TmMolStar/src/mol-model-props/computed/secondary-structure.ts

/**
 * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

import { Structure } from '../../mol-model/structure';
import { DSSPComputationParams, DSSPComputationProps, computeUnitDSSP } from './secondary-structure/dssp';
import { SecondaryStructure } from '../../mol-model/structure/model/properties/seconday-structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Unit } from '../../mol-model/structure/structure';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
import { CustomPropertyDescriptor } from '../../mol-model/structure/common/custom-property';

function getSecondaryStructureParams(data?: Structure) {
    let defaultType = 'model' as 'model' | 'dssp'
    if (data) {
        defaultType = 'dssp'
        for (let i = 0, il = data.models.length; i < il; ++i) {
            const m = data.models[i]
            if (MmcifFormat.is(m.sourceData)) {
                if (m.sourceData.data.db.struct_conf.id.isDefined ||
                    m.sourceData.data.db.struct_sheet_range.id.isDefined ||
                    m.sourceData.data.db.database_2.database_id.isDefined
                ) {
                    // if there is any secondary structure definition given or if there is
                    // an archival model, don't calculate dssp by default
                    defaultType = 'model'
                    break
                }
            }
        }
    }
    return {
        type: PD.MappedStatic(defaultType, {
            'model': PD.EmptyGroup({ label: 'Model' }),
            'dssp': PD.Group(DSSPComputationParams, { label: 'DSSP', isFlat: true })
        }, { options: [['model', 'Model'], ['dssp', 'DSSP']] })
    }
}

export const SecondaryStructureParams = getSecondaryStructureParams()
export type SecondaryStructureParams = typeof SecondaryStructureParams
export type SecondaryStructureProps = PD.Values<SecondaryStructureParams>

/** Maps `unit.id` to `SecondaryStructure` */
export type SecondaryStructureValue = Map<number, SecondaryStructure>

export const SecondaryStructureProvider: CustomStructureProperty.Provider<SecondaryStructureParams, SecondaryStructureValue> = CustomStructureProperty.createProvider({
    label: 'Secondary Structure',
    descriptor: CustomPropertyDescriptor({
        name: 'molstar_computed_secondary_structure',
        // TODO `cifExport` and `symbol`
    }),
    type: 'root',
    defaultParams: SecondaryStructureParams,
    getParams: getSecondaryStructureParams,
    isApplicable: (data: Structure) => true,
    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<SecondaryStructureProps>) => {
        const p = { ...PD.getDefaultValues(SecondaryStructureParams), ...props }
        switch (p.type.name) {
            case 'dssp': return await computeDssp(data, p.type.params)
            case 'model': return await computeModel(data)
        }
    }
})

async function computeDssp(structure: Structure, props: DSSPComputationProps): Promise<SecondaryStructureValue> {
    // TODO take inter-unit hbonds into account for bridge, ladder, sheet assignment
    // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
    const map = new Map<number, SecondaryStructure>()
    for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
        const u = structure.unitSymmetryGroups[i].units[0]
        if (Unit.isAtomic(u)) {
            const secondaryStructure = await computeUnitDSSP(u, props)
            map.set(u.invariantId, secondaryStructure)
        }
    }
    return map
}

async function computeModel(structure: Structure): Promise<SecondaryStructureValue> {
    const map = new Map<number, SecondaryStructure>()
    for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
        const u = structure.unitSymmetryGroups[i].units[0]
        if (Unit.isAtomic(u)) {
            const secondaryStructure = ModelSecondaryStructure.Provider.get(u.model)
            if (secondaryStructure) {
                map.set(u.invariantId, secondaryStructure)
            }
        }
    }
    return map
}