Sketch of atomIndex in bond-store

bond-store.js

/**
 * @file Bond Store
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @private
 */


import Store from "./store.js";
import BondProxy from "../proxy/bond-proxy.js";

function BondStore( sizeOrObject ){

    Store.call( this, sizeOrObject );

    this.atomAtomIndex = {};

}

BondStore.prototype = Object.assign( Object.create(

    Store.prototype ), {

    constructor: BondStore,

    type: "BondStore",

    __fields: [

        [ "atomIndex1", 1, "int32" ],
        [ "atomIndex2", 1, "int32" ],
        [ "bondOrder", 1, "int8" ],

    ],

    addBond: function( atom1, atom2, bondOrder ){

        this.growIfFull();

        var i = this.count;
        var aai = this.atomAtomIndex;
        var ai1 = atom1.index, ai2 = atom2.index;

        if( atom1.index < atom2.index ){
            this.atomIndex1[ i ] = atom1.index;
            this.atomIndex2[ i ] = atom2.index;
        }else{
            this.atomIndex2[ i ] = atom1.index;
            this.atomIndex1[ i ] = atom2.index;
        }
        if( bondOrder ) this.bondOrder[ i ] = bondOrder;

        aai[ ai1 ] = aai[ ai1 ] || {};
        aai[ ai1 ][ ai2 ] = i;
        aai[ ai2 ] = aai[ ai2 ] || {};
        aai[ ai2 ][ ai1 ] = i;

        this.count += 1;

    },

    addBondIfConnected: function( atom1, atom2, bondOrder ){

        if( atom1.connectedTo( atom2 ) ){
            this.addBond( atom1, atom2, bondOrder );
            return true;
        }

        return false;

    },

    getBondIndicesForAtom: function( atom1 ) {

        var bonds = [];
      
        var o = this.atomAtomIndex[atom1.index];
        if( o !== undefined ){
            for( var ai2 in o ){
                if( o.hasOwnProperty( ai2 ) ) {
                    bonds.push( o[ ai2 ] );
                }
            }
        }
      
        return bonds;
          
    },
   

    /** Invoke callback( bp ) for each bond for this atom */
    eachBondForAtom: function( atom1, callback ) {

        var bonds = this.getBondIndicesForAtom( atom1 );
        var bp = new BondProxy( atom1.structure, 0 );
        for( var i = 0; i < bonds.length; ++i ){
            bp.index = bonds[i];
            callback( bp );
        }
    },

    deduplicate: function() {
        
        // New arrays, or in place?

    }

    

} );


export default BondStore;