References

summary
public	C Script Script class
public	F setDebug()
public	F setExtensionFragDepth()
public	F setSupportsReadPixelsFloat()
public	F binarySearchIndexOf(array: Array, element: Anything, compareFunction: Function): Number Does a binary search to get the index of an element in the input array
public	F boolean()
public	F dataURItoImage()
public	F deepCopy()
public	F defaults()
public	F download()
public	F ensureArray()
public	F ensureBuffer()
public	F ensureFloat32Array()
public	F ensureMatrix4()
public	F ensureQuaternion()
public	F ensureVector2()
public	F ensureVector3()
public	F flatten()
public	F getAbsolutePath()
public	F getBrowser()
public	F getFileInfo()
public	F getProtocol()
public	F getQuery()
public	F getTypedArray()
public	F getUintArray()
public	F open()
public	F pick()
public	F rangeInSortedArray()
public	F submit()
public	F throttle()
public	F uint8ToLines()
public	F uint8ToString()
public	F uniqueArray()
private	V LeftMouseButton
public	V MiddleMouseButton
public	V RightMouseButton
public	V Browser: String \| false The browser name: "Opera", "Chrome", "Firefox", "Mobile Safari", "Internet Explorer", "Safari" or false.
public	V BufferRegistry
public	V ColormakerRegistry: ColormakerRegistry Global instance of src/color/colormaker-registry.js~ColormakerRegistry
public	V ComponentRegistry
public	V DatasourceRegistry
public	V Debug
public	V DecompressorRegistry
public	V ExtensionFragDepth: Boolean Flag indicating support for the `EXT_frag_depth` WebGL extension
public	V Log
public	V Mobile: Boolean Flag indicating a mobile browser
public	V ParserRegistry
public	V PickerRegistry
public	V RepresentationRegistry
public	V ScriptExtensions: String[] List of file extensions to be recognized as scripts
public	V ShaderRegistry
public	V SupportsPassiveEventHandler: Boolean Flag indicating support for the 'passive' option for event handler
public	V SupportsReadPixelsFloat
public	V WebglErrorMessage
public	V WorkerRegistry
public	V Version: String Version name
public	E Box3
public	E BufferGeometry
public	E Char
public	E Color
public	E Euler
public	E Float
public	E Integer
public	E Matrix3
public	E Matrix4
public	E Plane
public	E Quaternion
public	E Signal
public	E TypedArray
public	E Vector2
public	E Vector3

align

summary
public	C Alignment
public	C Superposition
public	F superpose(s1: Structure \| StructureView, s2: Structure \| StructureView, align: Boolean, sele1: String, sele2: String): undefined Perform structural superposition of two structures, optionally guided by a sequence alignment

animation

summary
public	C AnimationList Animation list.
public	C MoveAnimation Move animation.
public	C RockAnimation Rock animation.
public	C RotateAnimation Rotate animation.
public	C SpinAnimation Spin animation.
public	C TimeoutAnimation Timeout animation.
public	C ValueAnimation Value animation.
public	C ZoomAnimation Zoom animation.
public	I Animation Animation.

