layout: post
title: 构建表面修饰长链分子的纳米颗粒模型
categories:
- 科
tags:
- md
- bash
chem: true
- 2016-02-21 00:01:09 初稿
- 2016-08-16 22:58:21 修订, 增加随机选择, 指定法向功能
在进行与纳米颗粒有关的分子动力学模拟时, 有时候需要对纳米颗粒的表面进行修饰, 例如, 将一些长链的表面活性剂分子连接到颗粒的表面, 以改变纳米颗粒的亲水性. 这种模型的构建牵涉到两个问题, 一个是如何得到纳米颗粒的结构, 另一个是有了纳米颗粒的结构后, 如何将一些长链分子连接到颗粒的表面.
构建球形纳米颗粒
一般而言, 我们可以根据原子的晶胞结构来构建相应的晶体, 然后根据一定的条件去除不需要的原子, 就得到了一定形状的纳米颗粒. 对于球形的纳米颗粒, 这可以利用我编写的一个小工具来完成. 只要选择好晶胞类型(一般使用FCC或HCP, 因为这两种是最密堆积), 团簇类型球体, 设定好晶胞参数和球体半径, 点击创建就可以得到纳米颗粒的坐标文件了. 在坐标文件中, 正常位点以C表示, 面心位点以F表示, 六方位点以H表示, 表面原子则以S表示. 程序中表面原子的确定方法比较粗略, 你可以根据自己的需要自行决定将哪些原子指定为表面原子, 只要将相应的元素符号改为S即可.
作为示例, 我使用HCP晶胞类型, 其他参数默认, 得到的结构文件如下(中间部分省略):
<table class="highlighttable"><th colspan="2" style="text-align:left">HCP.xyz</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height: 125%"> 1
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HCP Sphere Radius<span style="color: #666666">=5</span>
H <span style="color: #666666">-7.500000</span> <span style="color: #666666">-11.258330</span> <span style="color: #666666">-2.449490</span>
H <span style="color: #666666">-7.500000</span> <span style="color: #666666">-11.258330</span> <span style="color: #666666">2.449490</span>
S <span style="color: #666666">-9.000000</span> <span style="color: #666666">-8.660254</span> <span style="color: #666666">-7.348469</span>
S <span style="color: #666666">-9.000000</span> <span style="color: #666666">-10.392305</span> <span style="color: #666666">-4.898979</span>
H <span style="color: #666666">-9.000000</span> <span style="color: #666666">-8.660254</span> <span style="color: #666666">-2.449490</span>
C <span style="color: #666666">-9.000000</span> <span style="color: #666666">-10.392305</span> <span style="color: #666666">0.000000</span>
H <span style="color: #666666">-9.000000</span> <span style="color: #666666">-8.660254</span> <span style="color: #666666">2.449490</span>
S <span style="color: #666666">-9.000000</span> <span style="color: #666666">-10.392305</span> <span style="color: #666666">4.898979</span>
S <span style="color: #666666">-9.000000</span> <span style="color: #666666">-8.660254</span> <span style="color: #666666">7.348469</span>
H <span style="color: #666666">-10.500000</span> <span style="color: #666666">-6.062178</span> <span style="color: #666666">-7.348469</span>
C <span style="color: #666666">-10.500000</span> <span style="color: #666666">-7.794229</span> <span style="color: #666666">-4.898979</span>
.....(<span style="border: 1px solid #FF0000">省略</span>)
S <span style="color: #666666">9.000000</span> <span style="color: #666666">10.392305</span> <span style="color: #666666">-4.898979</span>
C <span style="color: #666666">9.000000</span> <span style="color: #666666">10.392305</span> <span style="color: #666666">0.000000</span>
S <span style="color: #666666">9.000000</span> <span style="color: #666666">10.392305</span> <span style="color: #666666">4.898979</span>
</pre></div>
</td></tr></table>
为避免后面添加长链分子后, 分子其中的氢原子与颗粒中的`H`位点相混淆, 我们先将`H`原子类型替换为`C`. 如果颗粒的原子类型不是`C`的话, 你可能也需要将`C`改为你需要的原子类型, 以免与长链分子中的碳原子混淆.
将这个文件保存为`HCP.xyz`备用.
### 构建长链分子
长链分子的构建可采用你熟悉的分子编辑软件, 只要能输出xyz格式的结构文件即可.
我们以下面的分子作为示例:
<table class="highlighttable"><th colspan="2" style="text-align:left">C9.xyz</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height: 125%"> 1
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C9COOH
C <span style="color: #666666">8.79053824</span> <span style="color: #666666">1.01170907</span> <span style="color: #666666">-0.03365831</span>
C <span style="color: #666666">9.28080412</span> <span style="color: #666666">1.70826814</span> <span style="color: #666666">1.24932447</span>
C <span style="color: #666666">8.78721231</span> <span style="color: #666666">3.16696710</span> <span style="color: #666666">1.26214971</span>
H <span style="color: #666666">10.35034747</span> <span style="color: #666666">1.69339092</span> <span style="color: #666666">1.27681426</span>
H <span style="color: #666666">8.89485019</span> <span style="color: #666666">1.19360662</span> <span style="color: #666666">2.10434675</span>
C <span style="color: #666666">9.27747818</span> <span style="color: #666666">3.86352617</span> <span style="color: #666666">2.54513250</span>
H <span style="color: #666666">9.17316623</span> <span style="color: #666666">3.68162862</span> <span style="color: #666666">0.40712744</span>
H <span style="color: #666666">7.71766896</span> <span style="color: #666666">3.18184432</span> <span style="color: #666666">1.23465992</span>
C <span style="color: #666666">8.78388637</span> <span style="color: #666666">5.32222513</span> <span style="color: #666666">2.55795773</span>
H <span style="color: #666666">8.89152426</span> <span style="color: #666666">3.34886465</span> <span style="color: #666666">3.40015477</span>
H <span style="color: #666666">10.34702153</span> <span style="color: #666666">3.84864895</span> <span style="color: #666666">2.57262229</span>
H <span style="color: #666666">9.16984029</span> <span style="color: #666666">5.83688665</span> <span style="color: #666666">1.70293546</span>
H <span style="color: #666666">7.71434302</span> <span style="color: #666666">5.33710235</span> <span style="color: #666666">2.53046794</span>
C <span style="color: #666666">9.27415225</span> <span style="color: #666666">6.01878420</span> <span style="color: #666666">3.84094052</span>
C <span style="color: #666666">8.78056044</span> <span style="color: #666666">7.47748316</span> <span style="color: #666666">3.85376576</span>
H <span style="color: #666666">10.34369560</span> <span style="color: #666666">6.00390698</span> <span style="color: #666666">3.86843031</span>
H <span style="color: #666666">8.88819833</span> <span style="color: #666666">5.50412268</span> <span style="color: #666666">4.69596279</span>
C <span style="color: #666666">9.27082631</span> <span style="color: #666666">8.17404223</span> <span style="color: #666666">5.13674854</span>
H <span style="color: #666666">9.16651436</span> <span style="color: #666666">7.99214468</span> <span style="color: #666666">2.99874348</span>
H <span style="color: #666666">7.71101709</span> <span style="color: #666666">7.49236038</span> <span style="color: #666666">3.82627597</span>
H <span style="color: #666666">8.88487239</span> <span style="color: #666666">7.65938071</span> <span style="color: #666666">5.99177081</span>
