molstar
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A comprehensive macromolecular library.
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TypeScript
/**
* Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import * as Structure from '../../mol-model/structure.js';
import { DataLoci, Loci } from '../../mol-model/loci.js';
import { Volume } from '../../mol-model/volume.js';
import { Shape, ShapeGroup } from '../../mol-model/shape.js';
import * as LinearAlgebra3D from '../../mol-math/linear-algebra/3d.js';
import { PluginContext } from '../../mol-plugin/context.js';
import { PluginBehavior } from '../../mol-plugin/behavior.js';
import { PluginSpec } from '../../mol-plugin/spec.js';
import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects.js';
export declare const lib: {
structure: {
Time: typeof Structure.Time;
Coordinates: typeof Structure.Coordinates;
Topology: typeof Structure.Topology;
Model: typeof Structure.Model;
Types: typeof Structure.Types;
Symmetry: typeof Structure.Symmetry;
StructureSequence: typeof Structure.StructureSequence;
IndexedCustomProperty: typeof Structure.IndexedCustomProperty;
StructureElement: typeof Structure.StructureElement;
Bond: typeof Structure.Bond;
Structure: typeof Structure.Structure;
Unit: typeof Structure.Unit;
StructureSymmetry: typeof Structure.StructureSymmetry;
StructureProperties: {
constant: {
true: Structure.StructureElement.Property<boolean>;
false: Structure.StructureElement.Property<boolean>;
zero: Structure.StructureElement.Property<number>;
};
atom: {
key: Structure.StructureElement.Property<Structure.ElementIndex>;
x: Structure.StructureElement.Property<number>;
y: Structure.StructureElement.Property<number>;
z: Structure.StructureElement.Property<number>;
id: Structure.StructureElement.Property<number>;
occupancy: Structure.StructureElement.Property<number>;
B_iso_or_equiv: Structure.StructureElement.Property<number>;
sourceIndex: Structure.StructureElement.Property<number>;
type_symbol: Structure.StructureElement.Property<Structure.Types.ElementSymbol>;
label_atom_id: Structure.StructureElement.Property<string>;
auth_atom_id: Structure.StructureElement.Property<string>;
label_alt_id: Structure.StructureElement.Property<string>;
label_comp_id: Structure.StructureElement.Property<string>;
auth_comp_id: Structure.StructureElement.Property<string>;
pdbx_formal_charge: Structure.StructureElement.Property<number>;
vdw_radius: Structure.StructureElement.Property<number>;
};
residue: {
key: Structure.StructureElement.Property<Structure.ResidueIndex>;
group_PDB: Structure.StructureElement.Property<"ATOM" | "HETATM">;
label_comp_id: Structure.StructureElement.Property<string>;
auth_comp_id: Structure.StructureElement.Property<string>;
label_seq_id: Structure.StructureElement.Property<number>;
auth_seq_id: Structure.StructureElement.Property<number>;
pdbx_PDB_ins_code: Structure.StructureElement.Property<string>;
isNonStandard: Structure.StructureElement.Property<boolean>;
hasMicroheterogeneity: Structure.StructureElement.Property<boolean>;
microheterogeneityCompIds: Structure.StructureElement.Property<string[]>;
secondary_structure_type: Structure.StructureElement.Property<Structure.Types.SecondaryStructureType>;
secondary_structure_key: Structure.StructureElement.Property<number>;
chem_comp_type: Structure.StructureElement.Property<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
residueSourceIndex: Structure.StructureElement.Property<number>;
};
chain: {
key: Structure.StructureElement.Property<Structure.ChainIndex>;
label_asym_id: Structure.StructureElement.Property<string>;
auth_asym_id: Structure.StructureElement.Property<string>;
label_entity_id: Structure.StructureElement.Property<string>;
};
entity: {
key: Structure.StructureElement.Property<Structure.EntityIndex>;
id: Structure.StructureElement.Property<string>;
type: Structure.StructureElement.Property<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
src_method: Structure.StructureElement.Property<"nat" | "man" | "syn">;
pdbx_description: Structure.StructureElement.Property<string[]>;
formula_weight: Structure.StructureElement.Property<number>;
pdbx_number_of_molecules: Structure.StructureElement.Property<number>;
details: Structure.StructureElement.Property<string>;
pdbx_mutation: Structure.StructureElement.Property<string>;
pdbx_fragment: Structure.StructureElement.Property<string>;
pdbx_ec: Structure.StructureElement.Property<string[]>;
pdbx_parent_entity_id: Structure.StructureElement.Property<string>;
