmol.api that return LstModifier and TypeMethodDescriptionJmolAnnotationParser.catalogValidations(Viewer vwr, SV validation, int[] modelAtomIndices, Map<String, int[]> valResMap, Map<String, Integer> map, Map<String, Integer> modelMap) SymmetryInterface.generateCrystalClass(P3 pt0) JmolAnnotationParser.getAtomValidation(Viewer vwr, String type, Atom atom) SymmetryInterface.getEquivPoints(Point3fi pt, String flags, float packing) SymmetryInterface.getLatticeCentering()SymmetryInterface.getMoreInfo()JmolScriptManager.getScriptItem(boolean b, boolean startedByCommandThread) JmolScriptManager.getScriptQueue()JmolNMRInterface.getTensorInfo(String tensorType, String infoType, BS bs) JmolAdapterAtomIterator.getTensors()JmolAnnotationParser.initializeAnnotation(SV objAnn, int type, int modelIndex) Methods in org.jmol.api that return types with arguments of type LstMethods in org.jmol.api with parameters of type LstModifier and TypeMethodDescriptionJmolScriptManager.addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) JmolPropertyManager.extractProperty(Object property, Object args, int pt, Lst<Object> v2, boolean isCompiled) voidSymmetryInterface.getEquivPointList(int nIgnore, String flags, M4[] opsCtr, float packing, Lst<Point3fi> pts, SymmetryInterface uc) voidSmilesMatcherInterface.getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings) SymmetryInterface.getSubgroupJSON(String nameFrom, String nameTo, int index1, int index2, int flags, Map<String, Object> retMap, Lst<Object> retLst) voidJmolNavigatorInterface.navigateList(JmolScriptEvaluator eval, Lst<Object[]> list) booleanJmolJDXMOLParser.readACDAssignments(int nPoints, boolean isPeakAssignment, Lst<String[]> list) intJmolJDXMOLParser.setACDAssignments(String model, String mytype, int peakCount, Lst<String[]> acdlist, String molFile) -
Uses of Lst in org.jmol.awtjs.swing
Fields in org.jmol.awtjs.swing declared as Lst -
Uses of Lst in org.jmol.dssx
Methods in org.jmol.dssx that return LstModifier and TypeMethodDescriptionAnnotationParser.catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Returns a LstAnnotationParser.getAtomValidation(Viewer vwr, String type, Atom atom) Get all validation values corresponding to a specific validation type.AnnotationParser.initializeAnnotation(SV objAnn, int type, int modelIndex) We create a main list of mappings, where each mapping has _atoms and _pathMethods in org.jmol.dssx with parameters of type Lst -
Uses of Lst in org.jmol.export
Methods in org.jmol.export that return LstModifier and TypeMethodDescription___Exporter.getColorList(int i00, short[] colixes, int nVertices, BS bsSelected, Map<Short, Integer> htColixes) input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color indexMethods in org.jmol.export with parameters of type LstModifier and TypeMethodDescriptionprotected int[]__CartesianExporter.getNormalMap(T3[] normals, int nNormals, BS bsValid, Lst<String> vNormals) protected void_VrmlExporter.outputColors(Lst<Short> colorList) protected void_StlExporter.outputGeometry(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, BS bsPolygons, int faceVertexMax, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_VrmlExporter.outputGeometry(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, BS bsPolygons, int faceVertexMax, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_X3dExporter.outputGeometry(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, BS bsPolygons, int faceVertexMax, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_VrmlExporter.outputNormals(Lst<String> vNormals) protected void___Exporter.outputSurface(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_IdtfExporter.outputSurface(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_MayaExporter.outputSurface(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_PovrayExporter.outputSurface(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_TachyonExporter.outputSurface(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void_VrmlExporter.outputSurface(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected voidJSExporter.outputSurface(T3[] vertices, T3[] normals, short[] vertexColixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) -