H <span style="color: #666666">10.34036966</span> <span style="color: #666666">8.15916501</span> <span style="color: #666666">5.16423833</span>
C <span style="color: #666666">8.77723450</span> <span style="color: #666666">9.63274119</span> <span style="color: #666666">5.14957378</span>
O <span style="color: #666666">8.60383009</span> <span style="color: #666666">10.24786466</span> <span style="color: #666666">4.06554214</span>
O <span style="color: #666666">8.51594972</span> <span style="color: #666666">10.28824341</span> <span style="color: #666666">6.39333706</span>
H <span style="color: #666666">7.82155932</span> <span style="color: #666666">10.93991893</span> <span style="color: #666666">6.27192456</span>
</pre></div>
</td></tr></table><figure><script>var Mol1=new ChemDoodle.MovieCanvas3D('Mol-1',650,400);Mol1.specs.shapes_color = '#fff';Mol1.specs.backgroundColor = 'black';Mol1.specs.set3DRepresentation('Ball and Stick');Mol1.specs.projectionPerspective_3D = false;Mol1.specs.proteins_ribbonCartoonize = true;
/*Mol1.timeout = 15;
//Mol1.specs.atoms_resolution_3D = 15;
//Mol1.specs.bonds_resolution_3D = 15;
//Mol1.specs.crystals_unitCellLineWidth = 1.5;*/
Mol1.addFrame([ChemDoodle.readXYZ('26\nC9COOH\nC 8.79053824 1.01170907 -0.03365831\nC 9.28080412 1.70826814 1.24932447\nC 8.78721231 3.16696710 1.26214971\nH 10.35034747 1.69339092 1.27681426\nH 8.89485019 1.19360662 2.10434675\nC 9.27747818 3.86352617 2.54513250\nH 9.17316623 3.68162862 0.40712744\nH 7.71766896 3.18184432 1.23465992\nC 8.78388637 5.32222513 2.55795773\nH 8.89152426 3.34886465 3.40015477\nH 10.34702153 3.84864895 2.57262229\nH 9.16984029 5.83688665 1.70293546\nH 7.71434302 5.33710235 2.53046794\nC 9.27415225 6.01878420 3.84094052\nC 8.78056044 7.47748316 3.85376576\nH 10.34369560 6.00390698 3.86843031\nH 8.88819833 5.50412268 4.69596279\nC 9.27082631 8.17404223 5.13674854\nH 9.16651436 7.99214468 2.99874348\nH 7.71101709 7.49236038 3.82627597\nH 8.88487239 7.65938071 5.99177081\nH 10.34036966 8.15916501 5.16423833\nC 8.77723450 9.63274119 5.14957378\nO 8.60383009 10.24786466 4.06554214\nO 8.51594972 10.28824341 6.39333706\nH 7.82155932 10.93991893 6.27192456\n')],[]);Mol1.loadMolecule(Mol1.frames[0].mols[0]);Mol1.startAnimation();function setProj1(yesPers){Mol1.specs.projectionPerspective_3D = yesPers;Mol1.setupScene();Mol1.repaint()}function setModel1(model){Mol1.specs.set3DRepresentation(model);Mol1.setupScene();Mol1.repaint()}function setSpeed1(){Mol1.timeout=500-document.getElementById("spd1").value;Mol1.loadMolecule(Mol1.frames[0].mols[0]);Mol1.startAnimation()}</script><br><span class="meta">视图: <input type="radio" name="group2" onclick="setProj1(true)">投影<input type="radio" name="group2" onclick="setProj1(false)" checked="">正交 速度: <input type="range" id="spd1" min="1" max="500" onchange="setSpeed1()"/><br>模型: <input type="radio" name="model" onclick="setModel1('Ball and Stick')" checked="">球棍<input type="radio" name="model" onclick="setModel1('van der Waals Spheres')">范德华球<input type="radio" name="model" onclick="setModel1('Stick')">棍状<input type="radio" name="model" onclick="setModel1('Wireframe')">线框<input type="radio" name="model" onclick="setModel1('Line')">线型<input type="checkbox" onclick="Mol1.specs.atoms_displayLabels_3D=this.checked;Mol1.repaint()">名称<br>左键: 转动 滚轮: 缩放 双击: 开关自动旋转 Alt+左键: 移动</span><br><figurecaption>Fig.1</figurecaption></figure>我们可以利用C1和C23来指定这个分子的长轴方向. 由于C1会连接到纳米颗粒表面, 所以需要将本来与它相连的氢原子删除.
将结构保存为C9.xyz备用.
将长链分子连接到纳米颗粒表面
在进行表面修饰时, 我们要在指定为S的表面原子上连接长链分子. 连接时, 要使长链分子的长轴方向沿着表面的法向(对球体其法向即径向), 这样各个分子之间的重叠和交叉才最小. 手动进行这些操作也可以, 但当分子数较多时就变得很麻烦了. 因此, 我写了一个简单的bash脚本apdMol来完成这件事. 这个脚本在运行时需要两个结构文件, 一个是纳米颗粒的结构文件, 一个是长链分子的结构文件, 此外, 还需要给出长链分子中的两个原子编号来指定长链分子的长轴方向. 有了这些信息后, 脚本会自动将纳米颗粒中标为S的表面原子替换为长链分子, 并保证长链分子的长轴方向沿颗粒的法向.
原始脚本发布后, 有人希望能增加些功能
- 随机选取部分表面原子进行修饰
- 能够使用其他法向, 这样就能用于修饰表面
第二个功能实现起来并不复杂, 但对于第一个功能, 必须有些考虑, 想明白这里所说的"随机"是什么意思. 对于球形颗粒来说, 其表面随机分布的点看起来可能并不是均匀的, 有些地方疏, 有些地方密, 这可能并不是你需要的结果. 此外, 有些人所说的随机很可能指的是随机均匀分布, 需要把一定数量的点均匀分布在表面上, 使点与点之间的间距尽量相等且最大. 这两种随机方法实现起来都不简单, 就不详细说明了. 目前代码中实现的随机是最简单随机方法, 就是随机从表面点中选取一定数目的点. 严格说来这是一种很差的随机方法(甚至可说是错误的), 但容易实现, 对一般应用来说也不会引起多大问题. 在使用代码时, 请不要忘记这一点.
<table class="highlighttable"><th colspan="2" style="text-align:left">apdMol.bsh</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height: 125%"> 1
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144</pre></div></td><td class="code"><div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%">usage<span style="color: #666666">=</span><span style="color: #BB4444">"\</span>
<span style="color: #BB4444">>>>>>>>>>>>>>>>> apdMol <<<<<<<<<<<<<<<<</span>
<span style="color: #BB4444">>>>>>>>>>>>>>>>> Jerkwin@gmail.com <<<<<<<<<<<<<<<<</span>
<span style="color: #BB4444">>>>>>>>>>> 2016-02-20 23:20:36 初版 <<<<<<<<<</span>
<span style="color: #BB4444">>>>>>>>>>> 2016-08-16 22:58:21 修订 <<<<<<<<<</span>
<span style="color: #BB4444">>> 用法: bash $0 <MolA.xyz> <MolB.xyz> {Iatm} {Jatm} {Lsrf} {Apd#%} {Norm}</span>
<span style="color: #BB4444">>> 默认: bash $0 <MolA.xyz> <MolB.xyz> 1 2 S 50% COG</span>
<span style="color: #BB4444">>> MolA: 待修饰的团簇或表面</span>
<span style="color: #BB4444">>> MolB: 修饰到MolA的分子</span>
<span style="color: #BB4444">>> Iatm: MolB的#Iatm原子将重合到MolA中的某个表面原子</span>
<span style="color: #BB4444">>> Jatm: #Iatm->#Jatm原子定义MolB的主轴方向</span>
<span style="color: #BB4444">>> Lsrf: MolA中表面原子的标识符号</span>
<span style="color: #BB4444">>> Apd#%: MolA中要修饰的表面原子的个数或百分比</span>
<span style="color: #BB4444">>> Norm: MolA表面原子的法向</span>
<span style="color: #BB4444"> 对球形团簇可使用COG(到几何中心法向)</span>
<span style="color: #BB4444"> 对表面可使用X|Y|Z</span>
<span style="color: #BB4444"> 也可直接指定{x,y,z}(尚未实现)"</span>
[[ <span style="color: #666666">$</span><span style="color: #008800; font-style: italic"># -lt 2 ]] && { echo "$usage"; exit; }</span>
MolA<span style="color: #666666">=$1</span>; MolB<span style="color: #666666">=$2</span>
Iatm<span style="color: #666666">=1</span>; [[ x<span style="color: #666666">$3</span> <span style="color: #666666">!=</span> x ]] <span style="color: #666666">&&</span> { Iatm<span style="color: #666666">=$3</span>; }
Jatm<span style="color: #666666">=2</span>; [[ x<span style="color: #666666">$4</span> <span style="color: #666666">!=</span> x ]] <span style="color: #666666">&&</span> { Jatm<span style="color: #666666">=$4</span>; }
