Uses of Class
javajs.util.BS
Packages that use BS
Package
Description
Provides Binary Space Partitioning Functionality to spacially
separate data structures in n-dimensions
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
-
Uses of BS in javajs.util
Methods in javajs.util that return BSModifier and TypeMethodDescriptionstatic BS
fast copystatic BS
BS.newN
(int nbits) Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range0
throughnbits-1
.static BS
Methods in javajs.util with parameters of type BSModifier and TypeMethodDescriptionvoid
Performs a logical AND of this target bit set with the argument bit set.void
Clears all of the bits in thisBitSet
whose corresponding bit is set in the specifiedBitSet
.static BS
fast copystatic String
boolean
BS.intersects
(BS set) Returns true if the specifiedBitSet
has any bits set totrue
that are also set totrue
in thisBitSet
.void
Performs a logical OR of this bit set with the bit set argument.void
Performs a logical XOR of this bit set with the bit set argument. -
Uses of BS in jspecview.common
Methods in jspecview.common that return BS -
Uses of BS in org.jmol.adapter.readers.molxyz
Fields in org.jmol.adapter.readers.molxyz declared as BS -
Uses of BS in org.jmol.adapter.readers.quantum
Fields in org.jmol.adapter.readers.quantum declared as BS -
Uses of BS in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter declared as BSModifier and TypeFieldDescriptionBS[]
Structure.bsAll
AtomSetCollection.bsAtoms
protected BS
AtomSetCollectionReader.bsFilter
protected BS
AtomSetCollectionReader.bsModels
AtomSetCollection.bsStructuredModels
Atom.bsSymmetry
Methods in org.jmol.adapter.smarter that return BSModifier and TypeMethodDescriptionBS[]
StructureIterator.getBSAll()
AtomSetCollection.getBSAtoms
(int n) Create bsAtoms if it is null, and set bits if desired.StructureIterator.getStructuredModels()
Constructors in org.jmol.adapter.smarter with parameters of type BS -
Uses of BS in org.jmol.adapter.writers
Methods in org.jmol.adapter.writers with parameters of type BS -
Uses of BS in org.jmol.api
Methods in org.jmol.api that return BSModifier and TypeMethodDescriptionJmolScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) JmolAnnotationParser.getAtomBits
(Viewer vwr, String key, Object dssr, Map<String, Object> cache, int type, int modelIndex, BS bsModel) JmolScriptEvaluator.getAtomBitSet
(Object atomExpression) JmolScriptManager.getAtomBitSetEval
(JmolScriptEvaluator eval, Object atomExpression) abstract BS[]
JmolAdapterStructureIterator.getBSAll()
JmolEnvCalc.getBsSurfaceClone()
abstract BS
JmolViewer.getElementsPresentBitSet
(int modelIndex) abstract BS
JmolViewer.getSmartsMatch
(String smarts, BS bsSelected) abstract BS
JmolAdapterStructureIterator.getStructuredModels()
SmilesMatcherInterface.getSubstructureSet
(Object pattern, Object target, int ac, BS bsSelected, int flags) BS[]
SmilesMatcherInterface.getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) JmolAdapterAtomIterator.getSymmetry()
JmolNMRInterface.getUniqueTensorSet
(BS bs) An attempt to find unique atoms using tensors.abstract BS
JmolViewer.getVisibleFramesBitSet()
SymmetryInterface.notInCentroid
(ModelSet modelSet, BS bsAtoms, int[] minmax) SymmetryInterface.removeDuplicates
(ModelSet ms, BS bs, boolean highPrec) Methods in org.jmol.api with parameters of type BSModifier and TypeMethodDescriptionvoid
JmolScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) abstract void
JmolViewer.calcAtomsMinMax
(BS bs, BoxInfo boxInfo) void
JmolEnvCalc.calculate
(RadiusData rd, float maxRadius, BS bsSelected, BS bsIgnore, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel) void
SymmetryInterface.calculateCIPChiralityForAtoms
(Viewer vwr, BS bsAtoms) JmolAnnotationParser.calculateDSSRStructure
(Viewer vwr, BS bsAtoms) SmilesMatcherInterface.compileSearchTarget
(Node[] atoms, int atomCount, BS bitSet) void
JmolScriptEvaluator.deleteAtomsInVariables
(BS bsDeleted) void
JmolDataManager.deleteModelAtoms
(int firstAtomIndex, int nAtoms, BS bsDeleted) SymmetryInterface.findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) void
JmolPropertyManager.fixJMEFormalCharges
(BS bsAtoms, String s) JmolAnnotationParser.getAtomBits
(Viewer vwr, String key, Object dssr, Map<String, Object> cache, int type, int modelIndex, BS bsModel) JmolPropertyManager.getChimeInfo
(int tok, BS selectionSet) int[][]
SmilesMatcherInterface.getCorrelationMaps
(String pattern, Node[] atoms, int ac, BS bsSelected, int flags) JmolDataManager.getDefaultVdwNameOrData
(VDW type, BS bs) SymmetryInterface.getIterator
(Viewer vwr, Atom atom, BS bstoms, float radius) int[][]
SmilesMatcherInterface.getMapForJME
(String jme, Atom[] at, BS bsAtoms) void
SmilesMatcherInterface.getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings) JmolPropertyManager.getModelCml
(BS bs, int nAtomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories) JmolPropertyManager.getModelExtract
(BS atomBitSet, boolean doTransform, boolean isModelKit, String type, boolean allTrajectories) JmolPropertyManager.getModelFileInfo
(BS visibleFramesBitSet) abstract String
JmolViewer.getOpenSmiles
(BS atoms) JmolPropertyManager.getPdbAtomData
(BS bs, OC out, boolean asPQR, boolean doTransform, boolean allTrajectories) JmolPropertyManager.getPdbData
(int modelIndex, String type, BS bsA, Object[] parameters, OC oc, boolean addStructure) abstract BS
JmolViewer.getSmartsMatch
(String smarts, BS bsSelected) abstract String
SmilesMatcherInterface.getSubstructureSet
(Object pattern, Object target, int ac, BS bsSelected, int flags) BS[]
SmilesMatcherInterface.getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) JmolNMRInterface.getTensorInfo
(String tensorType, String infoType, BS bs) JmolNMRInterface.getUniqueTensorSet
(BS bs) An attempt to find unique atoms using tensors.SymmetryInterface.notInCentroid
(ModelSet modelSet, BS bsAtoms, int[] minmax) SymmetryInterface.removeDuplicates
(ModelSet ms, BS bs, boolean highPrec) void
JmolSelectionListener.selectionChanged
(BS selection) Called when the selected atoms changeSymmetryInterface.setPointGroup
(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) abstract void
JmolViewer.setSelectionSet
(BS newSelection) SymmetryInterface.staticTransformSpaceGroup
(BS bs, String cleg, Object paramsOrUC, SB sb) Method parameters in org.jmol.api with type arguments of type BS -
Uses of BS in org.jmol.atomdata
Fields in org.jmol.atomdata declared as BSModifier and TypeFieldDescriptionAtomData.bsIgnored
BS[]
AtomData.bsMolecules
AtomData.bsSelected
Methods in org.jmol.atomdata with parameters of type BSModifier and TypeMethodDescriptionAtomDataServer.getSelectedAtomIterator
(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel) void
AtomData.transformXYZ
(M4 mat, BS bs) allow for transformed XYZ -
Uses of BS in org.jmol.awtjs.swing
Methods in org.jmol.awtjs.swing with parameters of type BS -
Uses of BS in org.jmol.bspt
Methods in org.jmol.bspt with parameters of type BSModifier and TypeMethodDescriptionvoid
Bspf.initialize
(int modelIndex, P3[] atoms, BS modelAtomBitSet) static int
PointIterator.withinDistPoints
(float distance, P3 pt, P3[] ap3, P3[] ap31, BS bsSelected, Object[] ret) carry out various functions of the within() script function -
Uses of BS in org.jmol.dssx
Methods in org.jmol.dssx that return BSModifier and TypeMethodDescriptionAnnotationParser.getAtomBits
(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) DSSR1.getAtomBits