buffer

summary
public	C ArrowBuffer Arrow buffer.
public	C BoxBuffer Box buffer.
public	C ConeBuffer Cone buffer.
public	C ConeGeometryBuffer Cone geometry buffer.
public	C ContourBuffer Contour buffer.
public	C CylinderBuffer Cylinder buffer.
public	C CylinderGeometryBuffer Cylinder geometry buffer.
public	C CylinderImpostorBuffer Cylinder impostor buffer.
public	C DoubleSidedBuffer A double-sided mesh buffer.
public	C EllipsoidBuffer Ellipsoid buffer.
public	C EllipsoidGeometryBuffer Ellipsoid geometry buffer.
public	C HyperballStickBuffer Hyperball stick buffer.
public	C HyperballStickImpostorBuffer Hyperball stick impostor buffer.
public	C ImageBuffer Image buffer.
public	C LineBuffer Line buffer.
public	C MeshBuffer Mesh buffer.
public	C OctahedronBuffer Octahedron buffer.
public	C PointBuffer Point buffer.
public	C RibbonBuffer Ribbon buffer.
public	C SphereBuffer Sphere buffer.
public	C SphereGeometryBuffer Sphere geometry buffer.
public	C SphereImpostorBuffer Sphere impostor buffer.
public	C SurfaceBuffer Surface buffer.
public	C TetrahedronBuffer Tetrahedron buffer.
public	C TextBuffer Text buffer.
public	C TorusBuffer Torus geometry buffer.
public	C TraceBuffer Trace buffer.
public	C TubeMeshBuffer Tube mesh buffer.
public	C VectorBuffer Vector buffer.
public	C WideLineBuffer Wide Line buffer.
public	I Buffer Buffer class.
public	I GeometryBuffer Geometry buffer.
public	I MappedBuffer Mapped buffer.
public	I MappedAlignedBoxBuffer Mapped Aligned box buffer.
public	I MappedBoxBuffer Mapped Box buffer.
public	I MappedQuadBuffer Mapped Quad buffer.
public	T BufferParameters: Object Buffer parameter object.
public	T TextBufferParameters: Object Text buffer parameter object.

color

summary
public	C AtomindexColormaker Color by atom index.
public	C BfactorColormaker Color by b-factor.
public	C ChainidColormaker Color by chain id
public	C ChainindexColormaker Color by chain index
public	C ChainnameColormaker Color by chain name
public	C ColormakerRegistry Class for registering Colormakers.
public	C DensityfitColormaker Color by validation density fit
public	C ElectrostaticColormaker Color a surface by electrostatic charge.
public	C ElementColormaker Color by element
public	C EntityindexColormaker Color by entiry index
public	C EntitytypeColormaker Color by entity type
public	C GeoqualityColormaker Color by validation gometry quality
public	C HydrophobicityColormaker Color by hydrophobicity
public	C ModelindexColormaker Color by model index
public	C MoleculetypeColormaker Color by molecule type
public	C OccupancyColormaker Color by occupancy
public	C PartialchargeColormaker Color by partial charge.
public	C RandomColormaker Class by random color
public	C ResidueindexColormaker Color by residue index
public	C ResnameColormaker Color by residue name
public	C SelectionColormaker Color based on Selection
public	C SstrucColormaker Color by secondary structure
public	C UniformColormaker Color by uniform color
public	C ValueColormaker Color by volume value
public	C VolumeColormaker Color by volume position
public	I Colormaker Class for making colors.
public	T ColormakerParameters: Object Colormaker parameter object.

component

summary
public	C Annotation Annotation HTML element floating on top of a position rendered in 3d
private	C Collection
public	C ComponentCollection
public	C RepresentationCollection
public	C RepresentationComponent Component wrapping a Representation object
public	C ScriptComponent Component wrapping a Script object
public	C ShapeComponent Component wrapping a Shape object
public	C StructureComponent Component wrapping a Structure object
public	C SurfaceComponent Component wrapping a Surface object
public	C TrajectoryComponent Component wrapping a Trajectory object
public	C VolumeComponent Component wrapping a Volume object
public	I Component Base class for components
public	T ComponentParameters: Object Component parameter object.
public	T ComponentSignals: Object
public	T RepresentationComponentSignals: Object Extends ComponentSignals
public	T StructureComponentSignals: Object Extends ComponentSignals
public	T TrajectoryComponentParameters: Object Trajectory component parameter object.
public	T TrajectoryComponentSignals: Object Extends ComponentSignals