subtype: Structure.StructureElement.Property<import("../../mol-model/structure/model/properties/common.js").EntitySubtype>;
prd_id: Structure.StructureElement.Property<string>;
};
unit: {
id: Structure.StructureElement.Property<number>;
chainGroupId: Structure.StructureElement.Property<number>;
multiChain: Structure.StructureElement.Property<boolean>;
object_primitive: Structure.StructureElement.Property<"atomistic" | "sphere" | "gaussian">;
operator_name: Structure.StructureElement.Property<string>;
instance_id: Structure.StructureElement.Property<string>;
operator_key: Structure.StructureElement.Property<number>;
model_index: Structure.StructureElement.Property<number>;
model_label: Structure.StructureElement.Property<string>;
model_entry_id: Structure.StructureElement.Property<string>;
hkl: Structure.StructureElement.Property<LinearAlgebra3D.Vec3>;
spgrOp: Structure.StructureElement.Property<number>;
model_num: Structure.StructureElement.Property<number>;
pdbx_struct_assembly_id: Structure.StructureElement.Property<string>;
pdbx_struct_oper_list_ids: Structure.StructureElement.Property<any[]>;
struct_ncs_oper_id: Structure.StructureElement.Property<number>;
};
coarse: {
key: Structure.StructureElement.Property<Structure.ElementIndex>;
entityKey: Structure.StructureElement.Property<Structure.EntityIndex>;
x: Structure.StructureElement.Property<number>;
y: Structure.StructureElement.Property<number>;
z: Structure.StructureElement.Property<number>;
asym_id: Structure.StructureElement.Property<string>;
entity_id: Structure.StructureElement.Property<string>;
seq_id_begin: Structure.StructureElement.Property<number>;
seq_id_end: Structure.StructureElement.Property<number>;
sphere_radius: Structure.StructureElement.Property<number>;
sphere_rmsf: Structure.StructureElement.Property<number>;
gaussian_weight: Structure.StructureElement.Property<number>;
gaussian_covariance_matrix: Structure.StructureElement.Property<LinearAlgebra3D.Mat3>;
};
};
UnitRing: typeof Structure.UnitRing;
UnitRings: typeof Structure.UnitRings;
encode_mmCIF_categories(encoder: import("../../mol-io/writer/cif/encoder.js").Encoder, structures: Structure.Structure | Structure.Structure[], params?: {
exportCtx?: Structure.CifExportContext;
encoder?: import("../../mol-io/writer/cif/encoder.js").Encoder;
skipCategoryNames?: Set<string>;
includedCategoryNames?: Set<string>;
copyAllCategories?: boolean;
doNotReindexAtomSiteId?: boolean;
customProperties?: import("../../mol-model/custom-property.js").CustomPropertyDescriptor[];
extensions?: {
molstar_bond_site?: boolean;
};
}): void;
CifExportContext: typeof Structure.CifExportContext;
mmCIF_Export_Filters: {
onlyPositions: import("../../mol-io/writer/cif/encoder.js").Category.Filter;
};
to_mmCIF: typeof Structure.to_mmCIF;
Queries: {
generators: typeof import("../../mol-model/structure/query/queries/generators.js");
filters: typeof import("../../mol-model/structure/query/queries/filters.js");
modifiers: typeof import("../../mol-model/structure/query/queries/modifiers.js");
combinators: typeof import("../../mol-model/structure/query/queries/combinators.js");
pred: typeof import("../../mol-model/structure/query/predicates.js").Predicates;
internal: typeof import("../../mol-model/structure/query/queries/internal.js");
atomset: typeof import("../../mol-model/structure/query/queries/atom-set.js");
};
StructureSelection: typeof Structure.StructureSelection;
StructureQuery: typeof Structure.StructureQuery;
QueryContext: typeof Structure.QueryContext;
ArrayTrajectory: typeof Structure.ArrayTrajectory;
};
volume: {
Volume: typeof Volume;
};
shape: {
Shape: typeof Shape;
ShapeGroup: typeof ShapeGroup;
};
loci: {
Loci: typeof Loci;
DataLoci: typeof DataLoci;
EveryLoci: {
kind: "every-loci";
};
};
math: {
LinearAlgebra: {
Mat4: typeof LinearAlgebra3D.Mat4;
Mat3: typeof LinearAlgebra3D.Mat3;
Vec2: typeof LinearAlgebra3D.Vec2;
Vec3: typeof LinearAlgebra3D.Vec3;
Vec4: typeof LinearAlgebra3D.Vec4;
Quat: typeof LinearAlgebra3D.Quat;
EPSILON: 0.000001;
};
};
plugin: {
PluginContext: typeof PluginContext;
PluginConfig: {
item: <T>(key: string, defaultValue?: T) => import("../../mol-plugin/config.js").PluginConfigItem<T>;
General: {
IsBusyTimeoutMs: import("../../mol-plugin/config.js").PluginConfigItem<number>;
DisableAntialiasing: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
DisablePreserveDrawingBuffer: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
PixelScale: import("../../mol-plugin/config.js").PluginConfigItem<number>;
PickScale: import("../../mol-plugin/config.js").PluginConfigItem<number>;