(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) Methods in org.jmol.dssx with parameters of type BSModifier and TypeMethodDescriptionAnnotationParser.calculateDSSRStructure
(Viewer vwr, BS bsAtoms) DSSR1.calculateDSSRStructure
(Viewer vwr, BS bsAtoms) void
Adjusts _atoms bitset to account for added hydrogen atoms.AnnotationParser.getAtomBits
(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) DSSR1.getAtomBits
(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) -
Uses of BS in org.jmol.export
Methods in org.jmol.export with parameters of type BSModifier 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 indexprotected int
__CartesianExporter.getCoordinateMap
(T3[] vertices, int[] coordMap, BS bsValid) protected int[]
__CartesianExporter.getNormalMap
(T3[] normals, int nNormals, BS bsValid, Lst<String> vNormals) protected void
JSExporter.jsSurface
(Object applet, T3[] vertices, T3[] normals, int[][] indices, int nVertices, int nPolygons, int nFaces, BS bsPolygons, int faceVertexMax, int color, int[] vertexColors, int[] polygonColors) protected void
_VrmlExporter.outputColorIndices
(int[][] indices, int nPolygons, BS bsPolygons, int faceVertexMax, Map<Short, Integer> htColixes, short[] colixes, short[] polygonColixes) 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
__CartesianExporter.outputIndices
(int[][] indices, int[] map, int nPolygons, BS bsPolygons, int faceVertexMax) 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 void
JSExporter.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 BS in org.jmol.geodesic
Methods in org.jmol.geodesic that return BSModifier and TypeMethodDescriptionEnvelopeCalculation.getBsSurfaceClone()
BS[]
EnvelopeCalculation.getDotsConvexMaps()
Methods in org.jmol.geodesic with parameters of type BSModifier and TypeMethodDescriptionvoid
EnvelopeCalculation.calculate
(RadiusData rd, float maxRadius, BS bsSelected, BS bsIgnore, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel) void
EnvelopeCalculation.reCalculate
(BS bs, M3 m) problem prior to 12.3.18 was that dots once on the deodesic were not being moved.void
EnvelopeCalculation.setFromBits
(int index, BS bs) -
Uses of BS in org.jmol.inchi
Methods in org.jmol.inchi with parameters of type BS -
Uses of BS in org.jmol.jvxl.api
Methods in org.jmol.jvxl.api with parameters of type BSModifier and TypeMethodDescriptionP3[]
MeshDataServer.calculateGeodesicSurface
(BS bsSelected, float envelopeRadius) -
Uses of BS in org.jmol.jvxl.calc
Fields in org.jmol.jvxl.calc declared as BSModifier and TypeFieldDescriptionprotected BS
MarchingCubes.bsExcludedPlanes
protected BS
MarchingCubes.bsExcludedTriangles
protected BS
MarchingCubes.bsExcludedVertices
protected BS
MarchingCubes.bsValues
MarchingCubes.bsVoxels
Constructors in org.jmol.jvxl.calc with parameters of type BSModifierConstructorDescriptionMarchingCubes
(VertexDataServer surfaceReader, VolumeData volumeData, Parameters params, BS bsVoxels) -
Uses of BS in org.jmol.jvxl.data
Fields in org.jmol.jvxl.data declared as BSFields in org.jmol.jvxl.data with type parameters of type BSMethods in org.jmol.jvxl.data that return BSModifier and TypeMethodDescriptionBS[]
MeshData.getSurfaceSet()
static BS
JvxlCoder.jvxlDecodeBitSet
(String data) static BS
JvxlCoder.jvxlDecodeBitSetRange
(String data, int base, int range) Methods in org.jmol.jvxl.data with parameters of type BSModifier and TypeMethodDescriptionstatic Object
MeshData.calculateVolumeOrArea
(MeshData m, BS thisSet, boolean isArea, boolean getSets) void
MeshData.invalidateVertices
(BS bsInvalid) static String
JvxlCoder.jvxlEncodeBitSet
(BS bs) static int
JvxlCoder.jvxlEncodeBitSet0
(BS bs, int nPoints, SB sb) static int
JvxlCoder.jvxlEncodeBitSetBuffer
(BS bs, int nPoints, SB sb) void
JvxlData.setSurfaceInfoFromBitSet
(BS bs, P4 thePlane) void
JvxlData.setSurfaceInfoFromBitSetPts
(BS bs, P4 thePlane, P3 mapLattice) void
MeshData.updateInvalidatedVertices
(BS bs) -
Uses of BS in org.jmol.jvxl.readers
Fields in org.jmol.jvxl.readers declared as BSModifier and TypeFieldDescriptionBS[]
Parameters.bsExcluded
Parameters.bsIgnore
Parameters.bsSelected
Parameters.bsSolvent
SurfaceGenerator.bsVdw
protected BS
JvxlXmlReader.bsVoxelBitSet
BS[]
Parameters.intersection
protected BS
SurfaceReader.jvxlVoxelBitSet
Parameters.surfaceAtoms
Methods in org.jmol.jvxl.readers that return BSMethods in org.jmol.jvxl.readers with parameters of type BS -
Uses of BS in org.jmol.minimize
Fields in org.jmol.minimize declared as BSModifier and TypeFieldDescriptionMinAtom.bs14
Minimizer.bsAtoms
Minimizer.bsMinFixed
MinAtom.bsVdw
Methods in org.jmol.minimize with parameters of type BS -
Uses of BS in org.jmol.minimize.forcefield
Methods in org.jmol.minimize.forcefield with parameters of type BSModifier and TypeMethodDescriptionfloat[]
ForceFieldMMFF.calculatePartialCharges
(Bond[] bonds, int[] bTypes, Atom[] atoms, int[] aTypes, BS bsAtoms, boolean doRound) assign partial charges ala MMFF94boolean
ForceFieldMMFF.setArrays
(Atom[] atoms, BS bsAtoms, Bond[] bonds, int rawBondCount, boolean doRound, boolean allowUnknowns) abstract boolean
boolean
boolean
-
Uses of BS in org.jmol.modelkit
Fields in org.jmol.modelkit declared as BSModifier and TypeFieldDescriptionprotected final BS
ModelKit.bsKeyModels
a bitset indicating the presence of element keys for models; clearing a bit will cause a new key to be produced.protected final BS
ModelKit.bsKeyModelsOFF
tracks models for which the element key has been explicitly set OFF, overriding global SET elementKey ONMethods in org.jmol.modelkit with parameters of type BSModifier and TypeMethodDescriptionvoid
ModelKit.addLockedAtoms
(SymmetryInterface sg, BS bsLocked) Only for the current modelint
ModelKit.assignMoveAtoms
(BS bsSelected, int iatom, P3 p, P3[] pts, boolean allowProjection, boolean isMolecule, boolean isCommand) int
ModelKit.checkMovedAtoms
(BS bsFixed, BS bsAtoms, P3[] apos0) Something has changed atom positions.int
MODELKIT ADD @3 ...void
ModelKit.cmdAssignAtom
(BS bs, P3 pt, String type, String cmd) A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom via MODELKIT ASSIGN ATOMint
ModelKit.cmdAssignDeleteAtoms
(BS bs) Delete all atoms that are equivalent to this atom.int
ModelKit.cmdAssignMoveAtoms
(BS bsSelected, int iatom, P3 p, P3[] pts, boolean allowProjection, boolean isMolecule) void
ModelKit.cmdMinimize
(JmolScriptEvaluator eval, BS bsBasis, int steps, float crit, float rangeFixed, int flags) Minimize a unit cell with full symmetry constraints.int
ModelKit.cmdRotateAtoms
(BS bsAtoms, P3[] points, float endDegrees) void
ModelKit.minimizeEnd
(BS bsBasis2, boolean isEnd) int
ModelKit.moveMinConstrained
(int iatom, P3 p, BS bsAtoms) -
Uses of BS in org.jmol.modelset
Subclasses of BS in org.jmol.modelsetFields in org.jmol.modelset declared as BSModifier and TypeFieldDescriptionAtom.atomSymmetry
ModelSet.bboxModels
protected BS
ModelSet.bsAll
protected BS
BondCollection.bsAromatic
Model.bsAsymmetricUnit
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.Model.bsAtoms
Note that this bitset may or may not include bsAtomsDeletedModel.bsAtomsDeleted
AtomCollection.bsClickable
AtomCollection.bsModulated
AtomCollection.bsPartialCharges
MeasurementData.bsSelected
protected BS
ModelSet.bsSymmetry
AtomCollection.bsVisible
protected BS[]
ModelSet.elementsPresent
ModelLoader.structuresDefinedInFile
BS[]
AtomCollection.tainted