Uses of Lst in org.jmol.jsv
Methods in org.jmol.jsv with parameters of type LstModifier and TypeMethodDescriptionbooleanJDXMOLParser.readACDAssignments(int nPoints, boolean isPeakAssignment, Lst<String[]> list) intJDXMOLParser.setACDAssignments(String model, String mytype, int peakCount, Lst<String[]> acdlist, String molFile) -
Uses of Lst in org.jmol.jvxl.data
Fields in org.jmol.jvxl.data declared as LstMethods in org.jmol.jvxl.data with parameters of type LstModifier and TypeMethodDescriptionstatic voidJvxlCoder.set3dContourVector(Lst<Object> v, int[][] polygonIndexes, T3[] vertices) Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position. -
Uses of Lst in org.jmol.jvxl.readers
Fields in org.jmol.jvxl.readers declared as LstMethods in org.jmol.jvxl.readers with parameters of type Lst -
Uses of Lst in org.jmol.minimize
Fields in org.jmol.minimize declared as Lst -
Uses of Lst in org.jmol.modelset
Fields in org.jmol.modelset declared as LstModifier and TypeFieldDescriptionMeasurementData.pointsModelSet.stateScriptsModelSet.vibrationStepsFields in org.jmol.modelset with type parameters of type LstMethods in org.jmol.modelset that return LstModifier and TypeMethodDescriptionAtomCollection.generateCrystalClass(int atomIndex, P3 pt) AtomCollection.getAllAtomTensors(String type) AtomCollection.getAtomPointVector(BS bs) ModelSet.getModulationList(BS bs, char type, P3 t456) Methods in org.jmol.modelset with parameters of type LstModifier and TypeMethodDescriptionModelSet.addAtom(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, boolean isNegDisorder, byte specialAtomID, BS atomSymmetry, float bondRadius) ModelSet.addHydrogens(Lst<Atom> vConnections, P3[] pts) these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEWvoidModelSet.calcRasmolHydrogenBonds(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds) These are not actual hydrogen bonds.P3[][]AtomCollection.calculateHydrogens(BS bs, int[] nTotal, Lst<Atom> vConnect, int flags) get a list of potential H atom positions based on elemental valence and formal chargestatic intMeasurement.find(Lst<Measurement> measurements, Measurement m) P3[][]ModelSet.getCenterAndPoints(Lst<Object[]> vAtomSets, boolean addCenters) booleanAtom.getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) Used by SMILES to get vector of cross-linksbooleanGroup.getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) voidModelSet.getPolymerPointsAndVectors(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) voidAtomCollection.setAtomTensors(int atomIndex, Lst<Object> list) -
Uses of Lst in org.jmol.modelsetbio
Methods in org.jmol.modelsetbio that return LstModifier and TypeMethodDescriptionNucleicMonomer.getBasePairs()BioModel.getBioBranches(Lst<BS> biobranches) Methods in org.jmol.modelsetbio with parameters of type LstModifier and TypeMethodDescriptionprotected static intNucleicPolymer.addHydrogenBond(Lst<Bond> vAtoms, Atom atom1, Atom atom2) voidBioModelSet.calcAllRasmolHydrogenBonds(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int dsspVersion) only for base models, not trajectoriesvoidAminoPolymer.calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) voidBioPolymer.calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) voidNucleicPolymer.calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) voidBioModelSet.getAllPolymerPointsAndVectors(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) BioModel.getBioBranches(Lst<BS> biobranches) protected booleanMonomer.getCrossLinkGroup(int i, Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck) booleanMonomer.getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) booleanNucleicMonomer.getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) intBioPolymer.getPolymerPointsAndVectors(int last, BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) Method parameters in org.jmol.modelsetbio with type arguments of type Lst -
Uses of Lst in org.jmol.multitouch
Methods in org.jmol.multitouch that return Lst -
Uses of Lst in org.jmol.popup
Fields in org.jmol.popup declared as Lst -
Uses of Lst in org.jmol.quantum