controls

summary
public	C AnimationControls Animation controls
public	C ComponentControls Component controls
public	C KeyActions Key actions provided as static methods
public	C KeyControls Mouse controls
public	C MouseActions Mouse actions provided as static methods
public	C MouseControls Mouse controls
public	C PickingControls Picking controls
public	C PickingProxy Picking proxy class.
public	C TrackballControls Trackball controls
public	C ViewerControls Viewer controls
public	V KeyActionPresets
public	V MouseActionPresets
public	T TriggerString: String Strings to describe mouse events (including optional keyboard modifiers).
public	T PickingData: Object Picking data object.
public	T OrientationMatrix: Matrix4 Orientation matrix, a 4x4 transformation matrix with rotation part used for scene rotation, scale part for scene camera distance and position part for scene translation

datasource

summary
public	C MdsrvDatasource
public	C PassThroughDatasource
public	C PubchemDatasource
public	C RcsbDatasource
public	C StaticDatasource
public	I Datasource Datasource base class

geometry

summary
public	C Contact
public	C ArrowPrimitive Arrow geometry primitive
public	C BoxPrimitive Box geometry primitive
public	C ConePrimitive Cone geometry primitive
public	C CylinderPrimitive Cylinder geometry primitive
public	C EllipsoidPrimitive Ellipsoid geometry primitive
public	C OctahedronPrimitive Octahedron geometry primitive
public	C SpherePrimitive Sphere geometry primitive
public	C TetrahedronPrimitive Tetrahedron geometry primitive
public	C TextPrimitive Text geometry primitive
public	C TorusPrimitive Torus geometry primitive
public	C Shape Class for building custom shapes.
public	F polarBackboneContacts()
public	F polarContacts()
private	F Grid()
public	F Helixbundle()
public	F Helixorient()
public	F Kdtree()
private	F SpatialHash()
public	F Spline()

loader

summary
public	C Loader Loader base class
public	C ParserLoader Parser loader class
public	C PluginLoader Plugin loader class
public	C ScriptLoader Script loader class
public	F autoLoad(file: String \| File \| Blob, params: LoaderParameters): Promise Load a file
public	F getDataInfo()
public	T LoaderParameters: Object Loader parameter object.

math

summary
public	C PrincipalAxes Principal axes
public	F arrayMax()
public	F arrayMean()
public	F arrayMin()
public	F arrayRms()
public	F arraySorted()
public	F arraySortedCmp()
public	F arraySum()
public	F calculateCenterArray()
public	F calculateDirectionArray()
public	F calculateMeanArray()
public	F calculateMinArray()
public	F centerArray3()
public	F circularMean()
public	F copyArray()
public	F copyWithin()
public	F quickselectCmp()
public	F quicksortCmp()
public	F quicksortIP(arr: TypedArray, eleSize: Integer, orderElement: Integer, begin: Integer, end: Integer): TypedArray quicksortIP
public	F randomColorArray()
public	F replicateArray3Entries()
public	F serialArray()
public	F serialBlockArray()
public	F uniformArray()
public	F uniformArray3()
public	F almostIdentity()
public	F clamp()
public	F countSetBits()
private	F degToRad()
public	F generateUUID()
public	F lerp()
public	F normalize()
public	F pclamp()
public	F radToDeg()
public	F saturate()
public	F smootherstep()
public	F smootheststep()
public	F smoothstep()
public	F spline()
public	F Matrix()
public	F addCols()
public	F addRows()
public	F invert3x3()
public	F m3makeNormal()
public	F m3new()
public	F m4identity()
public	F m4makeRotationY()
public	F m4makeScale()
public	F m4makeTranslation()
public	F m4multiply()
public	F m4new()
public	F mat3x3determinant()
public	F meanCols()
public	F meanRows()
public	F multiply()
public	F multiply3x3()
public	F multiplyABt()
public	F multiplyAtB()
public	F subCols()
public	F subRows()
public	F svd()
public	F transpose()
public	F applyMatrix3toVector3array()
public	F applyMatrix4toVector3array()
public	F calculateMeanVector3()
public	F computeBoundingBox()
public	F isPointOnSegment()
public	F lineLineIntersect(p1: Vector3, p2: Vector3, p3: Vector3, p4: Vector3): Array<Vector3, Vector3> \| null Converted to JavaScript from http://paulbourke.net/geometry/pointlineplane/lineline.c
public	F normalizeVector3array()
public	F projectPointOnVector()
public	F v3add()
public	F v3addScalar()
public	F v3angle()
public	F v3ceil()
public	F v3cross()
public	F v3divide()
public	F v3divideScalar()
public	F v3dot()
public	F v3floor()
public	F v3forEach()
public	F v3fromArray()
public	F v3length()
public	F v3multiply()
public	F v3multiplyScalar()
public	F v3negate()
public	F v3new()
public	F v3normalize()
public	F v3round()
public	F v3sub()
public	F v3subScalar()
public	F v3toArray()
public	V DEG2RAD
private	V EPS
public	V RAD2DEG
public	V TwoPI