Lsrf<span style="color: #666666">=</span><span style="color: #BB4444">"S"</span>; [[ x<span style="color: #666666">$5</span> <span style="color: #666666">!=</span> x ]] <span style="color: #666666">&&</span> { Lsrf<span style="color: #666666">=$5</span>; }
Napd<span style="color: #666666">=</span><span style="color: #BB4444">"50%"</span>; [[ x<span style="color: #666666">$6</span> <span style="color: #666666">!=</span> x ]] <span style="color: #666666">&&</span> { Napd<span style="color: #666666">=$6</span>; }
Norm<span style="color: #666666">=</span><span style="color: #BB4444">"COG"</span>; [[ x<span style="color: #666666">$7</span> <span style="color: #666666">!=</span> x ]] <span style="color: #666666">&&</span> { Norm<span style="color: #666666">=$7</span>; }
awk <span style="color: #666666">-</span>v file<span style="color: #666666">=$</span>MolB <span style="color: #666666">-</span>v Iatm<span style="color: #666666">=$</span>Iatm <span style="color: #666666">-</span>v Jatm<span style="color: #666666">=$</span>Jatm <span style="border: 1px solid #FF0000">\</span>
<span style="color: #666666">-</span>v Lsrf<span style="color: #666666">=$</span>Lsrf <span style="color: #666666">-</span>v Napd<span style="color: #666666">=$</span>Napd <span style="color: #666666">-</span>v Norm<span style="color: #666666">=$</span>Norm <span style="border: 1px solid #FF0000">\</span>
<span style="color: #BB4444">'</span> <span style="color: #AA22FF">BEGIN</span>{ Pi<span style="color: #666666">=4*</span><span style="color: #AA22FF; font-weight: bold">atan2</span>(<span style="color: #666666">1</span>,<span style="color: #666666">1</span>)
<span style="color: #AA22FF; font-weight: bold">getline</span> NatmB <span style="color: #666666"><</span> file
<span style="color: #AA22FF; font-weight: bold">getline</span> <span style="color: #666666"><</span> file
<span style="color: #AA22FF; font-weight: bold">for</span>(i<span style="color: #666666">=1</span>; i<span style="color: #666666"><=</span>NatmB; i<span style="color: #666666">++</span>) {
<span style="color: #AA22FF; font-weight: bold">getline</span> <span style="color: #666666"><</span> file
SatmB[i]<span style="color: #666666">=$1</span>; XatmB[i]<span style="color: #666666">=$2</span>; YatmB[i]<span style="color: #666666">=$3</span>; ZatmB[i]<span style="color: #666666">=$4</span>
}
<span style="color: #008800; font-style: italic"># 使Iatm置于原点</span>
x<span style="color: #666666">=</span>XatmB[Iatm]; y<span style="color: #666666">=</span>YatmB[Iatm]; z<span style="color: #666666">=</span>ZatmB[Iatm]
<span style="color: #AA22FF; font-weight: bold">for</span>(i<span style="color: #666666">=1</span>; i<span style="color: #666666"><=</span>NatmB; i<span style="color: #666666">++</span>) {
XatmB[i] <span style="color: #666666">-=</span> x; YatmB[i] <span style="color: #666666">-=</span> y; ZatmB[i] <span style="color: #666666">-=</span> z
}
<span style="color: #008800; font-style: italic"># 获取分子主轴, 归一化</span>
Vij[<span style="color: #666666">1</span>]<span style="color: #666666">=</span>XatmB[Jatm]
Vij[<span style="color: #666666">2</span>]<span style="color: #666666">=</span>YatmB[Jatm]
Vij[<span style="color: #666666">3</span>]<span style="color: #666666">=</span>ZatmB[Jatm]
UniVect(Vij)
<span style="color: #008800; font-style: italic"># 表面原子法向</span>
Vatm[<span style="color: #666666">1</span>]<span style="color: #666666">=0</span>; Vatm[<span style="color: #666666">2</span>]<span style="color: #666666">=0</span>; Vatm[<span style="color: #666666">3</span>]<span style="color: #666666">=0</span>
<span style="color: #AA22FF; font-weight: bold">if</span>(Norm<span style="color: #666666">==</span><span style="color: #BB4444">"X"</span>) Vatm[<span style="color: #666666">1</span>]<span style="color: #666666">=1</span>
<span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #AA22FF; font-weight: bold">if</span>(Norm<span style="color: #666666">==</span><span style="color: #BB4444">"Y"</span>) Vatm[<span style="color: #666666">2</span>]<span style="color: #666666">=1</span>
<span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #AA22FF; font-weight: bold">if</span>(Norm<span style="color: #666666">==</span><span style="color: #BB4444">"Z"</span>) Vatm[<span style="color: #666666">3</span>]<span style="color: #666666">=1</span>
}
{ NatmA<span style="color: #666666">=$1</span>
<span style="color: #AA22FF; font-weight: bold">getline</span>
Nsrf<span style="color: #666666">=0</span>; Xcom<span style="color: #666666">=0</span>; Ycom<span style="color: #666666">=0</span>; Zcom<span style="color: #666666">=0</span>
<span style="color: #AA22FF; font-weight: bold">for</span>(i<span style="color: #666666">=1</span>; i<span style="color: #666666"><=</span>NatmA; i<span style="color: #666666">++</span>) {
<span style="color: #AA22FF; font-weight: bold">getline</span>
SatmA[i]<span style="color: #666666">=$1</span>; XatmA[i]<span style="color: #666666">=$2</span>; YatmA[i]<span style="color: #666666">=$3</span>; ZatmA[i]<span style="color: #666666">=$4</span>
Xcom <span style="color: #666666">+=</span> <span style="color: #666666">$2</span>; Ycom <span style="color: #666666">+=</span> <span style="color: #666666">$3</span>; Zcom <span style="color: #666666">+=</span> <span style="color: #666666">$4</span>
<span style="color: #AA22FF; font-weight: bold">if</span>(SatmA[i]<span style="color: #666666">==</span>Lsrf) { Nsrf<span style="color: #666666">++</span>; Isrf[Nsrf]<span style="color: #666666">=</span>i }
}
Xcom <span style="color: #666666">/=</span> NatmA; Ycom <span style="color: #666666">/=</span> NatmA; Zcom <span style="color: #666666">/=</span> NatmA
<span style="color: #008800; font-style: italic"># 随机混洗</span>
FisherYates(Isrf, Nsrf)
<span style="color: #AA22FF; font-weight: bold">if</span>(<span style="color: #AA22FF; font-weight: bold">index</span>(Napd, <span style="color: #BB4444">"%"</span>)) { <span style="color: #AA22FF; font-weight: bold">sub</span>(<span style="color: #BB4444">"%"</span>,<span style="color: #BB4444">""</span>,Napd); Napd<span style="color: #666666">=</span><span style="color: #AA22FF; font-weight: bold">int</span>(Nsrf<span style="color: #666666">*</span>Napd<span style="color: #666666">/100</span>) }
<span style="color: #AA22FF; font-weight: bold">if</span>(Napd<span style="color: #666666">></span>Nsrf) Napd<span style="color: #666666">=</span>Nsrf