Fields in org.jmol.modelset with type parameters of type BSMethods in org.jmol.modelset that return BSModifier and TypeMethodDescriptionModelSet.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 NEWModelSet.deleteModels
(BS bsModels) ModelSet.findAtomsInRectangle
(Rectangle rect) Atom.findAtomsLike
(String atomExpression) ModelSet.fixDeletedBonds
(BS bs) protected BS
ModelSet.getAtomBitsMaybeDeleted
(int tokType, Object specInfo) AtomCollection.getAtomBitsMDa
(int tokType, Object specInfo, BS bs) general unqualified lookup of atom set typeprotected BS
BondCollection.getAtomBitsMDb
(int tokType, Object specInfo) general lookup for integer type -- from EvalBondCollection.getAtomsConnected
(float min, float max, int intType, BS bs) AtomCollection.getAtomsFromAtomNumberInFrame
(int atomNumber) AtomCollection.getAtomsNearPlane
(float distance, P4 plane) ModelSet.getAtomsWithin
(float distance, T3 coord, BS bsResult, int modelIndex) ModelSet.getAtomsWithinRadius
(float distance, BS bs, boolean withinAllModels, RadiusData rd, BS bsSubset) Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atomsModelSet.getBitSetTrajectories()
BondCollection.getBondsForSelectedAtoms
(BS bsAtoms, boolean bondSelectionModeOr) BS[]
ModelSet.getBsBranches
(float[] dihedralList) Group.getBSSideChain()
AtomCollection.getChainBits
(int chainID) AtomCollection.getClickableSet
(boolean forceNew) ModelSet.getConformation
(int modelIndex, int conformationIndex, boolean doSet, BS bsSelected) ModelSet.getConnectingAtoms
(BS bsAtoms, BS bsFixed) ModelSet.getElementsPresentBitSet
(int modelIndex) ModelSet.getEquivalentAtoms
(int iatom) ModelSet.getGroupsWithin
(int nResidues, BS bs) ModelSet.getIterativeModels
(boolean allowJmolData) only some models can be iterated through.ModelSet.getModelAtomBitSetIncludingDeleted
(int modelIndex, boolean asCopy) Note that this method returns all atoms, included deleted ones.ModelSet.getModelAtomBitSetIncludingDeletedBs
(BS bsModels) note -- this method returns ALL atoms, including deleted.ModelSet.getModelBS
(BS atomList, boolean allTrajectories) Get the set of models associated with a set of atoms.ModelSet.getMoleculeBitSet
(BS bs) return cumulative sum of all atoms in molecules containing these atomsModelSet.getMoleculeBitSetForAtom
(int atomIndex) AtomCollection.getSeqcodeBits
(int seqcode, boolean returnEmpty) ModelSet.getSequenceBits
(String specInfo, BS bsAtoms, BS bsResult) AtomCollection.getSpecNameOrNull
(String name, boolean checkStar) ModelSet.getSymmetryEquivAtoms
(BS bsAtoms, SymmetryInterface sym, BS bsModelAtoms) Return a bitset of equivalent atomsAtomCollection.getTaintedAtoms
(int type) AtomCollection.getVisibleSet
(boolean forceNew) ModelSet.setConformation
(BS bsAtoms) Methods in org.jmol.modelset with parameters of type BSModifier 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) void
turns this into a SPHERICAL iterator for "within Distance" measuresvoid
BondCollection.addConnectedHAtoms
(Atom atom, BS bsAtoms) ModelSet.addStateScript
(String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions) void
BondCollection.assignAromaticBondsBs
(boolean isUserCalculation, BS bsBonds) algorithm discussed above.int
ModelSet.autoBondBs4
(BS bsA, BS bsB, BS bsExclude, BS bsBonds, short mad, boolean preJmol11_9_24, SB state) int
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.BondCollection.bondAtoms
(Atom atom1, Atom atom2, int order, short mad, BS bsBonds, float energy, boolean addGroup, boolean isNew) int
ModelSet.calcAtomsMinMax
(BS bs, BoxInfo boxInfo) void
ModelSet.calcBoundBoxDimensions
(BS bs, float scale) void
ModelSet.calcRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds) These are not actual hydrogen bonds.float
ModelSet.calcRotationRadiusBs
(BS bs) ModelSet.calculateChiralityForAtoms
(BS bsAtoms, boolean withReturn) 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 chargeModelSet.calculateMolecularDipole
(int modelIndex, BS bsAtoms) ModelSet.calculatePointGroup
(BS bsAtoms) protected void
ModelSet.calculatePolymers
(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded) ModelSet.calculateStructures
(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version) ModelSet.calculateStructuresAllExcept
(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) allows rebuilding of PDB structures; also accessed by ModelManager from Evalint
ModelSet.calculateStruts
(BS bs1, BS bs2) see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.P3[]
AtomCollection.calculateSurface
(BS bsSelected, float envelopeRadius) float
AtomCollection.calculateVolume
(BS bs, VDW vType) boolean
Text.checkObjectClicked
(boolean isAntialiased, int x, int y, BS bsVisible) static String
ModelLoader.createAtomDataSet
(Viewer vwr, ModelSet modelSet, int tokType, Object asc, BS bsSelected) protected void
Delete bonds, but don't shift arrays, just set bond to null, in order to allow for state.void
void
ModelSet.deleteAtoms
(BS bs) boolean
StateScript.deleteAtoms
(int modelIndex, BS bsBonds, BS bsAtoms) void
ModelSet.deleteBonds
(BS bsBonds, boolean isFullModel) protected int[]
BondCollection.deleteConnections
(float minD, float maxD, int order, BS bsA, BS bsB, boolean isBonds, boolean matchNull) protected void
AtomCollection.deleteModelAtoms
(int firstAtomIndex, int nAtoms, BS bsAtoms) ModelSet.deleteModels
(BS bsModels) protected void
AtomCollection.findNearest2
(int x, int y, Atom[] closest, BS bsNot, int min) int
ModelSet.findNearestAtomIndex
(int x, int y, BS bsNot, int min) ModelSet.fixDeletedBonds
(BS bs) int
AtomCollection.fixFormalCharges
(BS bs) void
Group.fixIndices
(int atomsDeleted, BS bsDeleted) void
Model.fixIndices
(int modelIndex, int nAtomsDeleted, BS bsDeleted) protected void
Model.fixIndicesM
(int modelIndex, int nAtomsDeleted, BS bsDeleted) AtomCollection.getAtomBitsMDa
(int tokType, Object specInfo, BS bs) general unqualified lookup of atom set typeQuat[]
ModelSet.getAtomGroupQuaternions
(BS bsAtoms, int nMax, char qtype) int[]
AtomCollection.getAtomIndices
(BS bs) AtomCollection.getAtomPointVector
(BS bs) BondCollection.getAtomsConnected
(float min, float max, int intType, BS bs) ModelSet.getAtomSetCenter
(BS bs) void
AtomCollection.getAtomsInFrame
(BS bsAtoms) ModelSet.getAtomsWithin
(float distance, T3 coord, BS bsResult, int modelIndex) ModelSet.getAtomsWithinRadius
(float distance, BS bs, boolean withinAllModels, RadiusData rd, BS bsSubset) Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atomsBondCollection.getBondIterator
(BS bsBonds) BondCollection.getBondIteratorForType
(int bondType, BS bsAtoms) BondCollection.getBondsForSelectedAtoms
(BS bsAtoms, boolean bondSelectionModeOr) ModelSet.getBoundBoxOrientation
(int type, BS bsAtoms, P3[] points) ModelSet.getBoxInfo
(BS bs, float scale) float[]
ModelSet.getCellWeights
(BS bsAtoms) ModelSet.getConformation
(int modelIndex, int conformationIndex, boolean doSet, BS bsSelected) ModelSet.getConnectingAtoms
(BS bsAtoms, BS bsFixed) ModelSet.getDefaultStructure
(BS bsAtoms, BS bsModified) int
AtomCollection.getFirstAtomIndexFromAtomNumber
(int atomNumber, BS bsVisibleFrames) P3[]
ModelSet.getFrameOffsets
(BS bsAtoms, boolean isFull) void
Atom.getGroupBits
(BS bs) ModelSet.getGroupsWithin
(int nResidues, BS bs) ModelSet.getModelAtomBitSetIncludingDeletedBs
(BS bsModels) note -- this method returns ALL atoms, including deleted.ModelSet.getModelBS
(BS atomList, boolean allTrajectories) Get the set of models associated with a set of atoms.void
Trajectory.getModelBS