Methods in org.jmol.quantum that return Lst -
Uses of Lst in org.jmol.script
Fields in org.jmol.script declared as LstFields in org.jmol.script with type parameters of type LstMethods in org.jmol.script that return LstModifier and TypeMethodDescriptionT.getAtomPropertiesLike(String type) SV.getList()ScriptParam.getPointOrCenterVector(T t) ScriptParam.getPointVector(T t, int i) ScriptManager.getScriptItem(boolean watching, boolean isByCommandWatcher) ScriptManager.getScriptQueue()ScriptParam.listParameter(int i, int nMin, int nMax) ScriptParam.listParameter4(int i, int nMin, int nMax, boolean allowString) ScriptParam.transformPoints(Lst<P3> vPts, M4 m4, P3 center) Methods in org.jmol.script that return types with arguments of type LstMethods in org.jmol.script with parameters of type LstModifier and TypeMethodDescriptionScriptManager.addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) Add hydrogens to a modelbooleanvoidScriptParam.getHklPlane(T3 pt, float offset, Lst<P3> pts) static doubleFills a 4x4 matrix with rotation-translation of mapped points A to B.ScriptEval.getUserFunctionResult(String name, Lst<SV> params, SV tokenAtom) static SVSV.getVariableList(Lst<?> v) ScriptParam.hklParameter(int i, Lst<P3> pts, boolean allowOffset) voidScriptManager.runScriptFromThread(Lst<Object> scriptItem) ScriptParam.transformPoints(Lst<P3> vPts, M4 m4, P3 center) -
Uses of Lst in org.jmol.scriptext
Methods in org.jmol.scriptext that return LstMethods in org.jmol.scriptext with parameters of type LstModifier and TypeMethodDescriptionfloatSmilesExt.getSmilesCorrelation(BS bsA, BS bsB, String smiles, Lst<P3> ptsA, Lst<P3> ptsB, M4 m4, Lst<BS> vReturn, boolean asMap, int[][] mapSet, P3 center, boolean bestMap, int flags) The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality. -
Uses of Lst in org.jmol.shape
Fields in org.jmol.shape declared as LstModifier and TypeFieldDescriptionMeshCollection.displayWithinPointsMesh.lineDatafinal Lst<Measurement> Measures.measurementsMethods in org.jmol.shape that return LstModifier and TypeMethodDescriptionMeshCollection.getMeshList(String key, boolean justOne) Get matching list of meshes, order reversedMethods in org.jmol.shape with parameters of type LstModifier and TypeMethodDescriptionstatic booleanMesh.checkWithin(T3 pti, Lst<P3> withinPoints, float withinDistance2, boolean isWithinNot) voidMesh.setShowWithin(Lst<P3> showWithinPoints, float showWithinDistance2, boolean isWithinNot) -
Uses of Lst in org.jmol.shapecgo
Fields in org.jmol.shapecgo declared as Lst -
Uses of Lst in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as Lst -
Uses of Lst in org.jmol.shapesurface
Methods in org.jmol.shapesurface that return LstMethods in org.jmol.shapesurface with parameters of type LstModifier and TypeMethodDescriptionstatic voidIsosurfaceMesh.addContourPoints(Lst<Object> v, BS bsContour, int i, SB fData, T3[] vertices, float[] vertexValues, int iA, int iB, int iC, float value) static voidIsosurfaceMesh.setContourVector(Lst<Object> v, int nPolygons, BS bsContour, float value, short colix, int color, SB fData) -
Uses of Lst in org.jmol.smiles
Methods in org.jmol.smiles with parameters of type LstModifier and TypeMethodDescriptionvoidSmilesSearch.SmilesTarget.finalizeAromatic(Lst<BS> lstAromatic) booleanSmilesAtom.getCrossLinkVector(Lst<Integer> vLinks, boolean crosslinkCovalent, boolean crosslinkHBond) voidSmilesMatcher.getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> ret, Lst<BS>[] vRings) called by ForceFieldMMFF.setAtomTypes only -
Uses of Lst in org.jmol.symmetry
Methods in org.jmol.symmetry that return LstModifier and TypeMethodDescriptionSymmetry.generateCrystalClass(P3 pt00) Symmetry.getEquivPoints(Point3fi pt, String flags, float packing) Symmetry.getLatticeCentering()SymmetryOperation.getLatticeCentering(SymmetryOperation[] ops) SymmetryOperation.getLatticeCenteringStrings(SymmetryOperation[] ops) Symmetry.getMoreInfo()SpaceGroup.setSpinList(String configuration) Methods in org.jmol.symmetry with parameters of type LstModifier and TypeMethodDescriptionbooleanSpaceGroup.addMagLatticeVectors(Lst<float[]> lattvecs) voidspin space groups onlyvoidSymmetry.getEquivPointList(int nInitial, String flags, M4[] opsCtr, float packing, Lst<Point3fi> pts, SymmetryInterface uc) Load a list of initial current points, and one or more starting points with equivalent points.Symmetry.getSubgroupJSON(String nameFrom, String nameTo, int i1, int i2, int flags, Map<String, Object> retMap, Lst<Object> retLst) Retrieve subgroup information for a space group.voidCLEG.ClegData.setReturnLst(Lst<Object> ret) -