Transparency: import("../../mol-plugin/config.js").PluginConfigItem<"blended" | "wboit" | "dpoit">;
PreferWebGl1: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
AllowMajorPerformanceCaveat: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
PowerPreference: import("../../mol-plugin/config.js").PluginConfigItem<WebGLPowerPreference | undefined>;
ResolutionMode: import("../../mol-plugin/config.js").PluginConfigItem<"auto" | "scaled" | "native">;
};
State: {
DefaultServer: import("../../mol-plugin/config.js").PluginConfigItem<string>;
CurrentServer: import("../../mol-plugin/config.js").PluginConfigItem<string>;
HistoryCapacity: import("../../mol-plugin/config.js").PluginConfigItem<number>;
};
VolumeStreaming: {
Enabled: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
DefaultServer: import("../../mol-plugin/config.js").PluginConfigItem<string>;
CanStream: import("../../mol-plugin/config.js").PluginConfigItem<(s: Structure.Structure, plugin: PluginContext) => boolean>;
EmdbHeaderServer: import("../../mol-plugin/config.js").PluginConfigItem<string>;
};
Viewport: {
ShowReset: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowExpand: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowToggleFullscreen: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowControls: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowSettings: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowSelectionMode: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowAnimation: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowTrajectoryControls: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowScreenshotControls: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowIllumination: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
ShowXR: import("../../mol-plugin/config.js").PluginConfigItem<"auto" | "always" | "never">;
};
Download: {
DefaultPdbProvider: import("../../mol-plugin/config.js").PluginConfigItem<"rcsb" | "pdbe" | "pdbj">;
DefaultEmdbProvider: import("../../mol-plugin/config.js").PluginConfigItem<import("../../mol-plugin-state/actions/volume.js").EmdbDownloadProvider>;
};
Structure: {
SizeThresholds: import("../../mol-plugin/config.js").PluginConfigItem<{
smallResidueCount: number;
mediumResidueCount: number;
largeResidueCount: number;
highSymmetryUnitCount: number;
fiberResidueCount: number;
}>;
DefaultRepresentationPreset: import("../../mol-plugin/config.js").PluginConfigItem<string>;
DefaultRepresentationPresetParams: import("../../mol-plugin/config.js").PluginConfigItem<import("../../mol-plugin-state/builder/structure/representation-preset.js").StructureRepresentationPresetProvider.CommonParams>;
SaccharideCompIdMapType: import("../../mol-plugin/config.js").PluginConfigItem<import("../../mol-model/structure/structure/carbohydrates/constants.js").SaccharideCompIdMapType>;
};
Background: {
Styles: import("../../mol-plugin/config.js").PluginConfigItem<[import("../../mol-util/param-definition.js").ParamDefinition.Values<{
variant: import("../../mol-util/param-definition.js").ParamDefinition.Mapped<import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<unknown>, "off"> | import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
coverage: "canvas" | "viewport";
opacity: number;
saturation: number;
lightness: number;
source: import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<any, "url"> | import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/assets.js").Asset.File | null, "file">;
blur: number;
}>, "image"> | import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
centerColor: import("../../mol-util/color/index.js").Color;
edgeColor: import("../../mol-util/color/index.js").Color;
ratio: number;
coverage: "canvas" | "viewport";
}>, "radialGradient"> | import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
opacity: number;
saturation: number;
lightness: number;
faces: import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
nx: /*elided*/ any;
ny: /*elided*/ any;
nz: /*elided*/ any;
px: /*elided*/ any;
py: /*elided*/ any;
pz: /*elided*/ any;
}>, "urls"> | import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
nx: /*elided*/ any;
ny: /*elided*/ any;
nz: /*elided*/ any;
px: /*elided*/ any;
py: /*elided*/ any;
pz: /*elided*/ any;
}>, "files">;
blur: number;
rotation: import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
x: /*elided*/ any;
y: /*elided*/ any;
z: /*elided*/ any;
}>;
}>, "skybox"> | import("../../mol-util/param-definition.js").ParamDefinition.NamedParams<import("../../mol-util/param-definition.js").ParamDefinition.Normalize<{
topColor: import("../../mol-util/color/index.js").Color;
