78 Three.js 导入PDB格式的模型

简介

PDB是一种非常特殊的格式,由Protein Data Bank(蛋白质数据银行)创建,用于定义蛋白质的形状。蛋白质数据银行(www.rcsb.org)包含了很多分子和蛋白质的详细信息,还可以用PDB格式下载这些分子的数据结构。在Three.js中有一种加载器可以加载PDB格式的文件。

实现案例

案例查看地址:http://www.wjceo.com/blog/threejs/2018-03-22/138.html

  • 首先,引入script加载器,在这里需要再引入CSS2DRenderer渲染器来绘制每个原子的名称。
<script src="/lib/js/renderers/CSS2DRenderer.js"></script>
<script src="/lib/js/loaders/PDBLoader.js"></script>
  • 然后,我们实例化一个THREE.PDBLoader对象,将想要加载的模型文件传递给它,还提供了一个回调函数,该函数会在模型加载完成之后调用。在返回的对象里面,我们可以获得geometryAtoms原子的数据,geometryBonds原子之间的键的数据,和json每个原子名称的数据。
    var loader = new THREE.PDBLoader();
    loader.load("/lib/models/molecules/caffeine.pdb", function (pdb) {
        //创建一个模型组
        var root = new THREE.Group();
        var offset = new THREE.Vector3();

        //获取到原子相关的数据
        var geometryAtoms = pdb.geometryAtoms;
        //获取到原子间的键的数据
        var geometryBonds = pdb.geometryBonds;
        //获取原子文字的数据
        var json = pdb.json;

        var boxGeometry = new THREE.BoxBufferGeometry( 1, 1, 1 );
        var sphereGeometry = new THREE.IcosahedronBufferGeometry( 1, 2 );

        //让模型居中
        geometryAtoms.computeBoundingBox();
        geometryAtoms.boundingBox.getCenter( offset ).negate();
        geometryAtoms.translate( offset.x, offset.y, offset.z );
        geometryBonds.translate( offset.x, offset.y, offset.z );

        //将原子和原子的文字添加到模型组当中
        var positions = geometryAtoms.getAttribute( 'position' );
        var colors = geometryAtoms.getAttribute( 'color' );
        var position = new THREE.Vector3();
        var color = new THREE.Color();
        for ( var i = 0; i < positions.count; i ++ ) {
            position.x = positions.getX( i );
            position.y = positions.getY( i );
            position.z = positions.getZ( i );
            color.r = colors.getX( i );
            color.g = colors.getY( i );
            color.b = colors.getZ( i );
            var material = new THREE.MeshPhongMaterial( { color: color } );
            var object = new THREE.Mesh( sphereGeometry, material );
            object.position.copy( position );
            object.position.multiplyScalar( 75 );
            object.scale.multiplyScalar( 25 );
            root.add( object );
            var atom = json.atoms[ i ];
            var text = document.createElement( 'div' );
            text.className = 'label';
            text.style.color = 'rgb(' + atom[ 3 ][ 0 ] + ',' + atom[ 3 ][ 1 ] + ',' + atom[ 3 ][ 2 ] + ')';
            text.style.textShadow = "1px 1px 1px #000";
            text.textContent = atom[ 4 ];
            var label = new THREE.CSS2DObject( text );
            label.position.copy( object.position );
            root.add( label );
        }

        //将原子之间的键添加到模型组当中
        positions = geometryBonds.getAttribute( 'position' );
        var start = new THREE.Vector3();
        var end = new THREE.Vector3();
        for ( var i = 0; i < positions.count; i += 2 ) {
            start.x = positions.getX( i );
            start.y = positions.getY( i );
            start.z = positions.getZ( i );
            end.x = positions.getX( i + 1 );
            end.y = positions.getY( i + 1 );
            end.z = positions.getZ( i + 1 );
            start.multiplyScalar( 75 );
            end.multiplyScalar( 75 );
            var object = new THREE.Mesh( boxGeometry, new THREE.MeshPhongMaterial( 0xffffff ) );
            object.position.copy( start );
            object.position.lerp( end, 0.5 );
            object.scale.set( 5, 5, start.distanceTo( end ) );
            object.lookAt( end );
            root.add( object );
        }