Uses of Lst in org.jmol.util
Fields in org.jmol.util declared as LstModifier and TypeFieldDescriptionprotected Lst<org.jmol.util.BZone.BZPoint> BZone.newLatticePtsBZone.newPlanesprotected Lst<org.jmol.util.BZone.Subzone> BZone.subzonesMethods in org.jmol.util that return LstModifier and TypeMethodDescriptionTriangulator.intersectPlane(P4 plane, T3[] vertices, int flags) a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.Methods in org.jmol.util with parameters of type LstModifier and TypeMethodDescriptionstatic Stringstatic BSJmolMolecule.getBranchBitSet(Node[] atoms, int atomIndex, BS bsToTest, Lst<BS> biobranches, int atomIndexNot, boolean allowCyclic, boolean allowBioResidue) given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.booleanNode.getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) voidMeshSlicer.getIntersection(float distance, P4 plane, P3[] ptCenters, Lst<P3[]> vData, float[] fData, BS bsSource, MeshSurface meshSurface, boolean andCap, boolean doClean, int tokType, boolean isGhost) static final JmolMolecule[]Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.ModulationSet.setMod(String id, P3 r00, P3 r0, int d, Lst<Modulation> mods, M3 gammaE, Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate) A collection of modulations for a specific atom.voidMeshSurface.slabPolygonsList(Lst<Object[]> slabInfo, boolean allowCap) -
Uses of Lst in org.jmol.viewer
Fields in org.jmol.viewer with type parameters of type LstMethods in org.jmol.viewer that return LstModifier and TypeMethodDescriptionPropertyManager.getAllAtomInfo(BS bs) PropertyManager.getAllBondInfo(Object bsOrArray) Viewer.getAtomValidation(String type, Atom atom) PropertyManager.getMoleculeInfo(Object atomExpression) Viewer.getStatusChanged(String statusNameList) Viewer.getSymmetryEquivPointList(Lst<Point3fi> pts, String flags) Viewer.getSymmetryEquivPoints(Point3fi pt, String flags) Viewer.parseJSONArray(String jsonArray) Methods in org.jmol.viewer that return types with arguments of type LstModifier and TypeMethodDescriptionPropertyManager.getAllChainInfo(BS bs) Viewer.getStatusChanged(String statusNameList) Viewer.getStatusChanged(String statusNameList) Methods in org.jmol.viewer with parameters of type LstModifier and TypeMethodDescriptionViewer.addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) PropertyManager.extractProperty(Object prop, Object args, int ptr, Lst<Object> v2, boolean isCompiled) P3[]Viewer.getAdditionalHydrogens(BS bsAtoms, Lst<Atom> vConnections, int flags) P3[][]Viewer.getCenterAndPoints(Lst<Object[]> atomSets, boolean addCenter) static voidvoidViewer.getPolymerPointsAndVectors(BS bs, Lst<P3[]> vList) Viewer.getSymmetryEquivPointList(Lst<Point3fi> pts, String flags) voidTransformManager.navigateList(JmolScriptEvaluator eval, Lst<Object[]> list) Viewer.newMeasurementData(String id, Lst<Object> points) booleanViewer.rotateAboutPointsInternal(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, Lst<P3> finalPoints, float[] dihedralList, M3 vectorMatrix, M4 m4, boolean useModelKit, P3[][] centerAndPoints) -
Uses of Lst in org.openscience.jvxl.simplewriter
Methods in org.openscience.jvxl.simplewriter with parameters of type LstModifier and TypeMethodDescriptionstatic StringASimpleJvxlWriter.jvxlGetData(VoxelDataCreator vdc, Parameters params, VolumeData volumeData, String[] title, Lst<P3> surfacePointsReturn, float[] areaVolumeReturn) Constructors in org.openscience.jvxl.simplewriter with parameters of type LstModifierConstructorDescriptionSimpleMarchingCubes(VoxelDataCreator vdc, VolumeData volumeData, Parameters params, JvxlData jvxlData, Lst<P3> surfacePointsReturn, float[] areaVolumeReturn)