<span style="color: #AA22FF; font-weight: bold">print</span> NatmA<span style="color: #666666">+</span>(NatmB<span style="color: #666666">-1</span>)<span style="color: #666666">*</span>Napd
<span style="color: #AA22FF; font-weight: bold">print</span> Napd<span style="color: #BB4444">"/"</span>Nsrf <span style="color: #BB4444">" Surface Atoms Appended with Another Molecule"</span>
<span style="color: #AA22FF; font-weight: bold">for</span>(i<span style="color: #666666">=1</span>; i<span style="color: #666666"><=</span>NatmA; i<span style="color: #666666">++</span>)
<span style="color: #AA22FF; font-weight: bold">printf</span><span style="color: #BB4444">"%4s %15.9f %15.9f %15.9f\n"</span>, SatmA[i], XatmA[i], YatmA[i], ZatmA[i]
<span style="color: #AA22FF; font-weight: bold">for</span>(i<span style="color: #666666">=1</span>; i<span style="color: #666666"><=</span>Napd; i<span style="color: #666666">++</span>) {
Itmp<span style="color: #666666">=</span>Isrf[i]
<span style="color: #AA22FF; font-weight: bold">if</span>(Norm<span style="color: #666666">==</span><span style="color: #BB4444">"COG"</span>) { <span style="color: #008800; font-style: italic"># 待转至的轴, 相对于分子几何中心的径向</span>
Vatm[<span style="color: #666666">1</span>]<span style="color: #666666">=</span>XatmA[Itmp]<span style="color: #666666">-</span>Xcom
Vatm[<span style="color: #666666">2</span>]<span style="color: #666666">=</span>YatmA[Itmp]<span style="color: #666666">-</span>Ycom
Vatm[<span style="color: #666666">3</span>]<span style="color: #666666">=</span>ZatmA[Itmp]<span style="color: #666666">-</span>Zcom
}
UniVect(Vatm)
<span style="color: #008800; font-style: italic"># 绕两轴中线旋转180度</span>
x<span style="color: #666666">=</span>(Vatm[<span style="color: #666666">1</span>]<span style="color: #666666">+</span>Vij[<span style="color: #666666">1</span>])<span style="color: #666666">/2</span>
y<span style="color: #666666">=</span>(Vatm[<span style="color: #666666">2</span>]<span style="color: #666666">+</span>Vij[<span style="color: #666666">2</span>])<span style="color: #666666">/2</span>
z<span style="color: #666666">=</span>(Vatm[<span style="color: #666666">3</span>]<span style="color: #666666">+</span>Vij[<span style="color: #666666">3</span>])<span style="color: #666666">/2</span>
AxiRotMat(Pi, x, y, z)
<span style="color: #008800; font-style: italic"># 追加分子</span>
<span style="color: #AA22FF; font-weight: bold">for</span>(j<span style="color: #666666">=2</span>; j<span style="color: #666666"><=</span>NatmB; j<span style="color: #666666">++</span>) {
V[<span style="color: #666666">1</span>] <span style="color: #666666">=</span> XatmB[j]
V[<span style="color: #666666">2</span>] <span style="color: #666666">=</span> YatmB[j]
V[<span style="color: #666666">3</span>] <span style="color: #666666">=</span> ZatmB[j]
RotVect(RotMat, V)
<span style="color: #AA22FF; font-weight: bold">printf</span><span style="color: #BB4444">"%4s %15.9f %15.9f %15.9f #%iMolB\n"</span>, SatmB[j], <span style="border: 1px solid #FF0000">\</span>
V[<span style="color: #666666">1</span>]<span style="color: #666666">+</span>XatmA[Itmp], V[<span style="color: #666666">2</span>]<span style="color: #666666">+</span>YatmA[Itmp], V[<span style="color: #666666">3</span>]<span style="color: #666666">+</span>ZatmA[Itmp], i
}
}
}
<span style="color: #AA22FF; font-weight: bold">function</span> Acos(x) { <span style="color: #AA22FF; font-weight: bold">return</span> <span style="color: #AA22FF; font-weight: bold">atan2</span>(<span style="color: #AA22FF; font-weight: bold">sqrt</span>(<span style="color: #666666">1-</span>x<span style="color: #666666">*</span>x),x) }
<span style="color: #AA22FF; font-weight: bold">function</span> Dot(A, B) { <span style="color: #AA22FF; font-weight: bold">return</span> A[<span style="color: #666666">1</span>]<span style="color: #666666">*</span>B[<span style="color: #666666">1</span>]<span style="color: #666666">+</span>A[<span style="color: #666666">2</span>]<span style="color: #666666">*</span>B[<span style="color: #666666">2</span>]<span style="color: #666666">+</span>A[<span style="color: #666666">3</span>]<span style="color: #666666">*</span>B[<span style="color: #666666">3</span>] }
<span style="color: #AA22FF; font-weight: bold">function</span> VectAng(A, B) { <span style="color: #AA22FF; font-weight: bold">return</span> Acos(Dot(A, B)<span style="color: #666666">/</span><span style="color: #AA22FF; font-weight: bold">sqrt</span>(Dot(A, A)<span style="color: #666666">*</span>Dot(B, B))) }
<span style="color: #AA22FF; font-weight: bold">function</span> UniVect(V, Rtmp) {
Rtmp<span style="color: #666666">=</span>Dot(V, V)
<span style="color: #AA22FF; font-weight: bold">if</span> (Rtmp<span style="color: #666666">!=0</span>) {
Rtmp<span style="color: #666666">=1/</span><span style="color: #AA22FF; font-weight: bold">sqrt</span>(Rtmp)
V[<span style="color: #666666">1</span>] <span style="color: #666666">*=</span> Rtmp; V[<span style="color: #666666">2</span>] <span style="color: #666666">*=</span> Rtmp; V[<span style="color: #666666">3</span>] <span style="color: #666666">*=</span> Rtmp
}
}
<span style="color: #AA22FF; font-weight: bold">function</span> RotVect(RotMat, V, Vx,Vy,Vz) { <span style="color: #008800; font-style: italic"># 按照矩阵RotMat旋转矢量V</span>
Vx <span style="color: #666666">=</span> V[<span style="color: #666666">1</span>]; Vy <span style="color: #666666">=</span> V[<span style="color: #666666">2</span>]; Vz <span style="color: #666666">=</span> V[<span style="color: #666666">3</span>]
V[<span style="color: #666666">1</span>]<span style="color: #666666">=</span> RotMat[<span style="color: #666666">1</span>,<span style="color: #666666">1</span>]<span style="color: #666666">*</span>Vx <span style="color: #666666">+</span> RotMat[<span style="color: #666666">1</span>,<span style="color: #666666">2</span>]<span style="color: #666666">*</span>Vy <span style="color: #666666">+</span> RotMat[<span style="color: #666666">1</span>,<span style="color: #666666">3</span>]<span style="color: #666666">*</span>Vz
V[<span style="color: #666666">2</span>]<span style="color: #666666">=</span> RotMat[<span style="color: #666666">2</span>,<span style="color: #666666">1</span>]<span style="color: #666666">*</span>Vx <span style="color: #666666">+</span> RotMat[<span style="color: #666666">2</span>,<span style="color: #666666">2</span>]<span style="color: #666666">*</span>Vy <span style="color: #666666">+</span> RotMat[<span style="color: #666666">2</span>,<span style="color: #666666">3</span>]<span style="color: #666666">*</span>Vz