parser

summary
public	C CifParser
public	C CsvParser CSV parser
public	C CubeParser
public	C DcdParser
public	C Dsn6Parser
public	C DxParser
public	C DxbinParser
public	C GroParser
public	C JsonParser
public	C MmtfParser
public	C Mol2Parser
public	C MrcParser
public	C MsgpackParser
public	C NctrajParser
public	C NetcdfParser
public	C ObjParser
public	C ParserRegistry
public	C Parser
public	C PdbParser
public	C PlyParser
public	C PqrParser
public	C PrmtopParser
public	C PsfParser
public	C SdfParser
public	C StructureParser
public	C SurfaceParser
public	C TextParser
public	C TopParser
public	C TrajectoryParser
public	C TrrParser
public	C ValidationParser
public	C VolumeParser
public	C XmlParser
public	C XplorParser
public	C XtcParser
public	V HelixTypes

proxy

summary
public	C AtomProxy Atom proxy
public	C BondProxy Bond proxy
public	C ChainProxy Chain proxy
public	C ModelProxy Model proxy
public	C Polymer Polymer
public	C ResidueProxy Residue proxy

representation

summary
public	C AngleRepresentation(structure: Structure, viewer: Viewer, params: AngleRepresentationParameters) Angle representation object
public	C AxesRepresentation Axes representation.
public	C BackboneRepresentation Backbone representation.
public	C BallAndStickRepresentation Ball And Stick representation.
public	C BaseRepresentation Base representation.
public	C BufferRepresentation Representation for showing buffer objects.
public	C CartoonRepresentation Cartoon representation.
public	C ContactRepresentation Contact representation.
public	C DihedralRepresentation(structure: Structure, viewer: Viewer, params: AngleRepresentationParameters) Dihedral representation object
public	C DistanceRepresentation Distance representation
public	C DotRepresentation Dot representation
public	C HelixorientRepresentation Helixorient Representation
public	C HyperballRepresentation Hyperball Representation
public	C LabelRepresentation Label representation
public	C LicoriceRepresentation Licorice representation object (BallAndStickRepresentation with `aspectRatio` fixed at 1.0)
public	C LineRepresentation Line representation
public	C MolecularSurfaceRepresentation Molecular Surface Representation
public	C PointRepresentation Point Representation
public	C RibbonRepresentation Ribbon Representation
public	C RocketRepresentation Rocket Representation
public	C RopeRepresentation Rope Representation
public	C SliceRepresentation Slice representation
public	C SpacefillRepresentation Spacefill Representation
public	C SurfaceRepresentation Surface representation
public	C TraceRepresentation Trace Representation
public	C TrajectoryRepresentation Trajectory representation
public	C TubeRepresentation Tube Representation
public	C UnitcellRepresentation Unitcell Representation
public	C ValidationRepresentation Validation representation
public	I Representation(object: Object, viewer: Viewer, params: RepresentationParameters) Representation object
public	I StructureRepresentation Structure representation
public	F calcArcPoint()
public	F parseNestedAtoms(sview: Structure, atoms: Array): Float32Array MeasurementRepresentations take atom[Pair\|Triple\|Quad] parameters.
public	F makeRepresentation()
public	T AngleRepresentationParameters: Object
public	T BallAndStickRepresentationParameters: Object Ball And Stick representation parameter object.
public	T DihedralRepresentationParameters: Object
public	T DistanceRepresentationParameters: Object Distance representation parameter object.
public	T DotRepresentationParameters: Object Dot representation parameter object.
public	T LabelRepresentationParameters: Object Label representation parameter object.
public	T MeasurementRepresentationParameters: Object Measurement representation parameter object.
public	T RepresentationParameters: Object Representation parameter object.
public	T SliceRepresentationParameters: Object Slice representation parameter object.
public	T StructureRepresentationParameters: Object Structure representation parameter object.
public	T SurfaceRepresentationParameters: Object Surface representation parameter object.
public	T TrajectoryRepresentationParameters: Object Trajectory representation parameter object.

