pfam-molstar/src/af-confidence/prop.ts

A component for embedding molstar 3D viewer in Pfam

/**
 * Copyright (c) 2018-2020 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 { Column, Table } from 'molstar/lib/mol-data/db';
import { toTable } from 'molstar/lib/mol-io/reader/cif/schema';
import { Model, ResidueIndex, Unit, IndexedCustomProperty } from 'molstar/lib/mol-model/structure';
import { StructureElement, Structure } from 'molstar/lib/mol-model/structure/structure';
import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
import { PropertyWrapper } from 'molstar/lib/mol-model-props/common/wrapper';
import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
import { CustomModelProperty } from 'molstar/lib/mol-model-props/common/custom-model-property';
import { CustomPropertyDescriptor } from 'molstar/lib/mol-model/custom-property';
import { dateToUtcString } from 'molstar/lib/mol-util/date';
import { arraySetAdd } from 'molstar/lib/mol-util/array';

export { AfConfidence };

type AfConfidence = PropertyWrapper<{
    score: IndexedCustomProperty.Residue<[number, string]>,
    category: string[]
}| undefined>

namespace AfConfidence {
    export const DefaultServerUrl = '';

    export function isApplicable(model?: Model): boolean {
        return !!model && Model.isFromPdbArchive(model);
    }

    export interface Info {
        timestamp_utc: string
    }

    export const Schema = {
        local_metric_values: {
            label_asym_id: Column.Schema.str,
            label_comp_id: Column.Schema.str,
            label_seq_id: Column.Schema.int,
            metric_id: Column.Schema.int,
            metric_value: Column.Schema.float,
            model_id: Column.Schema.int,
            ordinal_id: Column.Schema.int
        }
    };
    export type Schema = typeof Schema

    function tryGetInfoFromCif(categoryName: string, model: Model): undefined | Info {
        if (!MmcifFormat.is(model.sourceData) || !model.sourceData.data.frame.categoryNames.includes(categoryName)) {
            return;
        }

        const timestampField = model.sourceData.data.frame.categories[categoryName].getField('metric_value');
        if (!timestampField || timestampField.rowCount === 0) return;

        return { timestamp_utc: timestampField.str(0) || dateToUtcString(new Date()) };
    }

    export function fromCif(ctx: CustomProperty.Context, model: Model): AfConfidence | undefined {
        let info = tryGetInfoFromCif('ma_qa_metric_local', model);
        if (!info) return;
        const data = getCifData(model);
        const metricMap = createScoreMapFromCif(model, data.residues);
        return { info, data: metricMap };
    }

    export async function fromCifOrServer(ctx: CustomProperty.Context, model: Model, props: AfConfidenceProps): Promise<any> {
        const cif = fromCif(ctx, model);
        return { value: cif };
    }

    export function getConfidenceScore(e: StructureElement.Location) {
        if (!Unit.isAtomic(e.unit)) return [-1, 'No Score'];
        const prop = AfConfidenceProvider.get(e.unit.model).value;
        if (!prop || !prop.data) return [-1, 'No Score'];
        const rI = e.unit.residueIndex[e.element];
        return prop.data.score.has(rI) ? prop.data.score.get(rI)! : [-1, 'No Score'];
    }

    const _emptyArray: string[] = [];
    export function getCategories(structure?: Structure) {
        if (!structure) return _emptyArray;
        const prop = AfConfidenceProvider.get(structure.models[0]).value;
        if (!prop || !prop.data) return _emptyArray;
        return prop.data.category;
    }

    function getCifData(model: Model) {
        if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF.');
        return {
            residues: toTable(Schema.local_metric_values, model.sourceData.data.frame.categories.ma_qa_metric_local),
        };
    }
}

export const AfConfidenceParams = {
    serverUrl: PD.Text(AfConfidence.DefaultServerUrl, { description: 'JSON API Server URL' })
};
export type AfConfidenceParams = typeof AfConfidenceParams
export type AfConfidenceProps = PD.Values<AfConfidenceParams>

export const AfConfidenceProvider: CustomModelProperty.Provider<AfConfidenceParams, AfConfidence> = CustomModelProperty.createProvider({
    label: 'AF Confidence Score',
    descriptor: CustomPropertyDescriptor({
        name: 'af_confidence_score'
    }),
    type: 'static',
    defaultParams: AfConfidenceParams,
    getParams: (data: Model) => AfConfidenceParams,
    isApplicable: (data: Model) => AfConfidence.isApplicable(data),
    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<AfConfidenceProps>) => {
        const p = { ...PD.getDefaultValues(AfConfidenceParams), ...props };
        return await AfConfidence.fromCifOrServer(ctx, data, p);
    }
});

function createScoreMapFromCif(modelData: Model,
    residueData: Table<typeof AfConfidence.Schema.local_metric_values>): AfConfidence['data'] | undefined {

    const ret = new Map<ResidueIndex, [number, string]>();
    const { label_asym_id, label_seq_id, metric_value, _rowCount } = residueData;

    const categories: string[] = [];

    for (let i = 0; i < _rowCount; i++) {
        const confidenceScore = metric_value.value(i);
        const idx = modelData.atomicHierarchy.index.findResidue('1', label_asym_id.value(i), label_seq_id.value(i), '');

        let confidencyCategory = 'Very low';
        if(confidenceScore > 50 && confidenceScore <= 70) {
            confidencyCategory = 'Low';
        } else if(confidenceScore > 70 && confidenceScore <= 90) {
            confidencyCategory = 'Medium';
        } else if(confidenceScore > 90) {
            confidencyCategory = 'High';
        }

        ret.set(idx, [confidenceScore, confidencyCategory]);
        arraySetAdd(categories, confidencyCategory);
    }

    return {
        score: IndexedCustomProperty.fromResidueMap(ret),
        category: categories
    };
}