@jenskrumsieck/moleculesjs/dist/cif.js

Some TypeScript Molecule Parsers

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const atom_1 = require("./primitives/atom");
const molecule_1 = __importDefault(require("./primitives/molecule"));
const vector3_1 = require("./primitives/vector3");
class CIF {
    content;
    a;
    b;
    c;
    alpha;
    beta;
    gamma;
    constructor(content) {
        this.content = content.replace(/(?:[\r])/g, "");
        this.setParameters();
    }
    static parse(content) {
        var cif = new CIF(content);
        return cif.parse();
    }
    parse() {
        var loops = this.content.split('loop_');
        var molLoop = loops.find(s => s.includes('_atom_site_label'));
        var bondLoop = loops.find(s => s.includes('_geom_bond_atom_site_label_1'));
        var atoms = this.extractAtoms(molLoop);
        var bonds = this.extractBonds(bondLoop, atoms);
        return new molecule_1.default({ atoms, bonds });
    }
    extractAtoms(molLoop) {
        let lines = molLoop.split('\n');
        let headers = lines.filter(s => s.trim().startsWith('_'));
        let body = lines.filter(s => !s.trim().startsWith('_'));
        let disorderIndex = headers.indexOf('_atom_site_disorder_group');
        let data = [];
        for (var i = 0; i < body.length; i++) {
            var raw_data = body[i].split(' ');
            if (disorderIndex >= 0
                && disorderIndex < raw_data.length
                && raw_data[disorderIndex] == "2" || raw_data.length != headers.length)
                continue;
            data.push(raw_data);
        }
        return this.calculateCartesian(data);
    }
    extractBonds(bondLoop, atoms) {
        let lines = bondLoop.split('\n');
        let body = lines.filter(s => !s.trim().startsWith('_'));
        var bonds = [];
        for (var i = 0; i < body.length; i++) {
            var raw_data = body[i].split(" ");
            let atom1 = raw_data[0];
            let atom2 = raw_data[1];
            //check if atoms existing
            if (atoms.find(s => s.title == atom1) && atoms.find(s => s.title == atom2))
                bonds.push({ atom1: atoms.find(s => s.title == atom1), atom2: atoms.find(s => s.title == atom2) });
        }
        return bonds;
    }
    cellParameters(type) {
        let parameters = [];
        let lines = this.content.split('\n');
        for (var i = 0; i < lines.length; i++) {
            if (lines[i].startsWith("_" + type)) {
                //parameter value contains uncertainity in brackets, so strip that
                var tmp = lines[i].split(" ");
                var value = tmp[tmp.length - 1]; //last item
                parameters.push(value.split('(')[0]);
            }
        }
        return parameters;
    }
    setParameters() {
        var lengths = this.cellParameters('cell_length');
        var angles = this.cellParameters('cell_angle');
        this.a = parseFloat(lengths[0]);
        this.b = parseFloat(lengths[1]);
        this.c = parseFloat(lengths[2]);
        this.alpha = parseFloat(angles[0]);
        this.beta = parseFloat(angles[1]);
        this.gamma = parseFloat(angles[2]);
    }
    calculateCartesian(data) {
        //variables introduced to deconfuse
        var atoms = [];
        for (var i = 0; i < data.length; i++) {
            //get xyz in fractional coordinates
            //1 is label, 2 is x, 3 is y, 4 is z
            let xFrac = data[i][2].split('(')[0];
            let yFrac = data[i][3].split('(')[0];
            let zFrac = data[i][4].split('(')[0];
            let angle = Math.PI / 180;
            //transformation matrix: see https://en.wikipedia.org/wiki/Fractional_coordinates#Conversion_to_Cartesian_coordinates
            //a21, a31, a32 = 0
            //a11 = a
            //other matrix entries as below:
            let a12 = this.b * Math.cos(this.gamma * angle);
            let a13 = this.c * Math.cos(this.beta * angle);
            let a22 = this.b * Math.sin(this.gamma * angle);
            let a23 = this.c * (Math.cos(this.alpha * angle) - Math.cos(this.beta * angle) * Math.cos(this.gamma * angle)) / Math.sin(this.gamma * angle);
            let a33 = this.c * (Math.sqrt(1 - Math.pow(Math.cos(this.alpha * angle), 2) - Math.pow(Math.cos(this.beta * angle), 2) - Math.pow(Math.cos(this.gamma * angle), 2) + 2 * Math.cos(this.alpha * angle) * Math.cos(this.beta * angle) * Math.cos(this.gamma * angle))) / Math.sin(this.gamma * angle);
            //xyz = [A]*(xyz)_frac
            let x = this.a * xFrac + a12 * yFrac + a13 * zFrac;
            let y = a22 * yFrac + a23 * zFrac;
            let z = a33 * zFrac;
            let element = data[i][1];
            var atom = new atom_1.Atom(element, new vector3_1.Vector3(x, y, z));
            atom.title = data[i][0];
            atoms.push(atom);
        }
        return atoms;
    }
}
exports.default = CIF;