V[<span style="color: #666666">3</span>]<span style="color: #666666">=</span> RotMat[<span style="color: #666666">3</span>,<span style="color: #666666">1</span>]<span style="color: #666666">*</span>Vx <span style="color: #666666">+</span> RotMat[<span style="color: #666666">3</span>,<span style="color: #666666">2</span>]<span style="color: #666666">*</span>Vy <span style="color: #666666">+</span> RotMat[<span style="color: #666666">3</span>,<span style="color: #666666">3</span>]<span style="color: #666666">*</span>Vz
}
<span style="color: #AA22FF; font-weight: bold">function</span> AxiRotMat(tht, x, y, z, Rtmp, w) { <span style="color: #008800; font-style: italic"># 绕矢量(x,y,z)旋转tht弧度, 四元数方法</span>
Rtmp<span style="color: #666666">=</span>x<span style="color: #666666">*</span>x<span style="color: #666666">+</span>y<span style="color: #666666">*</span>y<span style="color: #666666">+</span>z<span style="color: #666666">*</span>z
<span style="color: #AA22FF; font-weight: bold">if</span>(Rtmp<span style="color: #666666">>1</span>E<span style="color: #666666">-6</span>) { Rtmp<span style="color: #666666">=1/</span><span style="color: #AA22FF; font-weight: bold">sqrt</span>(Rtmp); x <span style="color: #666666">*=</span> Rtmp; y <span style="color: #666666">*=</span> Rtmp; z <span style="color: #666666">*=</span> Rtmp }
Rtmp<span style="color: #666666">=</span><span style="color: #AA22FF; font-weight: bold">sin</span>(tht<span style="color: #666666">/2</span>); w<span style="color: #666666">=</span><span style="color: #AA22FF; font-weight: bold">cos</span>(tht<span style="color: #666666">/2</span>); x <span style="color: #666666">*=</span> Rtmp; y <span style="color: #666666">*=</span> Rtmp; z <span style="color: #666666">*=</span> Rtmp
RotMat[<span style="color: #666666">1</span>,<span style="color: #666666">1</span>]<span style="color: #666666">=1-2*</span>(y<span style="color: #666666">*</span>y<span style="color: #666666">+</span>z<span style="color: #666666">*</span>z); RotMat[<span style="color: #666666">1</span>,<span style="color: #666666">2</span>]<span style="color: #666666">=</span> <span style="color: #666666">2*</span>(x<span style="color: #666666">*</span>y<span style="color: #666666">-</span>w<span style="color: #666666">*</span>z); RotMat[<span style="color: #666666">1</span>,<span style="color: #666666">3</span>]<span style="color: #666666">=</span> <span style="color: #666666">2*</span>(x<span style="color: #666666">*</span>z<span style="color: #666666">+</span>w<span style="color: #666666">*</span>y)
RotMat[<span style="color: #666666">2</span>,<span style="color: #666666">1</span>]<span style="color: #666666">=</span> <span style="color: #666666">2*</span>(x<span style="color: #666666">*</span>y<span style="color: #666666">+</span>w<span style="color: #666666">*</span>z); RotMat[<span style="color: #666666">2</span>,<span style="color: #666666">2</span>]<span style="color: #666666">=1-2*</span>(x<span style="color: #666666">*</span>x<span style="color: #666666">+</span>z<span style="color: #666666">*</span>z); RotMat[<span style="color: #666666">2</span>,<span style="color: #666666">3</span>]<span style="color: #666666">=</span> <span style="color: #666666">2*</span>(y<span style="color: #666666">*</span>z<span style="color: #666666">-</span>w<span style="color: #666666">*</span>x)
RotMat[<span style="color: #666666">3</span>,<span style="color: #666666">1</span>]<span style="color: #666666">=</span> <span style="color: #666666">2*</span>(x<span style="color: #666666">*</span>z<span style="color: #666666">-</span>w<span style="color: #666666">*</span>y); RotMat[<span style="color: #666666">3</span>,<span style="color: #666666">2</span>]<span style="color: #666666">=</span> <span style="color: #666666">2*</span>(y<span style="color: #666666">*</span>z<span style="color: #666666">+</span>w<span style="color: #666666">*</span>x); RotMat[<span style="color: #666666">3</span>,<span style="color: #666666">3</span>]<span style="color: #666666">=1-2*</span>(x<span style="color: #666666">*</span>x<span style="color: #666666">+</span>y<span style="color: #666666">*</span>y)
}
<span style="color: #AA22FF; font-weight: bold">function</span> FisherYates(arr, len, i,j,tmp) {
<span style="color: #AA22FF; font-weight: bold">srand</span>()
<span style="color: #AA22FF; font-weight: bold">for</span>(i<span style="color: #666666">=</span>len; i<span style="color: #666666">>1</span>; i<span style="color: #666666">--</span>) {
j <span style="color: #666666">=</span> <span style="color: #AA22FF; font-weight: bold">int</span>(<span style="color: #AA22FF; font-weight: bold">rand</span>()<span style="color: #666666">*</span>i)<span style="color: #666666">+1</span>
tmp <span style="color: #666666">=</span> arr[i]
arr[i] <span style="color: #666666">=</span> arr[j]
arr[j] <span style="color: #666666">=</span> tmp
}
}
<span style="color: #BB4444">'</span> <span style="color: #666666">$</span>MolA <span style="color: #666666">></span> <span style="color: #666666">$</span>{MolA<span style="color: #666666">%</span>.<span style="color: #666666">*</span>}<span style="color: #666666">+$</span>{MolB<span style="color: #666666">%</span>.<span style="color: #666666">*</span>}.xyz
</pre></div>
</td></tr></table>使用bash apdMol.bsh HCP.xyz C9.xyz 1 23运行脚本, 会得到HCP+C9.xyz文件. 默认修饰了50%的表面原子.
<figure><script>var Mol2=new ChemDoodle.MovieCanvas3D('Mol-2',650,400);Mol2.specs.shapes_color = '#fff';Mol2.specs.backgroundColor = 'black';Mol2.specs.set3DRepresentation('Ball and Stick');Mol2.specs.projectionPerspective_3D = false;Mol2.specs.proteins_ribbonCartoonize = true;
/*Mol2.timeout = 15;
//Mol2.specs.atoms_resolution_3D = 15;
//Mol2.specs.bonds_resolution_3D = 15;
//Mol2.specs.crystals_unitCellLineWidth = 1.5;*/