bottomColor: import("../../mol-util/color/index.js").Color;
ratio: number;
coverage: "canvas" | "viewport";
}>, "horizontalGradient">>;
}>, string][]>;
};
};
PluginBehavior: typeof PluginBehavior;
PluginSpec: typeof PluginSpec;
PluginStateObject: typeof PluginStateObject;
PluginStateTransform: typeof PluginStateTransform;
StateTransforms: {
Data: typeof import("../../mol-plugin-state/transforms/data.js");
Misc: typeof import("../../mol-plugin-state/transforms/misc.js");
Model: typeof import("../../mol-plugin-state/transforms/model.js");
Volume: typeof import("../../mol-plugin-state/transforms/volume.js");
Representation: typeof import("../../mol-plugin-state/transforms/representation.js");
Shape: typeof import("../../mol-plugin-state/transforms/shape.js");
};
StateActions: {
Structure: typeof import("../../mol-plugin-state/actions/structure.js");
Volume: typeof import("../../mol-plugin-state/actions/volume.js");
DataFormat: typeof import("../../mol-plugin-state/actions/file.js");
};
DefaultPluginSpec: () => PluginSpec;
DefaultPluginUISpec: () => import("../../mol-plugin-ui/spec.js").PluginUISpec;
};
extensions: {
wwPDBStructConn: {
getStructConns(plugin: PluginContext, entry: string | undefined): {
[id: string]: import("../../extensions/wwpdb/struct-conn/index.js").StructConnRecord;
};
inspectStructConn(plugin: PluginContext, entry: string | undefined, structConnId: string, keepExisting?: boolean): Promise<number>;
clearStructConnInspections(plugin: PluginContext, entry: string | undefined): Promise<void>;
};
mvs: {
MVSData: {
SupportedVersion: number;
fromMVSJ(mvsjString: string): import("../mvs-stories/index.js").MVSData;
toMVSJ(mvsData: import("../mvs-stories/index.js").MVSData, space?: string | number): string;
toMVSX(mvsData: import("../mvs-stories/index.js").MVSData, options?: {
assets?: {
[uri: string]: Uint8Array<ArrayBuffer> | string;
};
baseUri?: string;
skipExternal?: boolean;
cache?: {
[absoluteUri: string]: Uint8Array<ArrayBuffer> | string;
};
}): Promise<Uint8Array<ArrayBuffer>>;
isValid(mvsData: import("../mvs-stories/index.js").MVSData, options?: {
noExtra?: boolean;
}): boolean;
validationIssues(mvsData: import("../mvs-stories/index.js").MVSData, options?: {
noExtra?: boolean;
}): string[] | undefined;
toPrettyString(mvsData: import("../mvs-stories/index.js").MVSData): string;
createBuilder(): import("../../extensions/mvs/tree/mvs/mvs-builder.js").Root;
createMultistate(snapshots: import("../../extensions/mvs/index.js").Snapshot[], metadata?: Pick<import("../../extensions/mvs/index.js").GlobalMetadata, "title" | "description" | "description_format">): import("../../extensions/mvs/index.js").MVSData_States;
stateToStates(state: import("../../extensions/mvs/index.js").MVSData_State): import("../../extensions/mvs/index.js").MVSData_States;
};
createBuilder: () => import("../../extensions/mvs/tree/mvs/mvs-builder.js").Root;
loadMVS: typeof import("../../extensions/mvs/index.js").loadMVS;
loadMVSData: typeof import("../../extensions/mvs/components/formats.js").loadMVSData;
util: {
queryMVSRef(plugin: PluginContext, ref: string): import("../../mol-state/index.js").StateSelection.CellSeq<import("../../mol-state/index.js").StateObjectCell<import("../../mol-state/index.js").StateObject<any, import("../../mol-state/index.js").StateObject.Type<any>>, import("../../mol-state/index.js").StateTransform<import("../../mol-state/index.js").StateTransformer<import("../../mol-state/index.js").StateObject<any, import("../../mol-state/index.js").StateObject.Type<any>>, import("../../mol-state/index.js").StateObject<any, import("../../mol-state/index.js").StateObject.Type<any>>, any>>>>;
createMVSRefMap(plugin: PluginContext): Map<string, import("../../mol-state/index.js").StateObjectSelector<import("../../mol-state/index.js").StateObject<any, import("../../mol-state/index.js").StateObject.Type<any>>, import("../../mol-state/index.js").StateTransformer<import("../../mol-state/index.js").StateObject<any, import("../../mol-state/index.js").StateObject.Type<any>>, import("../../mol-state/index.js").StateObject<any, import("../../mol-state/index.js").StateObject.Type<any>>, any>>[]>;
tryGetPrimitivesFromLoci(loci: Loci | undefined): import("../../extensions/mvs/tree/mvs/mvs-tree.js").MVSNode<"primitive">[] | undefined;
getCurrentMVSSnapshot(plugin: PluginContext): import("../../extensions/mvs/index.js").Snapshot | undefined;
};
};
modelArchive: {
qualityAssessment: {
config: {
EnablePairwiseScorePlot: import("../../mol-plugin/config.js").PluginConfigItem<boolean>;
};
};
};
};
};