        //缩放并将模型组添加到场景当中
        root.scale.set(0.1, 0.1, 0.1);
        scene.add(root);
    });
}

案例代码

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <title>Title</title>
    <style type="text/css">
        html, body {
            margin: 0;
            height: 100%;
        }

        canvas {
            display: block;
        }

    </style>
</head>
<body onload="draw();">

</body>
<script src="/lib/three.js"></script>
<script src="/lib/js/renderers/CSS2DRenderer.js"></script>
<script src="/lib/js/loaders/PDBLoader.js"></script>

<script src="/lib/js/controls/OrbitControls.js"></script>
<script src="/lib/js/libs/stats.min.js"></script>
<script src="/lib/js/libs/dat.gui.min.js"></script>
<script src="/lib/js/Detector.js"></script>

<script>
    var renderer,labelRenderer;
    function initRender() {
        renderer = new THREE.WebGLRenderer({antialias:true});
        renderer.setSize(window.innerWidth, window.innerHeight);
        //告诉渲染器需要阴影效果
        renderer.setClearColor(0x000000);
        document.body.appendChild(renderer.domElement);

        //实例化css2dRenderer
        labelRenderer = new THREE.CSS2DRenderer();
        labelRenderer.setSize( window.innerWidth, window.innerHeight );
        labelRenderer.domElement.style.position = 'absolute';
        labelRenderer.domElement.style.top = '0';
        labelRenderer.domElement.style.pointerEvents = 'none';
        document.body.appendChild( labelRenderer.domElement );
    }

    var camera;
    function initCamera() {
        camera = new THREE.PerspectiveCamera(45, window.innerWidth/window.innerHeight, 0.1, 1000);
        camera.position.set(0, 40, 50);
        camera.lookAt(new THREE.Vector3(0,0,0));
    }

    var scene;
    function initScene() {
        scene = new THREE.Scene();
    }

    //初始化dat.GUI简化试验流程
    var gui;
    function initGui() {
        //声明一个保存需求修改的相关数据的对象
        gui = {
        };
        var datGui = new dat.GUI();
        //将设置属性添加到gui当中,gui.add(对象,属性,最小值,最大值)
    }

    var light;
    function initLight() {
        scene.add(new THREE.AmbientLight(0x444444));

        light = new THREE.DirectionalLight(0xffffff);
        light.position.set(200, 200, 100);

        //告诉平行光需要开启阴影投射
        light.castShadow = true;

        scene.add(light);
    }

    function initModel() {

        //辅助工具
        var helper = new THREE.AxesHelper(50);
        scene.add(helper);

        var loader = new THREE.PDBLoader();
        loader.load("/lib/models/molecules/caffeine.pdb", function (pdb) {
            //创建一个模型组
            var root = new THREE.Group();
            var offset = new THREE.Vector3();

            //获取到原子相关的数据
            var geometryAtoms = pdb.geometryAtoms;
            //获取到原子间的键的数据
            var geometryBonds = pdb.geometryBonds;
            //获取原子文字的数据
            var json = pdb.json;

            var boxGeometry = new THREE.BoxBufferGeometry( 1, 1, 1 );
            var sphereGeometry = new THREE.IcosahedronBufferGeometry( 1, 2 );

            //让模型居中
            geometryAtoms.computeBoundingBox();
            geometryAtoms.boundingBox.getCenter( offset ).negate();
            geometryAtoms.translate( offset.x, offset.y, offset.z );
            geometryBonds.translate( offset.x, offset.y, offset.z );

