TmMolStar/src/mol-model/structure/model/model.ts

/**
 * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

import UUID from '../../../mol-util/uuid';
import StructureSequence from './properties/sequence';
import { AtomicHierarchy, AtomicConformation } from './properties/atomic';
import { ModelSymmetry } from './properties/symmetry';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities, ChemicalComponentMap, MissingResidues } from './properties/common';
import { CustomProperties } from '../common/custom-property';
import { SecondaryStructure } from './properties/seconday-structure';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from '../../../mol-model-formats/structure/format';
import { calcModelCenter } from './util';
import { Vec3 } from '../../../mol-math/linear-algebra';

/**
 * Interface to the "source data" of the molecule.
 *
 * "Atoms" are integers in the range [0, atomCount).
 */
export interface Model extends Readonly<{
    id: UUID,
    entryId: string,
    label: string,

    /** the name of the entry/file/collection the model is part of */
    entry: string,

    /** for IHM, corresponds to ihm_model_list.model_id */
    modelNum: number,

    sourceData: ModelFormat,

    symmetry: ModelSymmetry,
    entities: Entities,
    sequence: StructureSequence,

    atomicHierarchy: AtomicHierarchy,
    atomicConformation: AtomicConformation,

    properties: {
        /** secondary structure provided by the input file */
        readonly secondaryStructure: SecondaryStructure,
        /** maps modified residue name to its parent */
        readonly modifiedResidues: Readonly<{
            parentId: ReadonlyMap<string, string>,
            details: ReadonlyMap<string, string>
        }>,
        /** map that holds details about unobserved or zero occurrence residues */
        readonly missingResidues: MissingResidues,
        /** maps residue name to `ChemicalComponent` data */
        readonly chemicalComponentMap: ChemicalComponentMap
        /** maps residue name to `SaccharideComponent` data */
        readonly saccharideComponentMap: SaccharideComponentMap
    },

    customProperties: CustomProperties,

    /**
     * Not to be accessed directly, each custom property descriptor
     * defines property accessors that use this field to store the data.
     */
    _staticPropertyData: { [name: string]: any },
    _dynamicPropertyData: { [name: string]: any },

    coarseHierarchy: CoarseHierarchy,
    coarseConformation: CoarseConformation
}> {

} { }

export namespace Model {
    // TODO: is this enough?
    export type Trajectory = ReadonlyArray<Model>

    const CenterProp = '__Center__'
    export function getCenter(model: Model): Vec3 {
        if (model._dynamicPropertyData[CenterProp]) return model._dynamicPropertyData[CenterProp]
        const center = calcModelCenter(model.atomicConformation, model.coarseConformation)
        model._dynamicPropertyData[CenterProp] = center
        return center
    }
}