(int modelIndex, BS bs) set bits for all trajectories associated with this modelModelSet.getModelDataBaseName
(BS bsAtoms) ModelSet.getModelSetAuxiliaryInfo
(BS bsModels) Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.ModelSet.getModulationList
(BS bs, char type, P3 t456) ModelSet.getMoleculeBitSet
(BS bs) return cumulative sum of all atoms in molecules containing these atomsprotected Bond
BondCollection.getOrAddBond
(Atom atom, Atom atomOther, int order, short mad, BS bsBonds, float energy, boolean overrideBonding) ModelSet.getPointGroupAsString
(BS bsAtoms, String type, int index, float scale, P3[] pts, P3 center, String id) ModelSet.getPointGroupInfo
(BS bsAtoms) void
ModelSet.getPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) ModelSet.getProteinStructureState
(BS bsAtoms, int mode) ModelSet.getSelectedAtomIterator
(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean hemisphereOnly, boolean isMultiModel) ModelSet.getSequenceBits
(String specInfo, BS bsAtoms, BS bsResult) ModelSet.getSymmetryEquivAtoms
(BS bsAtoms, SymmetryInterface sym, BS bsModelAtoms) Return a bitset of equivalent atomsvoid
ModelSet.getSymmetryEquivAtomsForAtom
(int i, BS bsAtoms, BS bsCheck, BS bsEquiv) Set a bitset of the equivalent atoms of an atom.ModelSet.getUnitCellPointsWithin
(float distance, BS bs, P3 pt, boolean asMap) void
ModelSet.invertSelected
(P3 pt, P4 plane, int iAtom, BS bsAtoms) Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.boolean
Model.isContainedIn
(BS bs) boolean
Group.isSelected
(BS bs) int[]
ModelSet.makeConnections
(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy) int[]
ModelSet.makeConnections2
(float minD, float maxD, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy, SB state) void
ModelSet.morphAtoms
(BS bsAtoms, P3[][] points, int ipt, float f, P3 ptemp) void
ModelSet.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs, P3 center, boolean isInternal, boolean translationOnly) static BondSet
void
ModelSet.recalculatePolymers
(BS bsModelsExcluded) void
ModelSet.recalculatePositionDependentQuantities
(BS bsAtoms, M4 mat) void
Trajectory.selectDisplayed
(BS bs) Remove trajectories that are not currently displayed from the visible frames bitset.MeasurementData.set
(int tokAction, Map<String, Integer> htMin, RadiusData radiusData, String property, String strFormat, String units, TickInfo tickInfo, boolean mustBeConnected, boolean mustNotBeConnected, Boolean intramolecular, boolean isAll, int mad, short colix, Text text, float value, BS bsSelected) protected void
AtomCollection.setAPa
(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list) protected void
ModelSet.setAPm
(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list) Atom.setAtom
(int modelIndex, int atomIndex, P3 xyz, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, boolean isNegDisorder) void
Chain.setAtomBits
(BS bs) void
Group.setAtomBits
(BS bs) note that we may pick up additional bits here that were added latervoid
Structure.setAtomBits
(BS bs) void
Chain.setAtomBitsAndClear
(BS bs, BS bsOut) void
Group.setAtomBitsAndClear
(BS bs, BS bsOut) Setting and clearingvoid
Structure.setAtomBitsAndClear
(BS bs, BS bsOut) protected void
AtomCollection.setAtomCoord2
(BS bs, int tokType, Object xyzValues) void
ModelSet.setAtomCoords
(BS bs, int tokType, Object xyzValues) void
ModelSet.setAtomCoordsRelative
(T3 offset, BS bs) void
ModelSet.setAtomProperty
(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list) protected void
AtomCollection.setAtomsCoordRelative
(BS bs, float x, float y, float z) void
Trajectory.setBaseModels
(BS bsModels) set bits for all base models onlyvoid
AtomCollection.setBsHidden
(BS bs) void
ModelSet.setCentroid
(BS bs, int[] minmax) deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cellModelSet.setConformation
(BS bsAtoms) void
ModelSet.setDihedrals
(float[] dihedralList, BS[] bsBranches, float f) void
AtomCollection.setFormalCharges
(BS bs, int formalCharge) void
ModelSet.setFrameDelayMs
(long millis, BS bsModels) void
ModelSet.setFrameTitle
(BS bsFrames, Object title) void
ModelSet.setModulation
(BS bs, boolean isOn, P3 qtOffset, boolean isQ) Sets the modulation for all atoms in bs.void
ModelSet.setPdbConectBonding
(int baseAtomIndex, int baseModelIndex, BS bsExclude) void
ModelSet.setProteinType
(BS bs, STR type) void
ModelSet.setSpaceGroup
(int mi, SymmetryInterface sg, BS basis) Set up all the model-related fields in association with a new space group.void
AtomCollection.setTaintedAtoms
(BS bs, int type) void
ModelSet.setTrajectoryBs
(BS bsModels) void
AtomCollection.taintAtoms
(BS bsAtoms, int type) void
AtomCollection.unTaintAtoms
(BS bs, int type) Constructors in org.jmol.modelset with parameters of type BSModifierConstructorDescriptionAtomIteratorWithinModelSet
(BS bsModels) ModelLoader
(Viewer vwr, String modelSetName, SB loadScript, Object asc, ModelSet modelSet0, BS bsNew) -
Uses of BS in org.jmol.modelsetbio
Fields in org.jmol.modelsetbio declared as BSMethods in org.jmol.modelsetbio that return BSModifier and TypeMethodDescriptionBioModelSet.getAllSequenceBits
(String specInfo, BS bsAtoms, BS bsResult) BioModelSet.getAtomBitsBS
(int tokType, BS bsInfo, BS bs) BioModelSet.getAtomBitsStr
(int tokType, String specInfo, BS bs) AminoMonomer.getBSSideChain()
BioModelSet.getGroupsWithinAll
(int nResidues, BS bs) BioModelSet.getIdentifierOrNull
(String identifier) Methods in org.jmol.modelsetbio that return types with arguments of type BSMethods in org.jmol.modelsetbio with parameters of type BSModifier and TypeMethodDescriptionvoid
AlphaPolymer.addStructure
(STR type, String structureID, String serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, BS bsAssigned) void
BioModelSet.calcAllRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int dsspVersion) only for base models, not trajectoriesvoid
AminoPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
BioPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
NucleicPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
BioPolymer.calcSelectedMonomersCount
(BS bsSelected) void
BioModelSet.calculateAllPolymers
(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded) BioModelSet.calculateAllStructuresExcept
(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) BioModelSet.calculateAllStuctures
(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version) int
BioModelSet.calculateStruts
(BS bs1, BS bs2) ProteinStructure.findMonomer
(BS bsAtoms, boolean isFirst) void
BioPolymer.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BS bsNot) void
BioModel.fixIndices
(int modelIndex, int nAtomsDeleted, BS bsDeleted) BioResolver.fixPropertyValue
(BS bsAtoms, Object data, boolean toHydrogens) BioModelSet.getAllDefaultStructures
(BS bsAtoms, BS bsModified) void
void
BioModelSet.getAllPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) BioModelSet.getAllSequenceBits
(String specInfo, BS bsAtoms, BS bsResult) BioModelSet.getAtomBitsBS
(int tokType, BS bsInfo, BS bs) BioModelSet.getAtomBitsStr
(int tokType, String specInfo, BS bs) void
BioModel.getConformation
(int conformationIndex0, boolean doSet, BS bsAtoms, BS bsRet) BioModelSet.getFullProteinStructureState
(BS bsAtoms, int mode) BioModelSet.getGroupsWithinAll
(int nResidues, BS bs) void
BioModel.getPdbData
(String type, char ctype, boolean isDraw, BS bsSelected, OC out, LabelToken[] tokens, SB pdbCONECT, BS bsWritten) int
BioPolymer.getPolymerPointsAndVectors