            //将原子和原子的文字添加到模型组当中
            var positions = geometryAtoms.getAttribute( 'position' );
            var colors = geometryAtoms.getAttribute( 'color' );
            var position = new THREE.Vector3();
            var color = new THREE.Color();
            for ( var i = 0; i < positions.count; i ++ ) {
                position.x = positions.getX( i );
                position.y = positions.getY( i );
                position.z = positions.getZ( i );
                color.r = colors.getX( i );
                color.g = colors.getY( i );
                color.b = colors.getZ( i );
                var material = new THREE.MeshPhongMaterial( { color: color } );
                var object = new THREE.Mesh( sphereGeometry, material );
                object.position.copy( position );
                object.position.multiplyScalar( 75 );
                object.scale.multiplyScalar( 25 );
                root.add( object );
                var atom = json.atoms[ i ];
                var text = document.createElement( 'div' );
                text.className = 'label';
                text.style.color = 'rgb(' + atom[ 3 ][ 0 ] + ',' + atom[ 3 ][ 1 ] + ',' + atom[ 3 ][ 2 ] + ')';
                text.style.textShadow = "1px 1px 1px #000";
                text.textContent = atom[ 4 ];
                var label = new THREE.CSS2DObject( text );
                label.position.copy( object.position );
                root.add( label );
            }

            //将原子之间的键添加到模型组当中
            positions = geometryBonds.getAttribute( 'position' );
            var start = new THREE.Vector3();
            var end = new THREE.Vector3();
            for ( var i = 0; i < positions.count; i += 2 ) {
                start.x = positions.getX( i );
                start.y = positions.getY( i );
                start.z = positions.getZ( i );
                end.x = positions.getX( i + 1 );
                end.y = positions.getY( i + 1 );
                end.z = positions.getZ( i + 1 );
                start.multiplyScalar( 75 );
                end.multiplyScalar( 75 );
                var object = new THREE.Mesh( boxGeometry, new THREE.MeshPhongMaterial( 0xffffff ) );
                object.position.copy( start );
                object.position.lerp( end, 0.5 );
                object.scale.set( 5, 5, start.distanceTo( end ) );
                object.lookAt( end );
                root.add( object );
            }

            //缩放并将模型组添加到场景当中
            root.scale.set(0.1, 0.1, 0.1);
            scene.add(root);
        });
    }

    //初始化性能插件
    var stats;
    function initStats() {
        stats = new Stats();
        document.body.appendChild(stats.dom);
    }

    //用户交互插件 鼠标左键按住旋转,右键按住平移,滚轮缩放
    var controls;
    function initControls() {

        controls = new THREE.OrbitControls( camera, renderer.domElement );

        // 如果使用animate方法时,将此函数删除
        //controls.addEventListener( 'change', render );
        // 使动画循环使用时阻尼或自转 意思是否有惯性
        controls.enableDamping = true;
        //动态阻尼系数 就是鼠标拖拽旋转灵敏度
        //controls.dampingFactor = 0.25;
        //是否可以缩放
        controls.enableZoom = true;
        //是否自动旋转
        controls.autoRotate = true;
        controls.autoRotateSpeed = 0.5;
        //设置相机距离原点的最远距离
        controls.minDistance  = 1;
        //设置相机距离原点的最远距离
        controls.maxDistance  = 200;
        //是否开启右键拖拽
        controls.enablePan = true;
    }

    function render() {

        renderer.render( scene, camera );

        labelRenderer.render( scene, camera );
    }

    //窗口变动触发的函数
    function onWindowResize() {

        camera.aspect = window.innerWidth / window.innerHeight;
        camera.updateProjectionMatrix();
        render();
        renderer.setSize( window.innerWidth, window.innerHeight );

    }

    function animate() {
        //更新控制器
        render();

        //更新性能插件
        stats.update();

        controls.update();

        requestAnimationFrame(animate);
    }

    function draw() {
        //兼容性判断
        if ( ! Detector.webgl ) Detector.addGetWebGLMessage();

        initGui();
        initRender();
        initScene();
        initCamera();
        initControls();
        initLight();
        initModel();
        initStats();

        animate();
        window.onresize = onWindowResize;
    }
</script>
</html>
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