smiles-drawer/app.js

A SMILES drawer and parser. Generate molecular structure depictions in pure JavaScript.

// @ts-check
import Drawer         from './src/Drawer';
import GaussDrawer    from './src/GaussDrawer';
import Parser         from './src/Parser';
import ReactionDrawer from './src/ReactionDrawer';
import ReactionParser from './src/ReactionParser';
import SmiDrawer      from './src/SmilesDrawer';
import SvgDrawer      from './src/SvgDrawer';

/**
 * The SmilesDrawer namespace.
 * @typicalname SmilesDrawer
 */
const SmilesDrawerNS = {
    Version: '2.2.1',

    Drawer:         Drawer,
    GaussDrawer:    GaussDrawer,
    Parser:         Parser,
    ReactionDrawer: ReactionDrawer,
    ReactionParser: ReactionParser,
    SmiDrawer:      SmiDrawer,
    SvgDrawer:      SvgDrawer,
};

/**
* Cleans a SMILES string (removes non-valid characters)
*
* @static
* @param {String} smiles A SMILES string.
* @returns {String} The clean SMILES string.
*/
SmilesDrawerNS.clean = function(smiles) {
    return smiles.replace(/[^A-Za-z0-9@.+\-?!()[\]{}/\\=#$:*]/g, '');
};

/**
* Applies the smiles drawer draw function to each canvas element that has a smiles string in the data-smiles attribute.
*
* @static
* @param {Object} options SmilesDrawer options.
* @param {String} [selector='canvas[data-smiles]'] Selectors for the draw areas (canvas elements).
* @param {String} [themeName='light'] The theme to apply.
* @param {Function} [onError='null'] A callback function providing an error object.
*/
SmilesDrawerNS.apply = function(options, selector = 'canvas[data-smiles]', themeName = 'light', onError = null) {
    let smilesDrawer = new Drawer(options);
    let elements = document.querySelectorAll(selector);

    for (var i = 0; i < elements.length; i++) {
        let element = elements[i];

        SmilesDrawerNS.parse(element.getAttribute('data-smiles'), function(tree) {
            smilesDrawer.draw(tree, element, themeName, false);
        }, function(err) {
            if (onError) {
                onError(err);
            }
        });
    }
};

/**
* Parses the entered smiles string.
*
* @static
* @param {String} smiles A SMILES string.
* @param {Function} successCallback A callback that is called on success with the parse tree.
* @param {Function} errorCallback A callback that is called with the error object on error.
*/
SmilesDrawerNS.parse = function(smiles, successCallback, errorCallback) {
    try {
        if (successCallback) {
            successCallback(Parser.parse(smiles));
        }
    }
    catch (err) {
        if (errorCallback) {
            errorCallback(err);
        }
    }
};

/**
* Parses the entered reaction smiles string.
*
* @static
* @param {String} reactionSmiles A reaction SMILES string.
* @param {Function} successCallback A callback that is called on success with the parse tree.
* @param {Function} errorCallback A callback that is called with the error object on error.
*/
SmilesDrawerNS.parseReaction = function(reactionSmiles, successCallback, errorCallback) {
    try {
        if (successCallback) {
            successCallback(ReactionParser.parse(reactionSmiles));
        }
    }
    catch (err) {
        if (errorCallback) {
            errorCallback(err);
        }
    }
};

// Here be dragons (polyfills)
if (!Array.prototype.fill) {
    let fill = function(value) {
        // Steps 1-2.
        if (this == null) {
            throw new TypeError('this is null or not defined');
        }

        var O = Object(this);

        // Steps 3-5.
        var len = O.length >>> 0;

        // Steps 6-7.
        var start = arguments[1];
        var relativeStart = start >> 0;

        // Step 8.
        var k = relativeStart < 0
            ? Math.max(len + relativeStart, 0)
            : Math.min(relativeStart, len);

        // Steps 9-10.
        var end = arguments[2];
        var relativeEnd = end === undefined ? len : end >> 0;

        // Step 11.
        var final = relativeEnd < 0
            ? Math.max(len + relativeEnd, 0)
            : Math.min(relativeEnd, len);

        // Step 12.
        while (k < final) {
            O[k] = value;
            k++;
        }

        // Step 13.
        return O;
    };

    Object.defineProperty(Array.prototype, 'fill', {
        value:     fill,
        writeable: false,
    });
}

// If we're in a browser window, add the SmilesDrawer globals
if (typeof window !== 'undefined' && window.document && window.document.createElement) {
    window.SmilesDrawer = SmilesDrawerNS;
    window.SmiDrawer    = SmiDrawer;
}

// Finally - export time!
export default SmilesDrawerNS;