lookup3d.ts

import * as util from 'util'
import * as fs from 'fs'
import CIF from 'mol-io/reader/cif'

import { Structure, Model, Format } from 'mol-model/structure'

import { GridLookup3D } from 'mol-math/geometry';
// import { sortArray } from 'mol-data/util';
import { OrderedSet } from 'mol-data/int';

require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);

async function readData(path: string) {
    if (path.match(/\.bcif$/)) {
        const input = await readFileAsync(path)
        const data = new Uint8Array(input.byteLength);
        for (let i = 0; i < input.byteLength; i++) data[i] = input[i];
        return data;
    } else {
        return readFileAsync(path, 'utf8');
    }
}


export async function readCIF(path: string) {
    const input = await readData(path)
    const comp = typeof input === 'string' ? CIF.parseText(input) : CIF.parseBinary(input);
    const parsed = await comp.run();
    if (parsed.isError) {
        throw parsed;
    }

    const mmcif = Format.mmCIF(parsed.result.blocks[0]);
    const models = await Model.create(mmcif).run();
    const structures = models.map(Structure.ofModel);

    return { mmcif: mmcif.data, models, structures };
}

export async function test() {
    const { mmcif, structures } = await readCIF('e:/test/quick/1tqn_updated.cif');

    const lookup = GridLookup3D({ x: mmcif.atom_site.Cartn_x.toArray(), y: mmcif.atom_site.Cartn_y.toArray(), z: mmcif.atom_site.Cartn_z.toArray(),
        indices: OrderedSet.ofBounds(0, mmcif.atom_site._rowCount),
        //radius: [1, 1, 1, 1]
        //indices: [1]
    });
    console.log(lookup.boundary.box, lookup.boundary.sphere);

    const result = lookup.find(-30.07, 8.178, -13.897, 10);
    console.log(result.count)//, sortArray(result.indices));

    // const sl = structures[0].lookup3d;
    // const result1 = sl.find(-30.07, 8.178, -13.897, 10);
    // console.log(result1.count);//, result1.indices);

    console.log(structures[0].boundary);
    console.log(lookup.boundary);
}

test();