(int last, BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) void
BioPolymer.getPolymerSequenceAtoms
(int group1, int nGroups, BS bsInclude, BS bsResult) void
void
BioPolymer.getRangeGroups
(int nResidues, BS bsAtoms, BS bsResult) boolean
void
BioModelSet.recalculateAllPolymers
(BS bsModelsExcluded, Group[] groups) void
BioModel.resetRasmolBonds
(BS bs, int dsspVersion) from Trajectory.setAtomPositions base models only; not trajectoriesvoid
BioModelSet.setAllConformation
(BS bsAtoms) void
BioModelSet.setAllProteinType
(BS bs, STR type) called from state STRUCTURE commandvoid
BioPolymer.setAtomBits
(BS bs) void
ProteinStructure.setAtomBits
(BS bs) void
BioPolymer.setAtomBitsAndClear
(BS bs, BS bsOut) void
ProteinStructure.setAtomBitsAndClear
(BS bs, BS bsOut) void
BioPolymer.setConformation
(BS bsSelected) int
AlphaPolymer.setStructureBS
(int count, int dsspType, STR type, BS bs, boolean doOffset) bits in the bitset determines the typeMethod parameters in org.jmol.modelsetbio with type arguments of type BS -
Uses of BS in org.jmol.popup
Methods in org.jmol.popup with parameters of type BSModifier and TypeMethodDescriptionprotected void
JmolPopup.updateElementsComputedMenu
(BS elementsPresentBitSet) -
Uses of BS in org.jmol.quantum
Fields in org.jmol.quantum declared as BSMethods in org.jmol.quantum that return BSMethods in org.jmol.quantum with parameters of type BSModifier and TypeMethodDescriptionvoid
MepCalculation.assignPotentials
(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, String data) void
MlpCalculation.assignPotentials
(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, String data) void
MepCalculation.calculate
(VolumeData volumeData, BS bsSelected, P3[] xyz, Atom[] atoms, float[] potentials, int calcType) static NMRNoeMatrix
NMRNoeMatrix.createMatrix
(Viewer viewer, BS bsMol, String[] labelArray, NMRNoeMatrix.NOEParams params) NMRCalculation.getTensorInfo
(String tensorType, String infoType, BS bs) NMRCalculation.getUniqueTensorSet
(BS bsAtoms) void
boolean
MOCalculation.setupCalculation
(Map<String, Object> moData, boolean isSlaters, VolumeData volumeData, BS bsSelected, T3[] xyz, Atom[] atoms, int firstAtomOffset, int[][] dfCoefMaps, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, T3[] points) boolean
NciCalculation.setupCalculation
(VolumeData volumeData, BS bsSelected, BS bsExcluded, BS[] bsMolecules, T3[] atomCoordAngstroms, int firstAtomOffset, boolean isReducedDensity, T3[] points, float[] parameters, int testFlags) protected void
QuantumCalculation.setupCoordinates
(float[] originXYZ, float[] stepsXYZ, BS bsSelected, T3[] xyz, Atom[] atoms, T3[] points, boolean renumber) -
Uses of BS in org.jmol.render
Fields in org.jmol.render declared as BSModifier and TypeFieldDescriptionprotected BS
CageRenderer.bsPeriod
protected BS
CageRenderer.bsPeriod
protected BS
CageRenderer.bsPeriod
protected BS
MeshRenderer.bsPolygons
protected BS
MeshRenderer.bsPolygonsToExport
-
Uses of BS in org.jmol.renderbio
Fields in org.jmol.renderbio declared as BSModifier and TypeFieldDescriptionprotected BS
BioShapeRenderer.bsVisible
protected BS
BioShapeRenderer.bsVisible
protected BS
BioShapeRenderer.bsVisible
protected BS
BioShapeRenderer.bsVisible
protected BS
BioShapeRenderer.bsVisible
protected BS
BioShapeRenderer.bsVisible
protected BS
BioShapeRenderer.bsVisible
-
Uses of BS in org.jmol.renderspecial
Methods in org.jmol.renderspecial with parameters of type BSModifier and TypeMethodDescriptionprotected void
DotsRenderer.renderConvex
(short colix, BS map, int nPoints) generic renderer -- dots and geosurfaceprotected void
GeoSurfaceRenderer.renderConvex
(short colix, BS visibilityMap, int nPoints) -
Uses of BS in org.jmol.script
Methods in org.jmol.script that return BSModifier and TypeMethodDescriptionScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) Add hydrogens to a modelScriptEval.getAtomBitSet
(Object atomExpression) A general method to evaluate a string representing an atom set.ScriptManager.getAtomBitSetEval
(JmolScriptEvaluator eval, Object atomExpression) ScriptParam.getAtomsStartingAt
(int i) static BS
ScriptEval.lookupIdentifierValue
(String identifier) Methods in org.jmol.script with parameters of type BSModifier and TypeMethodDescriptionScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) Add hydrogens to a modelboolean
void
ScriptEval.deleteAtomsInVariables
(BS bsDeleted) void
ScriptEval.getPartialCharges
(BS bs) ScriptParam.getQuaternionParameter
(int i, BS bsAtoms, boolean divideByCurrent) protected void
ScriptEval.setAtomProp
(String prop, Object value, BS bs) void
ScriptEval.setShapePropertyBs
(int iShape, String propertyName, Object propertyValue, BS bs) void
ScriptEval.setShapeSizeBs
(int shapeType, int size, BS bs) void
ScriptEval.setShapeTranslucency
(int shapeType, String prefix, String translucency, float translucentLevel, BS bs) -
Uses of BS in org.jmol.scriptext
Methods in org.jmol.scriptext that return BSModifier and TypeMethodDescriptionprotected BS
ScriptExt.atomExpressionAt
(int i) MathExt.setContactBitSets
(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel) Methods in org.jmol.scriptext with parameters of type BSModifier and TypeMethodDescriptionprotected P3[]
protected void
ScriptExt.finalizeObject
(int shapeID, int colorArgb, float translucentLevel, int intScale, boolean doSet, Object data, int iptDisplayProperty, BS bs) CmdExt.getBitsetIdent
(BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll) CmdExt.getBitsetIdentFull
(BS bs, String label, boolean useAtomMap, int index, boolean isExplicitlyAll, String[] sout) float[]
CmdExt.getBitsetPropertyFloat
(BS bs, int tok, String property, float min, float max) float[]
SmilesExt.getFlexFitList
(BS bs1, BS bs2, String smiles1, boolean isSmarts) float
SmilesExt.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.SmilesExt.getSmilesMatches
(String pattern, Object smiles, BS bsSelected, BS bsMatch3D, int flags, boolean asOneBitset, boolean firstMatchOnly) MathExt.setContactBitSets
(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel) -
Uses of BS in org.jmol.shape
Fields in org.jmol.shape declared as BSModifier and TypeFieldDescriptionLabels.bsBgColixSet
Shape.bsColixSet
protected BS
MeshCollection.bsDisplay
Labels.bsFontSet
Halos.bsHighlight
Sticks.bsOrderSet
AtomShape.bsSizeDefault
Shape.bsSizeSet
protected BS
Mesh.bsTemp
Fields in org.jmol.shape with type parameters of type BSMethods in org.jmol.shape that return BSModifier and TypeMethodDescriptionMeasures.getSelected()
protected BS
Mesh.getVisibleVBS()
Mesh.getVisibleVertexBitSet()
Methods in org.jmol.shape with parameters of type BSModifier and TypeMethodDescriptionLabels.checkObjectClicked
(int x, int y, int modifiers, BS bsVisible, boolean drawPicking) Shape.checkObjectClicked
(int x, int y, int modifiers, BS bsVisible, boolean drawPicking) Sticks.checkObjectClicked
(int x, int y, int modifiers, BS bsVisible, boolean drawPicking) TextShape.checkObjectClicked
(int x, int y, int modifiers, BS bsVisible, boolean drawPicking) boolean
Labels.checkObjectDragged
(int prevX, int prevY, int x, int y, int dragAction, BS bsVisible) boolean
Shape.checkObjectDragged
(int prevX, int prevY, int x, int y, int dragAction, BS bsVisible) boolean
Frank.checkObjectHovered
(int x, int y, BS bsVisible) boolean
Shape.checkObjectHovered
(int x, int y, BS bsVisible) boolean
Sticks.checkObjectHovered
(int x, int y, BS bsVisible) boolean
TextShape.checkObjectHovered
(int x, int y, BS bsVisible) void