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-5.196152000 4.898979000\nS -12.000000000 -3.464102000 7.348469000\nS -13.500000000 -2.598076000 -4.898979000\nC -13.500000000 -0.866025000 -2.449490000\nC -13.500000000 -2.598076000 0.000000000\nC -13.500000000 -0.866025000 2.449490000\nS -13.500000000 -2.598076000 4.898979000\nS -15.000000000 0.000000000 0.000000000\nC -4.500000000 -11.258330000 -7.348469000\nS -4.500000000 -12.990381000 -4.898979000\nC -4.500000000 -11.258330000 -2.449490000\nC -4.500000000 -12.990381000 0.000000000\nC -4.500000000 -11.258330000 2.449490000\nS -4.500000000 -12.990381000 4.898979000\nC -4.500000000 -11.258330000 7.348469000\nC -6.000000000 -8.660254000 -7.348469000\nC -6.000000000 -10.392305000 -4.898979000\nC -6.000000000 -8.660254000 -2.449490000\nC -6.000000000 -10.392305000 0.000000000\nC -6.000000000 -8.660254000 2.449490000\nC -6.000000000 -10.392305000 4.898979000\nC -6.000000000 -8.660254000 7.348469000\nS -7.500000000 -7.794229000 -9.797959000\nC -7.500000000 -6.062178000 -7.348469000\nC 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#5MolB\nC 9.083726908 6.218946853 15.238151587 #5MolB\nH 8.257293425 4.269972314 14.872721318 #5MolB\nH 9.657300427 4.642715793 13.895936107 #5MolB\nC 10.004817211 5.738973736 16.375173344 #5MolB\nH 9.578842084 6.983524909 14.676741443 #5MolB\nH 8.178835082 6.610781430 15.653526654 #5MolB\nH 9.509702035 4.974395680 16.936583488 #5MolB\nH 10.909709037 5.347139160 15.959798277 #5MolB\nC 10.336135509 6.923370223 17.302013761 #5MolB\nC 11.257225817 6.443397115 18.439035519 #5MolB\nH 9.431243684 7.315204799 17.717388828 #5MolB\nH 10.831250686 7.687948279 16.740603617 #5MolB\nC 11.588544119 7.627793589 19.365875931 #5MolB\nH 10.762110637 5.678819050 19.000445662 #5MolB\nH 12.162117643 6.051562539 18.023660452 #5MolB\nH 12.083659296 8.392371645 18.804465787 #5MolB\nH 10.683652294 8.019628166 19.781250998 #5MolB\nC 12.509634427 7.147820482 20.502897689 #5MolB\nO 12.433579800 5.961579196 20.915956855 #5MolB\nO 13.451358269 8.050132626 21.089318180 #5MolB\nH 14.215651798 7.558495096 21.398749829 #5MolB\nC 10.785902769 3.011550741 -11.253602580 #6MolB\nC 12.306834792 3.022097380 -11.494962408 #6MolB\nH 10.389844939 3.989609996 -11.430911031 #6MolB\nH 10.323855873 2.313448013 -11.919984799 #6MolB\nC 12.592737563 3.435572109 -12.950605996 #6MolB\nH 12.768881689 3.720200097 -10.828580196 #6MolB\nH 12.702892622 2.044038125 -11.317653956 #6MolB\nC 14.113669587 3.446118751 -13.191965814 #6MolB\nH 12.130690665 2.737469393 -13.616988207 #6MolB\nH 12.196679733 4.413631364 -13.127914448 #6MolB\nH 14.575716485 4.144221468 -12.525583603 #6MolB\nH 14.509727417 2.468059496 -13.014657362 #6MolB\nC 14.399572355 3.859593489 -14.647609403 #6MolB\nC 15.920504378 3.870140129 -14.888969232 #6MolB\nH 14.003514525 4.837652744 -14.824917855 #6MolB\nH 13.937525457 3.161490773 -15.313991615 #6MolB\nC 16.206407150 4.283614860 -16.344612810 #6MolB\nH 16.382551277 4.568242848 -14.222587010 #6MolB\nH 16.316562208 2.892080874 -14.711660780 #6MolB\nH 15.744360253 3.585512144 -17.010995022 #6MolB\nH 15.810349321 5.261674115 -16.521921262 #6MolB\nC 17.727339173 4.294161500 -16.585972638 #6MolB\nO 18.513033286 4.554701164 -15.638146486 #6MolB\nO 18.246798962 4.007887011 -17.887167642 #6MolB\nH 19.112191483 3.600769341 -17.803795023 #6MolB\nC 13.484934805 -8.681358433 2.857072156 #7MolB\nC 13.996058971 -10.134061895 2.859252777 #7MolB\nH 13.591909486 -8.264150166 3.836558591 #7MolB\nH 14.054568830 -8.103884272 2.159260801 #7MolB\nC 15.480993785 -10.155166329 3.266834921 #7MolB\nH 13.426424955 -10.711536057 3.557064120 #7MolB\nH 13.889084290 -10.551270162 1.879766341 #7MolB\nC 15.992117942 -11.607869794 3.269015545 #7MolB\nH 16.050627801 -9.577692167 2.569023578 #7MolB\nH 15.587968466 -9.737958061 4.246321357 #7MolB\nH 15.422483926 -12.185343956 3.966826888 #7MolB\nH 15.885143261 -12.025078061 2.289529109 #7MolB\nC 17.477052756 -11.628974224 3.676597698 #7MolB\nC 17.988176923 -13.081677686 3.678778319 #7MolB\nH 17.584027437 -11.211765957 4.656084133 #7MolB\nH 18.046686773 -11.051500062 2.978786355 #7MolB\nC 19.473111727 -13.102782122 4.086360466 #7MolB\nH 17.418542897 -13.659151851 4.376589664 #7MolB\nH 17.881202241 -13.498885953 2.699291884 #7MolB\nH 20.042745743 -12.525307961 3.388549123 #7MolB\nH 19.580086408 -12.685573855 5.065846901 #7MolB\nC 19.984235893 -14.555485584 4.088541087 #7MolB\nO 19.194276837 -15.500048147 4.348034487 #7MolB\nO 21.356531925 -14.831057954 3.795687089 #7MolB\nH 21.428640282 -15.695533770 3.384491328 #7MolB\nC 9.321681270 -5.263645245 -11.302474140 #8MolB\nC 10.571294025 -6.136607880 -11.521572787 #8MolB\nH 9.506712166 -4.276771531 -11.672263049 #8MolB\nH 8.491918763 -5.690874664 -11.825799300 #8MolB\nC 10.892975289 -6.204101137 -13.026087933 #8MolB\nH 11.401056526 -5.709378473 -10.998247634 #8MolB\nH 10.386263129 -7.123481594 -11.151783878 #8MolB\nC 12.142588048 -7.077063769 -13.245186571 #8MolB\nH 10.063212788 -6.631330544 -13.549413087 #8MolB\nH 11.078006186 -5.217227423 -13.395876842 #8MolB\nH 12.972350550 -6.649834363 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#52MolB\nC 1.419239675 -2.537889168 18.571210659 #52MolB\nH 1.291431419 -4.020119823 17.021471754 #52MolB\nH 2.800134479 -3.138889812 17.039231189 #52MolB\nC 1.979549889 -3.518267086 19.618355166 #52MolB\nH 1.867583196 -1.575940888 18.707385488 #52MolB\nH 0.358880135 -2.457170899 18.689626053 #52MolB\nH 1.531206368 -4.480215366 19.482180336 #52MolB\nH 3.039909429 -3.598985355 19.499939771 #52MolB\nC 1.659014615 -2.997984711 21.031919242 #52MolB\nC 2.219324830 -3.978362622 22.079063756 #52MolB\nH 0.598655075 -2.917266442 21.150334636 #52MolB\nH 2.107358136 -2.036036431 21.168094072 #52MolB\nC 1.898789564 -3.458080254 23.492627824 #52MolB\nH 1.770981308 -4.940310909 21.942888919 #52MolB\nH 3.279684370 -4.059080891 21.960648361 #52MolB\nH 2.347133085 -2.496131974 23.628802654 #52MolB\nH 0.838430025 -3.377361985 23.611043218 #52MolB\nC 2.459099780 -4.438458165 24.539772338 #52MolB\nO 2.547296859 -5.664454444 24.270096667 #52MolB\nO 2.879163876 -3.955631488 25.818570425 #52MolB\nH 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-15.371985054 -6.824379477 #53MolB\nH -14.747527532 -15.737820780 -9.246118468 #53MolB\nH -13.423384217 -16.877867147 -9.243790738 #53MolB\nC -15.186957700 -17.585169672 -8.241510815 #53MolB\nO -15.001759277 -18.203009774 -7.160980518 #53MolB\nO -16.295320655 -17.925187404 -9.078660440 #53MolB\nH -17.017788551 -18.250503960 -8.536618668 #53MolB\nC -5.550662900 -6.002349604 13.371783478 #54MolB\nC -5.293736446 -7.141613051 14.375609963 #54MolB\nH -6.528875672 -6.110744461 12.951961699 #54MolB\nH -5.480969998 -5.060819508 13.875334860 #54MolB\nC -6.344399341 -7.081784649 15.499944453 #54MolB\nH -5.363429343 -8.083143140 13.872058593 #54MolB\nH -4.315523675 -7.033218194 14.795431742 #54MolB\nC -6.087472883 -8.221048102 16.503770931 #54MolB\nH -6.274706444 -6.140254560 16.003495823 #54MolB\nH -7.322612113 -7.190179506 15.080122674 #54MolB\nH -6.157165780 -9.162578191 16.000219561 #54MolB\nH -5.109260112 -8.112653244 16.923592710 #54MolB\nC -7.138135787 -8.161219700 17.628105416 #54MolB\nC -6.881209334 -9.300483148 18.631931901 #54MolB\nH -8.116348559 -8.269614557 17.208283637 #54MolB\nH -7.068442890 -7.219689611 18.131656786 #54MolB\nC -7.931872225 -9.240654750 19.756266384 #54MolB\nH -6.950902227 -10.242013242 18.128380524 #54MolB\nH -5.902996562 -9.192088291 19.051753680 #54MolB\nH -7.862179328 -8.299124661 20.259817754 #54MolB\nH -8.910084996 -9.349049608 19.336444605 #54MolB\nC -7.674945771 -10.379918198 20.760092869 #54MolB\nO -7.158130483 -11.458555346 20.368922279 #54MolB\nO -8.023661308 -10.212081646 22.136729480 #54MolB\nH -7.428205567 -10.730221594 22.683139090 #54MolB\nC 11.421765041 -1.973613430 10.861911862 #55MolB\nC 12.300195532 -3.072277622 11.488726734 #55MolB\nH 10.827149610 -1.514418703 11.623799445 #55MolB\nH 12.046489566 -1.235570737 10.403750027 #55MolB\nC 13.221960586 -2.447815049 12.552679591 #55MolB\nH 11.675471020 -3.810320312 11.946888564 #55MolB\nH 12.894810963 -3.531472348 10.726839151 #55MolB\nC 14.100391070 -3.546479247 13.179494461 #55MolB\nH 13.846685098 -1.709772359 12.094517761 #55MolB\nH 12.627345155 -1.988620322 13.314567174 #55MolB\nH 13.475666558 -4.284521937 13.637656291 #55MolB\nH 14.695006501 -4.005673974 12.417606878 #55MolB\nC 15.022156118 -2.922016670 14.243447325 #55MolB\nC 15.900586609 -4.020680862 14.870262197 #55MolB\nH 14.427540687 -2.462821944 15.005334908 #55MolB\nH 15.646880631 -2.183973980 13.785285495 #55MolB\nC 16.822351656 -3.396218296 15.934215052 #55MolB\nH 15.275862090 -4.758723559 15.328424025 #55MolB\nH 16.495202041 -4.479875588 14.108374614 #55MolB\nH 17.447076168 -2.658175606 15.476053222 #55MolB\nH 16.227736225 -2.937023569 16.696102635 #55MolB\nC 17.700782147 -4.494882487 16.561029924 #55MolB\nO 17.270586267 -5.674702547 16.641817929 #55MolB\nO 19.005326543 -4.174366047 17.051267748 #55MolB\nH 19.576160349 -4.941634598 16.967316916 #55MolB\nC 14.386835737 5.319149980 -3.228563748 #56MolB\nC 15.865620802 5.066334482 -2.880887066 #56MolB\nH 14.123793938 6.321190762 -2.960938485 #56MolB\nH 14.238588090 5.179945018 -4.279061072 #56MolB\nC 16.752456544 6.055357456 -3.659960826 #56MolB\nH 16.013868455 5.205539439 -1.830389753 #56MolB\nH 16.128662601 4.064293700 -3.148512329 #56MolB\nC 18.231241606 5.802541955 -3.312284135 #56MolB\nH 16.604208891 5.916152500 -4.710458138 #56MolB\nH 16.489414745 7.057398238 -3.392335563 #56MolB\nH 18.379489259 5.941746911 -2.261786822 #56MolB\nH 18.494283405 4.800501173 -3.579909397 #56MolB\nC 19.118077346 6.791564938 -4.091357892 #56MolB\nC 20.596862410 6.538749440 -3.743681210 #56MolB\nH 18.855035547 7.793605720 -3.823732629 #56MolB\nH 18.969829693 6.652359982 -5.141855205 #56MolB\nC 21.483698150 7.527772411 -4.522754961 #56MolB\nH 20.745110060 6.677954393 -2.693183888 #56MolB\nH 20.859904209 5.536708658 -4.011306473 #56MolB\nH 21.335450497 7.388567454 -5.573252273 #56MolB\nH 21.220656351 8.529813193 -4.255129698 #56MolB\nC 22.962483214 7.274956913 -4.175078279 #56MolB\nO 23.274820661 6.829888455 -3.040208261 #56MolB\nO 23.980711841 7.545959277 -5.141860662 #56MolB\nH 24.719810238 6.949006659 -5.004088612 #56MolB\nC 4.040129078 -6.716343591 -13.563574412 #57MolB\nC 5.272393173 -7.144776653 -14.381847184 #57MolB\nH 3.463446193 -6.014047416 -14.128478768 #57MolB\nH 3.441107772 -7.575479919 -13.344580665 #57MolB\nC 4.812522250 -7.798942258 -15.697972594 #57MolB\nH 5.871414478 -6.285640339 -14.600840929 #57MolB\nH 5.849076057 -7.847072828 -13.816942828 #57MolB\nC 6.044786350 -8.227375312 -16.516245362 #57MolB\nH 4.213500945 -8.658078571 -15.478978849 #57MolB\nH 4.235839366 -7.096646083 -16.262876950 #57MolB\nH 6.643807656 -7.368238999 -16.735239108 #57MolB\nH 6.621469235 -8.929671487 -15.951341006 #57MolB\nC 5.584915423 -8.881540910 -17.832370778 #57MolB\nC 6.817179517 -9.309973973 -18.650643550 #57MolB\nH 5.008232538 -8.179244736 -18.397275134 #57MolB\nH 4.985894117 -9.740677224 -17.613377033 #57MolB\nC 6.357308600 -9.964139570 -19.966768956 #57MolB\nH 7.416200828 -8.450837651 -18.869637291 #57MolB\nH 7.393862402 -10.012270147 -18.085739194 #57MolB\nH 5.758287295 -10.823275884 -19.747775211 #57MolB\nH 5.780625716 -9.261843395 -20.531673312 #57MolB\nC 7.589572695 -10.392572632 -20.785041728 #57MolB\nO 8.665942443 -9.748281862 -20.685602603 #57MolB\nO 7.510670477 -11.522551924 -21.657865441 #57MolB\nH 8.372888005 -11.940149937 -21.719451476 #57MolB\nC -2.173179219 -2.126944164 15.999421979 #58MolB\nC -1.762278370 -3.057756620 17.155427464 #58MolB\nH -3.236297795 -2.153081723 15.881118474 #58MolB\nH -1.863285095 -1.126728426 16.219499524 #58MolB\nC -2.435457581 -2.586624775 18.457911451 #58MolB\nH -2.072172486 -4.057972349 16.935349927 #58MolB\nH -0.699159794 -3.031619060 17.273730970 #58MolB\nC -2.024556731 -3.517437239 19.613916930 #58MolB\nH -2.125563465 -1.586409046 18.677988989 #58MolB\nH -3.498576157 -2.612762335 18.339607946 #58MolB\nH -2.334450846 -4.517652968 19.393839393 #58MolB\nH -0.961438155 -3.491299679 19.732220435 #58MolB\nC -2.697735951 -3.046305395 20.916400916 #58MolB\nC -2.286835102 -3.977117851 22.072406401 #58MolB\nH -3.760854527 -3.072442955 20.798097411 #58MolB\nH -2.387841835 -2.046089666 21.136478453 #58MolB\nC -2.960014311 -3.505986014 23.374890382 #58MolB\nH -2.596729216 -4.977333588 21.852328857 #58MolB\nH -1.223716526 -3.950980291 22.190709906 #58MolB\nH -2.650120196 -2.505770285 23.594967919 #58MolB\nH -4.023132887 -3.532123574 23.256586876 #58MolB\nC -2.549113462 -4.436798470 24.530895867 #58MolB\nO -2.282788628 -5.645111779 24.301504064 #58MolB\nO -2.470204535 -3.928041013 25.865002019 #58MolB\nH -1.801799935 -4.413827145 26.353721908 #58MolB\nC -11.693385875 10.268584377 1.819876734 #59MolB\nC -12.353471022 11.170769431 2.879098027 #59MolB\nH -12.407814359 9.556754692 1.462398849 #59MolB\nH -11.349497513 10.869328857 1.003943600 #59MolB\nC -13.546856894 11.913074821 2.249484757 #59MolB\nH -12.697359380 10.570024964 3.695031158 #59MolB\nH -11.639042538 