molstar
Version:
A comprehensive macromolecular library.
152 lines (151 loc) • 6.5 kB
TypeScript
/**
* Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Structure, Unit } from '../../../mol-model/structure';
import { Features } from './features';
import { InteractionsIntraContacts, InteractionsInterContacts } from './common';
import { IntMap } from '../../../mol-data/int';
import { CustomProperty } from '../../common/custom-property';
import { DataLocation } from '../../../mol-model/location';
import { Sphere3D } from '../../../mol-math/geometry';
import { DataLoci } from '../../../mol-model/loci';
export { Interactions };
interface Interactions {
/** Features of each unit */
unitsFeatures: IntMap<Features>;
/** Interactions of each unit */
unitsContacts: IntMap<InteractionsIntraContacts>;
/** Interactions between units */
contacts: InteractionsInterContacts;
}
declare namespace Interactions {
type StructureInteractions = {
readonly structure: Structure;
readonly interactions: Interactions;
};
export interface Element {
unitA: Unit;
/** Index into features of unitA */
indexA: Features.FeatureIndex;
unitB: Unit;
/** Index into features of unitB */
indexB: Features.FeatureIndex;
}
export interface Location extends DataLocation<StructureInteractions, Element> {
}
export function Location(interactions: Interactions, structure: Structure, unitA?: Unit, indexA?: Features.FeatureIndex, unitB?: Unit, indexB?: Features.FeatureIndex): Location;
export function isLocation(x: any): x is Location;
export function areLocationsEqual(locA: Location, locB: Location): boolean;
export function locationLabel(location: Location): string;
export interface Loci extends DataLoci<StructureInteractions, Element> {
}
export function Loci(structure: Structure, interactions: Interactions, elements: ReadonlyArray<Element>): Loci;
export function isLoci(x: any): x is Loci;
export function getBoundingSphere(interactions: Interactions, elements: ReadonlyArray<Element>, boundingSphere: Sphere3D): Sphere3D;
export function getLabel(structure: Structure, interactions: Interactions, elements: ReadonlyArray<Element>): string;
export {};
}
export declare const ContactProviderParams: {
ionic: PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
}, "on">>;
'pi-stacking': PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
offsetMax: PD.Numeric;
angleDevMax: PD.Numeric;
}, "on">>;
'cation-pi': PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
offsetMax: PD.Numeric;
}, "on">>;
'halogen-bonds': PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
angleMax: PD.Numeric;
}, "on">>;
'hydrogen-bonds': PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
water: PD.BooleanParam;
sulfurDistanceMax: PD.Numeric;
distanceMax: PD.Numeric;
backbone: PD.BooleanParam;
accAngleDevMax: PD.Numeric;
ignoreHydrogens: PD.BooleanParam;
donAngleDevMax: PD.Numeric;
accOutOfPlaneAngleMax: PD.Numeric;
donOutOfPlaneAngleMax: PD.Numeric;
}, "on">>;
'weak-hydrogen-bonds': PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
backbone: PD.BooleanParam;
accAngleDevMax: PD.Numeric;
ignoreHydrogens: PD.BooleanParam;
donAngleDevMax: PD.Numeric;
accOutOfPlaneAngleMax: PD.Numeric;
donOutOfPlaneAngleMax: PD.Numeric;
}, "on">>;
hydrophobic: PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
}, "on">>;
'metal-coordination': PD.Mapped<PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
}, "on">>;
};
export declare const InteractionsParams: {
providers: PD.Group<PD.Normalize<{
ionic: PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
}, "on">;
'pi-stacking': PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
offsetMax: PD.Numeric;
angleDevMax: PD.Numeric;
}, "on">;
'cation-pi': PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
offsetMax: PD.Numeric;
}, "on">;
'halogen-bonds': PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
angleMax: PD.Numeric;
}, "on">;
'hydrogen-bonds': PD.NamedParams<{}, "off"> | PD.NamedParams<{
water: PD.BooleanParam;
sulfurDistanceMax: PD.Numeric;
distanceMax: PD.Numeric;
backbone: PD.BooleanParam;
accAngleDevMax: PD.Numeric;
ignoreHydrogens: PD.BooleanParam;
donAngleDevMax: PD.Numeric;
accOutOfPlaneAngleMax: PD.Numeric;
donOutOfPlaneAngleMax: PD.Numeric;
}, "on">;
'weak-hydrogen-bonds': PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
backbone: PD.BooleanParam;
accAngleDevMax: PD.Numeric;
ignoreHydrogens: PD.BooleanParam;
donAngleDevMax: PD.Numeric;
accOutOfPlaneAngleMax: PD.Numeric;
donOutOfPlaneAngleMax: PD.Numeric;
}, "on">;
hydrophobic: PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
}, "on">;
'metal-coordination': PD.NamedParams<{}, "off"> | PD.NamedParams<{
distanceMax: PD.Numeric;
}, "on">;
}>>;
contacts: PD.Group<PD.Normalize<{
lineOfSightDistFactor: number;
}>>;
};
export type InteractionsParams = typeof InteractionsParams;
export type InteractionsProps = PD.Values<InteractionsParams>;
export interface ComputeInterctionsOptions {
skipIntraContacts?: boolean;
unitPairTest?: (unitA: Unit, unitB: Unit) => boolean;
}
export declare function computeInteractions(ctx: CustomProperty.Context, structure: Structure, props: Partial<InteractionsProps>, options?: ComputeInterctionsOptions): Promise<Interactions>;