selection

summary
public	C Selection Selection
public	F parseSele()
public	F makeAtomTest()
public	F makeChainTest()
public	F makeModelTest()
public	F makeResidueTest()
public	V AcidicResname
public	V AliphaticResname
public	V AmideResname
public	V AromaticResname
public	V AtomOnlyKeywords
public	V BasicResname
public	V ChainKeywords
public	V ChargedResname
public	V CyclicResname
public	V HydrophobicResname
public	V NonpolarResname
public	V NucleophilicResname
public	V PolarResname
public	V SelectAllKeyword
public	V SmallResname
private	V kwd

shader

summary
public	F getShader()

stage

summary
private	C AnimationBehavior
public	C KeyBehavior
private	C MouseBehavior
public	C MouseObserver Mouse observer
private	C PickingBehavior
public	C Stage Stage class, central for creating molecular scenes with NGL.
public	T MouseSignals: Object
public	T StageParameters: Object Stage parameter object.
public	T StageSignals: Object

store

summary
public	C AtomMap
public	C AtomStore Atom store
public	C AtomType Atom type
public	C BondHash
public	C BondStore Bond store
public	C ChainStore Chain store
public	C ModelStore Model store
public	C ResidueMap
public	C ResidueStore Residue store
public	C ResidueType Residue type
public	I Store Store base class

streamer

summary
public	C BinaryStreamer
public	C FileStreamer
public	C NetworkStreamer
public	C Streamer
public	C StringStreamer

structure

summary
public	C Entity Entity of a Structure
public	C StructureView View on the structure, restricted to the selection
public	C Structure Structure
public	C Validation
private	F StructureBuilder()
public	F assignResidueTypeBonds(structure: Structure): undefined Assigns ResidueType bonds.
public	F assignSecondaryStructure()
public	F buildUnitcellAssembly()
public	F calculateBonds()
public	F calculateBondsBetween()
public	F calculateBondsWithin()
public	F calculateChainnames()
public	F calculateResidueBonds()
public	F getChainname()
public	F guessElement()
public	F reorderAtoms()
public	V AA1
public	V AA3
public	V CgDnaBackboneType
public	V CgProteinBackboneType
public	V CgRnaBackboneType
public	V ChemCompDna
public	V ChemCompHetero
public	V ChemCompNonPolymer
public	V ChemCompOther
public	V ChemCompProtein
public	V ChemCompRna
public	V ChemCompSaccharide
public	V CovalentRadii
public	V DefaultCovalentRadius
public	V DefaultResidueHydrophobicity
public	V DefaultResidueRadius
public	V DefaultVdwRadius
public	V DnaBackboneType
public	V DnaBases
public	V DnaType
public	V IonNames
public	V IonType
public	V MacrolideEntity
public	V NonPolymerEntity
public	V NucleicBackboneAtoms
public	V PolymerEntity
public	V ProteinBackboneAtoms
public	V ProteinBackboneType
public	V ProteinType
public	V PurinBases
public	V ResidueHydrophobicity
public	V ResidueRadii
public	V ResidueTypeAtoms
public	V RnaBackboneType
public	V RnaBases
public	V RnaType
public	V SaccharideNames
public	V SaccharideType
public	V SecStrucHelix
public	V SecStrucSheet
public	V SecStrucTurn
public	V UnknownBackboneType
private	V UnknownEntity
public	V UnknownType
public	V VdwRadii
public	V WaterEntity
public	V WaterNames
public	V WaterType
public	V calculateSecondaryStructure
public	T StructureExtraData: Object Structure extra data.
public	T StructureHeader: Object Structure header object.