Shape.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, BS bsNot) void
Bbcage.setModelVisibilityFlags
(BS bs) void
Halos.setModelVisibilityFlags
(BS bs) void
MeshCollection.setModelVisibilityFlags
(BS bsModels) void
Shape.setModelVisibilityFlags
(BS bsModels) void
TextShape.setModelVisibilityFlags
(BS bsModels) protected void
void
Axes.setProperty
(String propertyName, Object value, BS bs) void
Balls.setProperty
(String propertyName, Object value, BS bs) void
Bbcage.setProperty
(String propertyName, Object value, BS bs) void
Echo.setProperty
(String propertyName, Object value, BS bs) void
Frank.setProperty
(String propertyName, Object value, BS bs) void
Halos.setProperty
(String propertyName, Object value, BS bs) void
Hover.setProperty
(String propertyName, Object value, BS bsSelected) void
Labels.setProperty
(String propertyName, Object value, BS bs) void
Measures.setProperty
(String propertyName, Object value, BS bsAtoms) abstract void
Shape.setProperty
(String propertyName, Object value, BS bsSelected) void
Stars.setProperty
(String propertyName, Object value, BS bs) void
Sticks.setProperty
(String propertyName, Object value, BS bs) void
Uccage.setProperty
(String propertyName, Object value, BS bs) protected void
protected void
protected void
void
Shape.setShapeSizeRD
(int size, RadiusData rd, BS bsSelected) protected void
protected void
protected void
protected void
protected void
sets the size of a bond, or sets the selectedBonds setprotected void
protected void
AtomShape.setSizeRD
(RadiusData rd, BS bsSelected) protected void
Balls.setSizeRD
(RadiusData rd, BS bsSelected) protected void
Shape.setSizeRD
(RadiusData rd, BS bsSelected) -
Uses of BS in org.jmol.shapebio
Methods in org.jmol.shapebio with parameters of type BSModifier and TypeMethodDescriptionvoid
BioShape.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, BS bsNot) void
BioShapeCollection.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, BS bsNot) void
BioShapeCollection.setModelVisibilityFlags
(BS bsModels) void
protected void
BioShapeCollection.setPropBSC
(String propertyName, Object value, BS bsSelected) void
Backbone.setProperty
(String propertyName, Object value, BS bsSelected) void
BioShape.setProperty
(String propertyName, Object value, BS bsSelected) void
BioShapeCollection.setProperty
(String propertyName, Object value, BS bsSelected) void
Trace.setProperty
(String propertyName, Object value, BS bsSelected) void
Backbone.setShapeSizeRD
(int size, RadiusData rd, BS bsSelected) void
BioShapeCollection.setShapeSizeRD
(int size, RadiusData rd, BS bsSelected) -
Uses of BS in org.jmol.shapecgo
Methods in org.jmol.shapecgo with parameters of type BSModifier and TypeMethodDescriptionvoid
CGO.setModelVisibilityFlags
(BS bsModels) void
CGO.setProperty
(String propertyName, Object value, BS bs) -
Uses of BS in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as BSMethods in org.jmol.shapespecial with parameters of type BSModifier and TypeMethodDescriptionDraw.checkObjectClicked
(int x, int y, int action, BS bsVisible, boolean drawPicking) Ellipsoids.checkObjectClicked
(int x, int y, int action, BS bsModels, boolean drawPicking) boolean
Draw.checkObjectDragged
(int prevX, int prevY, int x, int y, int dragAction, BS bsVisible) boolean
Draw.checkObjectHovered
(int x, int y, BS bsVisible) boolean
Ellipsoids.checkObjectHovered
(int x, int y, BS bsModels) void
Dipoles.setModelVisibilityFlags
(BS bsModels) void
Draw.setModelVisibilityFlags
(BS bsModels) void
Ellipsoids.setModelVisibilityFlags
(BS bsModels) void
Polyhedra.setModelVisibilityFlags
(BS bsModels) void
Dipoles.setProperty
(String propertyName, Object value, BS bs) void
Dots.setProperty
(String propertyName, Object value, BS bs) void
Draw.setProperty
(String propertyName, Object value, BS bs) void
Ellipsoids.setProperty
(String propertyName, Object value, BS bs) void
Polyhedra.setProperty
(String propertyName, Object value, BS bs) void
Vectors.setProperty
(String propertyName, Object value, BS bsSelected) protected void
protected void
Dots.setSizeRD
(RadiusData rd, BS bsSelected) -
Uses of BS in org.jmol.shapesurface
Methods in org.jmol.shapesurface that return BSMethods in org.jmol.shapesurface with parameters of type BSModifier and TypeMethodDescriptionstatic void
IsosurfaceMesh.addContourPoints
(Lst<Object> v, BS bsContour, int i, SB fData, T3[] vertices, float[] vertexValues, int iA, int iB, int iC, float value) P3[]
Isosurface.calculateGeodesicSurface
(BS bsSelected, float envelopeRadius) Isosurface.checkObjectClicked
(int x, int y, int action, BS bsVisible, boolean drawPicking) boolean
Isosurface.checkObjectHovered
(int x, int y, BS bsVisible) static String
Isosurface.getPolygonColorData
(int ccount, short[] colixes, int[][] polygons, BS bsSlabDisplay) float[]
IsosurfaceMesh.getValidValues
(BS bs) T3[]
IsosurfaceMesh.getValidVertices
(BS bs) static void
IsosurfaceMesh.setContourVector
(Lst<Object> v, int nPolygons, BS bsContour, float value, short colix, int color, SB fData) void
Contact.setProperty
(String propertyName, Object value, BS bs) void
Isosurface.setProperty
(String propertyName, Object value, BS bs) void
LcaoCartoon.setProperty
(String propertyName, Object value, BS bs) void
MolecularOrbital.setProperty
(String propertyName, Object value, BS bs) protected void
void
IsosurfaceMesh.updateCoordinates
(M4 m, BS bs) bs will be null if this is a set from the new isosurface MOVE [mat4] command -
Uses of BS in org.jmol.smiles
Methods in org.jmol.smiles that return BSModifier and TypeMethodDescriptionSmilesAtom.findAtomsLike
(String substring) SmilesMatcher.getSubstructureSet
(Object pattern, Object target, int ac, BS bsSelected, int flags) Returns a bitset matching the pattern within a set of Jmol atoms.BS[]
SmilesMatcher.getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) Returns a vector of bitsets indicating which atoms match the pattern.Methods in org.jmol.smiles with parameters of type BSModifier and TypeMethodDescriptionSmilesMatcher.compileSearchTarget
(Node[] atoms, int atomCount, BS bsSelected) SmilesMatcher.getAtropisomerKeys
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) called by SmilesParser to get nn in ^nn- base on match to actual structureint[][]
SmilesMatcher.getCorrelationMaps
(String pattern, Node[] atoms, int atomCount, BS bsSelected, int flags) Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.void
SmilesAtom.getGroupBits
(BS bs) int[][]
SmilesMatcher.getMapForJME
(String jme, Atom[] at, BS bsAtoms) void
SmilesMatcher.getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> ret, Lst<BS>[] vRings) called by ForceFieldMMFF.setAtomTypes onlyinternal to Jmol -- called by org.jmol.Viewer.getSmilesSmilesMatcher.getSubstructureSet
(Object pattern, Object target, int ac, BS bsSelected, int flags) Returns a bitset matching the pattern within a set of Jmol atoms.BS[]
SmilesMatcher.getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) Returns a vector of bitsets indicating which atoms match the pattern.void
Method parameters in org.jmol.smiles with type arguments of type BS -
Uses of BS in org.jmol.symmetry
Methods in org.jmol.symmetry that return BSModifier and TypeMethodDescriptionprotected BS[]
Retrieve an array of bit sets that match a given SMARTSprotected BS[]
protected BS
Return a bit set corresponding to a SMARTSprotected BS
Symmetry.notInCentroid
(ModelSet modelSet, BS bsAtoms, int[] minmax) Symmetry.removeDuplicates
