化学/化学信息学/化学信息学简介.html

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<div id="content">
<header>
<h1 class="title">化学信息学简介</h1>
</header><nav id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgheadline1">1. 化学信息学定义</a></li>
<li><a href="#orgheadline2">2. MDL</a></li>
<li><a href="#orgheadline3">3. 线性标记法</a></li>
<li><a href="#orgheadline4">4. WLN</a></li>
<li><a href="#orgheadline5">5. SMILES</a></li>
<li><a href="#orgheadline6">6. InChI</a></li>
<li><a href="#orgheadline7">7. SMARTS</a></li>
<li><a href="#orgheadline11">8. name</a>
<ul>
<li><a href="#orgheadline8">8.1. IUPAC name</a></li>
<li><a href="#orgheadline9">8.2. Trade name</a></li>
<li><a href="#orgheadline10">8.3. Common name</a></li>
</ul>
</li>
<li><a href="#orgheadline13">9. 子结构搜索</a>
<ul>
<li><a href="#orgheadline12">9.1. 预先建立索引</a></li>
</ul>
</li>
<li><a href="#orgheadline14">10. 参考资料</a></li>
</ul>
</div>
</nav>


<div class="outline-2">
<h2 id="orgheadline1">化学信息学定义</h2>
<div class="outline-text-2" id="text-1">
<p>
化学信息学(cheminformatics)，是计算机学科和化学的结合学科，其主要研究对化学物质的信息进行存储和检索这一过程。
</p>

<p>
化学信息学主要解决如下四个问题：
</p>
<ol class="org-ol">
<li>如何存储分子</li>
<li>如何精确找到这个分子</li>
<li>分子结构中子结构的查找</li>
<li>各分子的相似性搜索</li>
</ol>
</div>
</div>

<div class="outline-2">
<h2 id="orgheadline2">MDL</h2>
<div class="outline-text-2" id="text-2">
<p>
3D坐标表示法，各个原子，具体的x，y，z坐标信息都列入其中了。
</p>
</div>
</div>


<div class="outline-2">
<h2 id="orgheadline3">线性标记法</h2>
</div>
<div class="outline-2">
<h2 id="orgheadline4">WLN</h2>
<div class="outline-text-2" id="text-4">
<p>
Wiswesser Line Notation，魏氏线性标记法。由William J. Wisswesser于十九世纪50年代早期发明。
</p>
</div>
</div>

<div class="outline-2">
<h2 id="orgheadline5">SMILES</h2>
<div class="outline-text-2" id="text-5">
<p>
Simplified molecular input line entry specification，简化分子线性输入规范。这应该是目前应用最广最为大家熟知的线性标记法了。下面详细介绍一下这个线性标记法的规则，更多细节请参看 <a href="http://www.opensmiles.org/spec/open-smiles-3-input.html">这个网页</a> 。
</p>

<ol class="org-ol">
<li>原子：[Na] [Cl] ，然后原子的同位素表示如下[2H]，[13C]。</li>
<li>离子：[Na+] [Cl-] [Cu+2] 或者 [Cu++]也是可以的。</li>
<li>离子化合物： 点符号 “.” 表示两个原子之间不成键，比如氯化钠 <code>[Na+].[Cl-]</code> 。</li>
<li>单质：氢气 <code>[H][H]</code> , 氧气  <code>[O]=[O]</code> ，氮气 <code>[N]#[N]</code> ，这里各个原子外面默认用单键连接，然后 = 表示双键， # 表示三键。</li>
<li>上面的氧气和氮气可以简写为 O=O 和 N#N ，但是氢气不行。因为氢原子比较特殊，其是会自动加上的，这是符合我们日常有机化学各个结构式的表达风格，比如双氧水 表达为 <code>OO</code> 即可。关于如何加氢的规则我觉得就不用多说了，学过有机化学的应该是清楚的。这里值得一提的就是方括号里面是不自动加氢的，于是有[H]就是一个氢原子，而[OH2]就是两个氢原子，这是水分子。</li>
<li>有机化合物：接着上面的讨论，一些基本的有机化合物表达式大家应该能猜出了，比如：CCCC 就是丁烷， CCO 就是乙醇。分支的处理：一是整个有机化合物顺序链根据有机化学中学习的IUPAC命名法来；二是圆括号表示分支子基团() 。比如异丁烷表示为 <code>CC(C)C</code> ，新戊烷表示为 <code>CC(C)(C)C</code> ，醋酸表示为 <code>CC(=O)O</code> ，比如那个双键。</li>

<li>环的表示： 比如环己烷 <code>C1CCCCC1</code> ,其核心理念就是后面相同编号的原子连键。比如化合物萘：</li>
</ol>


<figure>
<p><img src="images/Naphthalene.png" alt="Naphthalene.png">
</p>
</figure>

<p>
其SMILES表达就是：
</p>

<pre>
c1ccc2ccccc2c1
</pre>

<p>
这其中涉及到萘的具体IUPAC编号问题，按照顺时针从右上那个1开始，然后到4之后跳到5，再678，然后中间那两个碳必须跳一下，这个知识就比较冷门了。这里数字1或2可以互换，是任意的。
</p>

<p>
这个例子还涉及到一个知识点，那就是有芳香性的原子（也就是苯环上的C，或者其他杂环原子ONS等等）都要小写。这样苯你应该知道怎么写了： <code>c1ccccc1</code> 。
</p>

<ol class="org-ol">
<li>立体化学 在双键的两端 <code>/C=C/</code> 或者 <code>\C=C\</code> 表示反(trans)双键， 然后 <code>/C=C\</code> 或者 <code>\C=C/</code> 表示顺(cis)。</li>
</ol>

<p>
手性我还不是很熟悉，暂时略过。
</p>
</div>
</div>


<div class="outline-2">
<h2 id="orgheadline6">InChI</h2>
</div>


<div class="outline-2">
<h2 id="orgheadline7">SMARTS</h2>
</div>

<div class="outline-2">
<h2 id="orgheadline11">name</h2>
<div class="outline-text-2" id="text-8">
</div><div class="outline-3">
<h3 id="orgheadline8">IUPAC name</h3>
<div class="outline-text-3" id="text-8-1">
<p>
这个学习有机化学的应该都清楚什么是IUPAC命名法了。
</p>
</div>
</div>

<div class="outline-3">
<h3 id="orgheadline9">Trade name</h3>
<div class="outline-text-3" id="text-8-2">
<p>
商用名
</p>
</div>
</div>

<div class="outline-3">
<h3 id="orgheadline10">Common name</h3>
<div class="outline-text-3" id="text-8-3">
<p>
常用名，比如醋酸等，也叫俗名吧。
</p>
</div>
</div>
</div>

<div class="outline-2">
<h2 id="orgheadline13">子结构搜索</h2>
<div class="outline-text-2" id="text-9">
</div><div class="outline-3">
<h3 id="orgheadline12">预先建立索引</h3>
</div>
</div>


<div class="outline-2">
<h2 id="orgheadline14">参考资料</h2>
<div class="outline-text-2" id="text-10">
<ol class="org-ol">
<li>An introduction to the computer science and chemistry of chemical information systems ， 2009 by Craig A. James</li>
<li><a href="http://zh.wikipedia.org/zh/%E7%AE%80%E5%8C%96%E5%88%86%E5%AD%90%E7%BA%BF%E6%80%A7%E8%BE%93%E5%85%A5%E8%A7%84%E8%8C%83">维基百科SMILES</a></li>
<li><a href="http://www.opensmiles.org/spec/open-smiles.html">open smiles 官方文档</a></li>
</ol>
</div>
</div>
</div>
</body>
</html>