@ccp-nc/crystvis-js/lib/data.js

A Three.js based crystallographic visualisation tool

'use strict';

import {
    PeriodicTable as PeriodicTable
} from 'mendeleev';

import nmrData from './nmrdata.js';
import { shiftCpkColor } from './utils.js';

/**
 * @fileoverview Various data arrays and structures storing useful information
 * @private
 */

// Van der Waals radii by atomic number
const vdwRadii = [1.77, // Z = 0 is used as the default
    1.2, 1.4, 1.82, 1.7, 2.08,
    1.95, 1.55, 1.7, 1.73, 1.54, 2.27, 1.73, 2.05,
    2.1, 2.08, 2.0, 1.97, 1.88, 2.75, 1.973, 1.7,
    1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.63, 1.4, 1.39,
    1.87, 1.7, 1.85, 1.9, 2.1, 2.02, 1.7, 1.7, 1.7,
    1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.63, 1.72, 1.58,
    1.93, 2.17, 2.2, 2.06, 2.15, 2.16, 1.7, 1.7,
    1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7,
    1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7,
    1.7, 1.7, 1.7, 1.72, 1.66, 1.55, 1.96, 2.02,
    1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7,
    1.86, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7,
    1.7, 1.7, 1.7
];

const cpkColors = [0xff1493, // Z = 0 is used as the default
    0xffffff, 0xd9ffff, 0xcc80ff, 0xc2ff00, 0xffb5b5, 0x909090, 0x3050f8, 0xff0d0d,
    0x90e050, 0xb3e3f5, 0xab5cf2, 0x8aff00, 0xbfa6a6, 0xf0c8a0, 0xff8000, 0xffff30,
    0x1ff01f, 0x80d1e3, 0x8f40d4, 0x3dff00, 0xe6e6e6, 0xbfc2c7, 0xa6a6ab, 0x8a99c7,
    0x9c7ac7, 0xe06633, 0xf090a0, 0x50d050, 0xc88033, 0x7d80b0, 0xc28f8f, 0x668f8f,
    0xbd80e3, 0xffa100, 0xa62929, 0x5cb8d1, 0x702eb0, 0x00ff00, 0x94ffff, 0x94e0e0,
    0x73c2c9, 0x54b5b5, 0x3b9e9e, 0x248f8f, 0x0a7d8c, 0x006985, 0xc0c0c0, 0xffd98f,
    0xa67573, 0x668080, 0x9e63b5, 0xd47a00, 0x940094, 0x429eb0, 0x57178f, 0x00c900,
    0x70d4ff, 0xffffc7, 0xd9ffc7, 0xc7ffc7, 0xa3ffc7, 0x8fffc7, 0x61ffc7, 0x45ffc7,
    0x30ffc7, 0x1fffc7, 0x00ff9c, 0x00e675, 0x00d452, 0x00bf38, 0x00ab24, 0x4dc2ff,
    0x4da6ff, 0x2194d6, 0x267dab, 0x266696, 0x175487, 0xd0d0e0, 0xffd123, 0xb8b8d0,
    0xa6544d, 0x575961, 0x9e4fb5, 0xab5c00, 0x754f45, 0x428296, 0x420066, 0x007d00,
    0x70abfa, 0x00baff, 0x00a1ff, 0x008fff, 0x0080ff, 0x006bff, 0x545cf2, 0x785ce3,
    0x8a4fe3, 0xa136d4, 0xb31fd4, 0xb31fba, 0xb30da6, 0xbd0d87, 0xc70066, 0xcc0059,
    0xd1004f, 0xd90045, 0xe00038, 0xe6002e, 0xeb0026
];


function getVdwRadius(symbol) {
    var el = PeriodicTable.getElement(symbol);
    var Z = (el ? el.number : 0);
    return vdwRadii[Z];
}

function getCpkColor(symbol, isotope=null) {
    var el = PeriodicTable.getElement(symbol);
    var Z = (el ? el.number : 0);
    var cpkc = cpkColors[Z];

    if (isotope !== null) {
        // We apply an isotope correction
        var edata = nmrData[symbol];
        if (isotope != edata.maxiso) {
            // Then a correction is necessary
            var isolist = getIsotopeList(symbol);
            var imax = isolist.indexOf(edata.maxiso);
            var ic = isolist.indexOf(isotope.toString());
            var shift = (ic-imax)/isolist.length;
            cpkc = shiftCpkColor(cpkc, shift);
        }
    }

    return cpkc;
}

function getIsotopeList(symbol) {
    const data = nmrData[symbol];
    if (!data) {
        return null;
    }

    // If we do have it though...
    return Object.keys(data.isotopes).sort();
}

function getElementData(symbol) {
    return nmrData[symbol];
}

function getIsotopeData(symbol, iso=null) {
    const eldata = nmrData[symbol];

    if (eldata == null) {
        return null;
    }

    if (iso === null) {
        // Make it the most common one
        iso = eldata.maxiso;
    }
    else if (iso === 'nmr') {
        iso = eldata.maxiso_NMR;
    }
    else if (iso === 'Q') {
        iso = eldata.maxiso_Q;
    }

    if (iso === null) {
        // No such isotope
        return null;
    }

    return eldata.isotopes[iso];
}

export {
    vdwRadii,
    cpkColors,
    getVdwRadius,
    getCpkColor,
    getIsotopeList,
    getElementData,
    getIsotopeData
}