(ModelSet ms, BS bs, boolean highPrec) Methods in org.jmol.symmetry with parameters of type BSModifier and TypeMethodDescriptionvoid
void
Symmetry.calculateCIPChiralityForAtoms
(Viewer vwr, BS bsAtoms) SpaceGroupFinder.checkSupercell
(Viewer vwr, Symmetry uc, BS bsPoints, int abc, P3 scaling) Look for a supercell and adjust lattice down if necessary.Symmetry.findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) Symmetry.getIterator
(Viewer vwr, Atom atom, BS bsAtoms, float radius) Symmetry.notInCentroid
(ModelSet modelSet, BS bsAtoms, int[] minmax) Symmetry.removeDuplicates
(ModelSet ms, BS bs, boolean highPrec) Actual constructor.UnitCellIterator.set
(SymmetryInterface unitCell, Atom atom, Atom[] atoms, BS bsAtoms, float distance) Symmetry.setPointGroup
(Viewer vwr, SymmetryInterface siLast, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) Symmetry.staticTransformSpaceGroup
(BS bs, String cleg, Object paramsOrUC, SB sb) -
Uses of BS in org.jmol.util
Fields in org.jmol.util declared as BSModifier and TypeFieldDescriptionJmolMolecule.atomList
MeshSurface.bsDisplay
MeshSurface.bsPolygons
MeshSurface.bsSlabDisplay
MeshSurface.bsSlabGhost
static final BS
BSUtil.emptySet
MeshSurface.surfaceAtoms
BS[]
MeshSurface.surfaceSet
Methods in org.jmol.util that return BSModifier and TypeMethodDescriptionstatic BS
static BS
static BS
static BS
BSUtil.copyInvert
(BS bs, int n) static BS
BSUtil.deleteBits
(BS bs, BS bsDelete) this one slides deleted bits out of a pattern.Node.findAtomsLike
(String substring) static BS
JmolMolecule.getBitSetForMF
(Atom[] at, BS bsAtoms, String mf) static BS
JmolMolecule.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.static BS
JmolMolecule.getBranchesForInversion
(Node[] at, int atomIndex, BS bsToTest) static BS
BSUtil.invertInPlace
(BS bs, int n) inverts the bitset bits 0 through n-1, and returns a reference to the modified bitsetstatic BS
BSUtil.newAndSetBit
(int i) static BS
BSUtil.newBitSet2
(int i0, int i1) static BS
Normix.newVertexBitSet()
static BS
BSUtil.setAll
(int n) static BS
BSUtil.toggleInPlace
(BS a, BS b) a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.Methods in org.jmol.util with parameters of type BSModifier and TypeMethodDescriptionstatic final JmolMolecule[]
JmolMolecule.addMolecule
(JmolMolecule[] molecules, int iMolecule, Node[] atoms, int iAtom, BS bsBranch, int modelIndex, int indexInModel, BS bsExclude) int
MeshSurface.addPolygon
(int[] polygon, BS bs) protected int
MeshSurface.addPolygonC
(int[] polygon, int color, BS bs, boolean isExplicit) static BS
static boolean
static int
BSUtil.cardinalityOf
(BS bs) cardinality = "total number of set bits"static BS
static BS
static BS
BSUtil.copyInvert
(BS bs, int n) static BS
BSUtil.deleteBits
(BS bs, BS bsDelete) this one slides deleted bits out of a pattern.static String
static String
static short
Normix.get2SidedNormix
(V3 v, BS bsTemp) static BS
JmolMolecule.getBitSetForMF
(Atom[] at, BS bsAtoms, String mf) static BS
JmolMolecule.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.static BS
JmolMolecule.getBranchesForInversion
(Node[] at, int atomIndex, BS bsToTest) void
Node.getGroupBits
(BS bs) void
MeshSlicer.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 String
JmolMolecule.getMolecularFormulaAtoms
(Node[] atoms, BS bsSelected, float[] wts, boolean isEmpirical) static final JmolMolecule[]
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.static short
Normix.getNormixV
(V3 v, BS bsTemp) static boolean
BSUtil.haveCommon
(BS a, BS b) static BS
BSUtil.invertInPlace
(BS bs, int n) inverts the bitset bits 0 through n-1, and returns a reference to the modified bitsetboolean
Tensor.isSelected
(BS bsSelected, int iAtom) static void
offset the bitset in place by the specified number of bits starting at a given positionstatic int
Parser.parseFloatArrayBsData
(String[] tokens, BS bs, float[] data) static float[]
Parser.parseFloatArrayFromMatchAndField
(String str, BS bs, int fieldMatch, int fieldMatchColumnCount, int[] matchData, int field, int fieldColumnCount, float[] data, int firstLine) the major lifter here.static int
Parser.parseStringInfestedFloatArray
(String str, BS bs, float[] data) parses a "dirty" string for floats.void
MeshSurface.setTranslucentVertices
(BS bsVertices) Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygonsstatic void
this one slides bits to higher positions based on a pattern.static BS
BSUtil.toggleInPlace
(BS a, BS b) a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.Method parameters in org.jmol.util with type arguments of type BSModifier and TypeMethodDescriptionstatic BS
JmolMolecule.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.static final JmolMolecule[]
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.static void
BSUtil.setMapBitSet
(Map<String, BS> ht, int i1, int i2, String key) -
Uses of BS in org.jmol.viewer
Fields in org.jmol.viewer declared as BSModifier and TypeFieldDescriptionSelectionManager.bsDeleted
TransformManager.bsFrameOffsets
final BS
ShapeManager.bsRenderableAtoms
final BS
ShapeManager.bsSlabbedInternal
SelectionManager.bsSubset
Viewer.movableBitSet
Methods in org.jmol.viewer that return BSModifier and TypeMethodDescriptionViewer.addHydrogens
(BS bsAtoms, int flags) Viewer.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) Viewer.bsA()
SelectionManager.excludeAtoms
(BS bs, boolean ignoreSubset) Viewer.getAllAtoms()
Viewer.getAtomBitSet
(Object atomExpression) Viewer.getAtomsNearPt
(float distance, P3 coord, BS bs) Viewer.getBaseModelBitSet()
Viewer.getBondsForSelectedAtoms
(BS bsAtoms) Viewer.getBranchBitSet
(int atomIndex, int atomIndexNot, boolean allowCyclic) 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.Viewer.getDefinedAtomSet
(String name) Viewer.getElementsPresentBitSet
(int modelIndex) Viewer.getFrameAtoms()
Viewer.getGroupsWithin
(int nResidues, BS bs) SelectionManager.getHiddenSet()
Viewer.getModelUndeletedAtomsBitSet
(int modelIndex) Viewer.getModelUndeletedAtomsBitSetBs
(BS bsModels) SelectionManager.getMotionFixedAtoms()
Viewer.getMotionFixedAtoms
(SymmetryInterface sym, BS bsFixed) For the current SINGLE model only.Viewer.getSmartsMatch
(String smarts, BS bsSelected) Viewer.getSmartsMatchForNodes
(String smarts, Node[] atoms) BS[]
Viewer.getSubstructureSetArray
(String pattern, BS bsSelected, int flags) BS[]
Viewer.getSubstructureSetArrayForNodes
(String pattern, Node[] nodes, int flags) Viewer.getThisModelAtoms()
Viewer.getVisibleFramesBitSet()
Viewer.restrictToModel
(BS bs, int mi) Restrict this bitset to the current model or its initial atom's model.Methods in org.jmol.viewer with parameters of type BSModifier and TypeMethodDescriptionViewer.addHydrogens
(BS bsAtoms, int flags) Viewer.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) int
void
Viewer.calcAtomsMinMax
(BS bs, BoxInfo boxInfo) void
Viewer.calcBoundBoxDimensions
(BS bs, float scale) Viewer.calculateChirality
(BS bsAtoms) int
Viewer.calculateFormalCharges
(BS bs) Viewer.calculateMolecularDipole
(BS bsAtoms) void
Viewer.calculatePartialCharges
(BS bsSelected) Viewer.calculateStructures
(BS bsAtoms, boolean asDSSP, boolean setStructure, int version) int
Viewer.calculateStruts
(BS bs1, BS bs2) P3[]
Viewer.calculateSurface
(BS bsSelected, float envelopeRadius) void
Viewer.checkCoordinatesChanged
(BS bsAtoms) int
Viewer.deleteAtoms
(BS bsAtoms, boolean fullModels) void
Viewer.deleteBonds
(BS bsDeleted) void
DataManager.deleteModelAtoms