11.882599116 3.236575912 #59MolB\nC -14.206942037 12.815259868 3.308706057 #59MolB\nH -13.202968535 12.513819287 1.433551627 #59MolB\nH -14.261285377 11.201245135 1.892006872 #59MolB\nH -14.550830396 12.214515402 4.124639188 #59MolB\nH -13.492513554 13.527089554 3.666183942 #59MolB\nC -15.400327916 13.557565252 2.679092784 #59MolB\nC -16.060413062 14.459750305 3.738314077 #59MolB\nH -16.114756399 12.845735566 2.321614899 #59MolB\nH -15.056439557 14.158309718 1.863159654 #59MolB\nC -17.253798931 15.202055689 3.108700814 #59MolB\nH -16.404301418 13.859005832 4.554247215 #59MolB\nH -15.345984579 15.171579991 4.095791962 #59MolB\nH -16.909910572 15.802800156 2.292767684 #59MolB\nH -17.968227414 14.490226003 2.751222929 #59MolB\nC -17.913884077 16.104240742 4.167922107 #59MolB\nO -17.880901605 15.776476663 5.382439885 #59MolB\nO -18.564300360 17.314443173 3.771350892 #59MolB\nH -18.502889589 17.958096887 4.480955444 #59MolB\nC 1.118406530 16.125996802 1.943533227 #60MolB\nC 1.742583160 17.190885015 2.864411418 #60MolB\nH 0.053461931 16.229746139 1.948925281 #60MolB\nH 1.484536853 16.257561735 0.946768827 #60MolB\nC 1.360989700 18.594449823 2.358454638 #60MolB\nH 1.376452847 17.059320087 3.861175811 #60MolB\nH 2.807527759 17.087135678 2.859019364 #60MolB\nC 1.985166331 19.659338030 3.279332837 #60MolB\nH 1.727120014 18.726014751 1.361690245 #60MolB\nH 0.296045101 18.698199160 2.363846692 #60MolB\nH 1.619036017 19.527773102 4.276097229 #60MolB\nH 3.050110929 19.555588693 3.273940782 #60MolB\nC 1.603572861 21.062902838 2.773376056 #60MolB\nC 2.227749491 22.127791052 3.694254248 #60MolB\nH 0.538628262 21.166652175 2.778768110 #60MolB\nH 1.969703174 21.194467766 1.776611664 #60MolB\nC 1.846156031 23.531355852 3.188297474 #60MolB\nH 1.861619178 21.996226117 4.691018648 #60MolB\nH 3.292694090 22.024041715 3.688862193 #60MolB\nH 2.212286344 23.662920781 2.191533082 #60MolB\nH 0.781211432 23.635105189 3.193689529 #60MolB\nC 2.470332662 24.596244066 4.109175666 #60MolB\nO 2.662360656 24.341026434 5.326369068 #60MolB\nO 2.831711609 25.875088858 3.581102520 #60MolB\nH 3.577941899 26.225233317 4.073178955 #60MolB\nC 2.817035594 8.239620152 13.033775309 #61MolB\nC 3.515573734 8.120086130 14.401019289 #61MolB\nH 1.773490452 8.424375449 13.181352457 #61MolB\nH 3.248108205 9.049097174 12.482573559 #61MolB\nC 3.332609339 9.431503290 15.187345597 #61MolB\nH 3.084501135 7.310609116 14.952221038 #61MolB\nH 4.559118877 7.935330833 14.253442142 #61MolB\nC 4.031147479 9.311969259 16.554589577 #61MolB\nH 3.763681939 10.240980305 14.636143848 #61MolB\nH 2.289064197 9.616258587 15.334922745 #61MolB\nH 3.600074879 8.502492245 17.105791326 #61MolB\nH 5.074692621 9.127213962 16.407012429 #61MolB\nC 3.848183074 10.623386421 17.340915886 #61MolB\nC 4.546721215 10.503852399 18.708159867 #61MolB\nH 2.804637932 10.808141717 17.488493034 #61MolB\nH 4.279255673 11.432863435 16.789714137 #61MolB\nC 4.363756818 11.815269549 19.494486174 #61MolB\nH 4.115648614 9.694375375 19.259361616 #61MolB\nH 5.590266357 10.319097102 18.560582719 #61MolB\nH 4.794829418 12.624746563 18.943284425 #61MolB\nH 3.320211676 12.000024846 19.642063322 #61MolB\nC 5.062294959 11.695735527 20.861730154 #61MolB\nO 5.158122942 10.573710419 21.423377039 #61MolB\nO 5.602042074 12.859768176 21.493078741 #61MolB\nH 6.358117713 12.611157737 22.029867791 #61MolB\nC 10.135004845 -10.720155191 5.886844496 #62MolB\nC 10.532213281 -12.200719682 5.739351218 #62MolB\nH 9.800947231 -10.538425695 6.886984435 #62MolB\nH 10.981687257 -10.100972819 5.675557725 #62MolB\nC 11.667218139 -12.528569872 6.727216707 #62MolB\nH 9.685530882 -12.819902053 5.950637983 #62MolB\nH 10.866270895 -12.382449178 4.739211278 #62MolB\nC 12.064426565 -14.009134365 6.579723426 #62MolB\nH 12.513900537 -11.909387500 6.515929942 #62MolB\nH 11.333160525 -12.346840375 7.727356647 #62MolB\nH 11.217744166 -14.628316736 6.791010191 #62MolB\nH 12.398484179 -14.190863861 5.579583487 #62MolB\nC 13.199431420 -14.336984554 7.567588925 #62MolB\nC 13.596639855 -15.817549044 7.420095647 #62MolB\nH 12.865373806 -14.155255057 8.567728864 #62MolB\nH 14.046113818 -13.717802182 7.356302160 #62MolB\nC 14.731644704 -16.145399237 8.407961133 #62MolB\nH 12.749957447 -16.436731418 7.631382409 #62MolB\nH 13.930697469 -15.999278541 6.419955707 #62MolB\nH 15.578327102 -15.526216865 8.196674368 #62MolB\nH 14.397587090 -15.963669740 9.408101073 #62MolB\nC 15.128853139 -17.625963727 8.260467855 #62MolB\nO 14.271198175 -18.474993302 7.903890638 #62MolB\nO 16.472297446 -18.035967262 8.528711195 #62MolB\nH 16.689810630 -18.795827136 7.983824975 #62MolB\n')],[]);Mol2.loadMolecule(Mol2.frames[0].mols[0]);Mol2.startAnimation();function setProj2(yesPers){Mol2.specs.projectionPerspective_3D = yesPers;Mol2.setupScene();Mol2.repaint()}function setModel2(model){Mol2.specs.set3DRepresentation(model);Mol2.setupScene();Mol2.repaint()}function setSpeed2(){Mol2.timeout=500-document.getElementById("spd2").value;Mol2.loadMolecule(Mol2.frames[0].mols[0]);Mol2.startAnimation()}</script><br><span class="meta">视图: <input type="radio" name="group2" onclick="setProj2(true)">投影<input type="radio" name="group2" onclick="setProj2(false)" checked="">正交 速度: <input type="range" id="spd2" min="1" max="500" onchange="setSpeed2()"/><br>模型: <input type="radio" name="model" onclick="setModel2('Ball and Stick')" checked="">球棍<input type="radio" name="model" onclick="setModel2('van der Waals Spheres')">范德华球<input type="radio" name="model" onclick="setModel2('Stick')">棍状<input type="radio" name="model" onclick="setModel2('Wireframe')">线框<input type="radio" name="model" onclick="setModel2('Line')">线型<input type="checkbox" onclick="Mol2.specs.atoms_displayLabels_3D=this.checked;Mol2.repaint()">名称<br>左键: 转动 滚轮: 缩放 双击: 开关自动旋转 Alt+左键: 移动</span><br><figurecaption>Fig.2</figurecaption></figure>将得到的构型稍加修改, 就可以用于模拟了.
代码下载
点击这里下载脚本及示例文件及代码.
网络资料
- 如何测试洗牌程序
- 等概率随机排列数组（洗牌算法）
- 洗牌算法汇总以及测试洗牌程序的正确性
评论
- 2016-03-10 08:19:06
刘小康 好厉害！！！
2016-03-11 15:21:43 Jerkwin 谢谢鼓励.
2016-03-11 21:27:51 赞 赞
2016-03-14 23:30:35 Jerkwin 谢.
2016-07-26 09:48:24 小和尚 老师您好，我需要对表面进行部分接枝，能否实现随机选取表面原子进行部分接枝？
2016-07-26 10:35:39 Jerkwin 可以, 只要指定相应的原子即可. 至于如何随机, 那要看你的定义.
2016-08-03 13:13:45 张蕴瀚 老师您好，我需要对一个金表面进行修饰巯基分子，但只需要一层金原子，这样是不是没了法向？这个脚本应该如何修改？
2016-08-04 10:35:09 Jerkwin 表面的话更简单, 手动做也不麻烦. 使用这个脚本的话, 你要修改法向的代码, 使其指向表面的法向.
2016-11-07 18:23:35 franklinly 这个很有用，谢谢李老师。