surface

summary
public	C FilteredVolume
public	C MolecularSurface Create Molecular surfaces
public	C Surface Surface
public	C VolumeSlice
public	C Volume Volume
public	F AVHash(atomsX: Float32Array, atomsY: Float32Array, atomsZ: Float32Array, atomsR: Float32Array, min: Float32Array, max: Float32Array, maxDistance: Float) Modifed from SpatialHash
public	F AVSurface()
public	F EDTSurface()
public	F MarchingCubes()
public	F computeVertexNormals()
public	F getRadiusDict()
public	F getSurfaceGrid()
public	F laplacianSmooth()
public	F VolumeSurface()
public	T MolecularSurfaceParameters: Object Molecular surface parameter object.

symmetry

summary
public	C Assembly Assembly of transformed parts of a Structure
public	C Unitcell Unitcell class
public	F getSymmetryOperations()
public	V EncodedSymOp
private	V SymOpCode

trajectory

summary
public	C FramesTrajectory Frames trajectory class.
private	C Frames
public	C RemoteTrajectory Remote trajectory class.
public	C StructureTrajectory Structure trajectory class.
public	C TrajectoryPlayer Trajectory player for animating coordinate frames
public	I Trajectory Base class for trajectories, tying structures and coordinates together
public	F makeTrajectory()
public	T TrajectoryPlayerParameters: Object Trajectory player parameter object.
public	T TrajectoryParameters: Object Trajectory parameter object.
public	T TrajectorySignals: Object

utils

summary
public	C BitArray Bit array
public	C Counter Counter class for keeping track of counts
public	C IOBuffer Class for writing and reading binary data
public	C NetcdfReader Reads a NetCDF v3.x file https://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html
public	C ArrowPicker
public	C AtomPicker
public	C AxesPicker
public	C BondPicker
public	C BoxPicker
public	C ClashPicker
public	C ConePicker
public	C ContactPicker
public	C CylinderPicker
public	C DistancePicker
public	C EllipsoidPicker
public	C IgnorePicker
public	C MeshPicker
public	C OctahedronPicker
public	C SlicePicker
public	C SpherePicker
public	C SurfacePicker
public	C TetrahedronPicker
public	C TorusPicker
public	C UnitcellPicker
public	C UnknownPicker
public	C VolumePicker
public	C Registry
public	I Picker Picker class
public	I ShapePicker Shape picker class
public	F BinaryHeap(scoreFunction: Function) Binary heap implementation
public	F Kdtree(points: Float32Array, metric: Function) Kdtree
public	F LabelFactory()
public	F parseXml()
private	F Queue()
public	F RadiusFactory()

viewer

summary
public	C GeometryGroup
public	F Stats()
private	F TiledRenderer()
public	F makeImage(viewer: Viewer, params: ImageParameters): Promise Make image from what is shown in a viewer canvas
public	F sortProjectedPosition()
public	F testTextureSupport()
public	F updateMaterialUniforms()
public	F Viewer(idOrElement: String \| Element) Viewer class
public	V JitterVectors
public	T ImageParameters: Object Image parameter object.

worker

summary
public	C WorkerRegistry
public	F WorkerPool()
public	F makeWorkerBlob()
public	F Worker()

writer

summary
public	C PdbWriter Create a PDB file from a Structure object
public	C SdfWriter
public	C StlWriter Create an STL File from a surface Object (e.g.
public	I Writer Base class for writers

Directories