(int firstAtomIndex, int nAtoms, BS bsDeleted) void
Viewer.deleteModelAtoms
(int modelIndex, int firstAtomIndex, int nAtoms, BS bsModelAtoms) int
Viewer.deleteModels
(int modelIndex, BS bsAtoms) called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1void
ShapeManager.deleteShapeAtoms
(Object[] value, BS bs) void
Viewer.displayAtoms
(BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet) SelectionManager.excludeAtoms
(BS bs, boolean ignoreSubset) int[]
ShapeManager.finalizeAtoms
(BS bsTranslateSelected, boolean finalizeParams) void
ShapeManager.findNearestShapeAtomIndex
(int x, int y, Atom[] closest, BS bsNot) Viewer.findSpaceGroup
(SymmetryInterface sym, BS bsAtoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) PropertyManager.fixJMEFormalCharges
(BS bsAtoms, String jme) Fix a JME string returned from NCI CIR to have the proper formal charges.P3[]
Viewer.getAdditionalHydrogens
(BS bsAtoms, Lst<Atom> vConnections, int flags) PropertyManager.getAllAtomInfo
(BS bs) PropertyManager.getAllChainInfo
(BS bs) Quat[]
Viewer.getAtomGroupQuaternions
(BS bsAtoms, int nMax) Viewer.getAtomsNearPt
(float distance, P3 coord, BS bs) Viewer.getBioSmiles
(BS bs) Viewer.getBondsForSelectedAtoms
(BS bsAtoms) Viewer.getChemicalInfo
(String smiles, String info, BS bsAtoms) PropertyManager.getChimeInfo
(int tok, BS bs) Viewer.getCoordinateState
(BS bsSelected) Viewer.getDataObj
(String key, BS bsSelected, int dataType) Retrieve a data objectDataManager.getDefaultVdwNameOrData
(VDW type, BS bs) Viewer.getDefaultVdwNameOrData
(int mode, VDW type, BS bs) Viewer.getFormulaForAtoms
(BS bs, String type, boolean isEmpirical) Get formula -- MF or CELLFORMULA, possibly empiricalViewer.getGroupsWithin
(int nResidues, BS bs) Get an InChI or InChIKey for a set of atoms or MOL data.PropertyManager.getModelCml
(BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories) Viewer.getModelCml
(BS bs, int nAtomsMax, boolean addBonds, boolean doTransform) PropertyManager.getModelExtract
(BS bs, boolean doTransform, boolean isModelKit, String type, boolean allTrajectories) V3000, SDF, MOL, JSON, CD (ChemDoodle), XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON, PWMAT, XSF MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)PropertyManager.getModelFileInfo
(BS frames) Viewer.getModelUndeletedAtomsBitSetBs
(BS bsModels) Viewer.getMotionFixedAtoms
(SymmetryInterface sym, BS bsFixed) For the current SINGLE model only.Viewer.getOpenSmiles
(BS bs) float[]
Viewer.getOrCalcPartialCharges
(BS bsSelected, BS bsIgnore) Viewer.getOrientation
(int type, String name, BS bs, P3[] points) PropertyManager.getPdbAtomData
(BS bs, OC out, boolean isPQR, boolean doTransform, boolean allTrajectories) PDB or PQR onlyViewer.getPdbAtomData
(BS bs, OC out, boolean asPQR, boolean doTransform) PropertyManager.getPdbData
(int modelIndex, String type, BS bsSelected, Object[] parameters, OC out, boolean addStructure) Viewer.getPdbData
(int modelIndex, String type, BS bsAtoms, Object[] parameters, OC oc, boolean getStructure) void
Viewer.getPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList) Viewer.getSelectedAtomIterator
(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel) int[][]
Viewer.getSmartsMap
(String smilesOrSmarts, BS bsSelected, int flags) Viewer.getSmartsMatch
(String smarts, BS bsSelected) NOT getting aromatic smilesViewer.getSmilesOpt
(BS bsSelected, int index1, int index2, int flags, String options) returns the SMILES string for a sequence or atom set does not include attached protons on groupsBS[]
Viewer.getSubstructureSetArray
(String pattern, BS bsSelected, int flags) void
void
Viewer.invertAtomCoord
(P3 pt, P4 plane, BS bs, int ringAtomIndex, boolean isClick) void
Viewer.invertSelected
(P3 pt, P4 plane, int iAtom, BS bsAtoms) int[]
Viewer.makeConnections
(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy) void
Viewer.minimize
(JmolScriptEvaluator eval, int steps, float crit, BS bsSelected, BS bsFixed, BS bsInFrame, float rangeFixed, int flags) From the MINIMIZE command and other sources.void
Viewer.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly, boolean useModelKit) int
Viewer.moveAtomWithHydrogens
(int atomIndex, int deltaX, int deltaY, int deltaZ, P3 ptNew, BS bsAtoms) void
ShapeManager.notifyAtomPositionsChanged
(int baseModel, BS bs, M4 mat) void
ShapeManager.notifyAtoms
(String prop, BS[] atomsAndModels) void
ShapeManager.resetBioshapes
(BS bsAllAtoms) Viewer.restrictToModel
(BS bs, int mi) Restrict this bitset to the current model or its initial atom's model.protected void
TransformManager.rotate3DBall
(float xDeg, float yDeg, BS bsAtoms) boolean
Viewer.rotateAboutPointsInternal
(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, Lst<P3> finalPoints, float[] dihedralList, M4 m4, boolean useModelKit, P3[][] centerAndPoints) boolean
Viewer.rotateAxisAngleAtCenter
(JmolScriptEvaluator eval, P3 rotCenter, V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected) void
TransformManager.rotateAxisAngleRadiansFixed
(float angleRadians, BS bsAtoms) void
TransformManager.rotateAxisAngleRadiansInternal
(float radians, BS bsAtoms, M4 m4, boolean useModelKit) void
TransformManager.rotateXRadians
(float angleRadians, BS bsAtoms) protected void
TransformManager.rotateXYBy
(float degX, float degY, BS bsAtoms) protected void
TransformManager4D.rotateXYBy
(float xDelta, float yDelta, BS bsAtoms) void
TransformManager.rotateYRadians
(float angleRadians, BS bsAtoms) void
StateManager.saveCoordinates
(String saveName, BS bsSelected) void
StateManager.saveSelection
(String saveName, BS bsSelected) void
void
Viewer.selectBonds
(BS bs) void
Viewer.selectStatus
(BS bs, boolean isGroup, int addRemove, boolean isQuiet, boolean reportStatus) "SELECT" starting with comma triggers the SELECT callback from a SELECT command.void
Viewer.setAnimDisplay
(BS bs) void
Viewer.setAtomCoords
(BS bs, int tokType, Object xyzValues) void
Viewer.setAtomCoordsRelative
(T3 offset, BS bs) void
Viewer.setAtomProperty
(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list) void
Viewer.setCenterBitSet
(BS bsCenter, boolean doScale) void
Viewer.setDihedrals
(float[] dihedralList, BS[] bsBranches, float rate) void
Viewer.setFrameOffsets
(BS bsAtoms, boolean isFull) void
void
Viewer.setModulation
(BS bs, boolean isOn, P3 t1, boolean isQ) void
Viewer.setMotionFixed
(BS bs) void
Viewer.setMotionFixedAtoms
(BS bs) void
ColorManager.setPropertyColorRangeData
(float[] data, BS bs) void
Viewer.setProteinType
(STR type, BS bs) void
Viewer.setSelectionSet
(BS set) void
SelectionManager.setSelectionSubset
(BS bs) void
ShapeManager.setShapePropertyBs
(int shapeID, String propertyName, Object value, BS bsSelected) void
Viewer.setShapeSize
(int shapeID, int madOrMad10, BS bsSelected) void
ShapeManager.setShapeSizeBs
(int shapeID, int size, RadiusData rd, BS bsSelected) void
Viewer.setStatusAtomMoved
(boolean andCheckMinimize, BS bs) void
Viewer.setStatusSelect
(BS bs) Make the SelectCallback call and reset the hasSelected value to false.void
StatusManager.setStatusStructureModified
(int atomIndex, int modelIndex, int mode, String msg, int n, BS bsAtoms) void
Method parameters in org.jmol.viewer with type arguments of type BS -
Uses of BS in org.openscience.jmol.app.janocchio
Constructors in org.openscience.jmol.app.janocchio with parameters of type BSModifierConstructorDescriptionNmrMolecule
(NMR_JmolPanel nmrPanel, BS bsMol, String[] labelArray, boolean forNOE)