化学/化学信息学/小分子结构显示/小分子结构显示.html

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<script type="text/javascript">
  window.MathJax = {
    tex2jax: {
      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
      processEscapes: true
    },
        TeX: {
               extensions: ["AMSmath.js","AMSsymbols.js","noErrors.js","noUndefined.js","mhchem.js"]
             }
  };
</script>

<script type="text/javascript" src="http://cdn.bootcss.com/mathjax/2.6.0/MathJax.js?config=TeX-MML-AM_CHTML"></script>


</head>
<body>
<div id="content">
<header>
<h1 class="title">小分子结构显示</h1>
</header><nav id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgheadline6">1. 使用mhchem宏包</a>
<ul>
<li><a href="#orgheadline1">1.1. 数字</a></li>
<li><a href="#orgheadline2">1.2. 数学环境</a></li>
<li><a href="#orgheadline3">1.3. 键</a></li>
<li><a href="#orgheadline4">1.4. 化学反应式</a></li>
<li><a href="#orgheadline5">1.5. 上下箭头</a></li>
</ul>
</li>
<li><a href="#orgheadline9">2. mathjax简介</a>
</li>
<li><a href="#orgheadline10">3. 参考资料</a></li>
</ul>
</div>
</nav>


<div class="outline-2">
<h2 id="orgheadline6">使用mhchem宏包</h2>
<div class="outline-text-2" id="text-1">
<p>
latex可以用基于tikz的chemfig宏包来处理小分子结构显示问题，包括大型有机分子的结构显示问题，然后一些简单的小分子显示推荐 <strong>mhchem</strong> 宏包。
</p>

<p>
mhchem看得出来是通过latex的数学环境来显示小分子结构的，所以马上就被html上的mathjax支持了，而chemfig是通过tikz机制，这可能以后永远都不会被mathjax支持（或者通过svg途径？）。首先是加载宏包：
</p>

<div class="highlight"><pre><span></span><span class="k">\usepackage</span><span class="na">[version=3]</span><span class="nb">{</span>mhchem<span class="nb">}</span>
</pre></div>

<p>
目前是第三版，作者说第四版正在开发中（2015年2月）。
</p>

<p>
就作为一般使用来说，假定读者对latex的数学环境内的语法都很熟悉了，那么可以简单理解为mhchem宏包就是在数学环境下，加入了一个新命令 <code>\ce{ }</code> ，在这个ce命令里面上标和下标语法是类似数学环境内的语法表示的，不过对于具体化学表达式的显示会更加美观一些。
</p>

<p>
比如 <code>$\ce{H_2O}$</code> 将显示为 $\ce{H_2O}$ ，然后 <code>$\ce{AgCl_2^-}$</code> 将显示为 $\ce{AgCl_2^-}$ 。
</p>

<p>
此外还有一种简写写法：比如 <code>$\ce{H2O}$</code> 将显示为 $\ce{H2O}$ ，然后 <code>$\ce{AgCl2-}$</code> 将显示为 $\ce{AgCl2-}$ 。
</p>

<p>
我们可以看一下没有经过ce命令包装的纯数学环境表达的显示效果： \(H_2O\) 和 \(AgCl_2^-\) 。区别还是有点的。
</p>

<p>
关于上面的简写表达，我暂时还没找到规律，如果不在这个ce命令中，你使用这样的语句 <code>$H_2_{(aq)}$</code> 是会报错的，但是放入ce命令中就不会了， \(\ce{H_2_{(aq)}}\) ，同时我们看到 <code>\ce{H_{2(aq)}}</code> \(\ce{H_{2(aq)}}\) 和上面的 <code>\ce{H_2_{(aq)}}</code> 显示效果稍微有点差异（在pdf即latex那边又没有区别！）。初步的理解是，后面跟着的数字默认进入下标，然后加减号默认进入上标，这在输入上确实带来了很大的便捷，因为化学表达式的数学很多都是进入下标的。
</p>

<p>
关于数字进入上标和加减号自动情况见这两个例子： <code>$\ce{Y^{99}+}$</code>  \(\ce{Y^{99}+}\) 和  <code>$\ce{Y^{99+}}$</code>  \(\ce{Y^{99+}}\) 。同样在latex那边这两个表达式的显示效果没有差异，而在html这边加减号自动处理（第一个）的情况显示效果稍微美观一点。
</p>
</div>

<div class="outline-3">
<h3 id="orgheadline1">数字</h3>
<div class="outline-text-3" id="text-1-1">
<p>
数字就直接写上即可 <code>$\ce{0.5H2O}$</code>  \(\ce{0.5H2O}\) ，值得一提的是，前面的数字分数形式会自动处理： <code>$\ce{1/2 H2O}$</code> \(\ce{1/2 H2O}\) 。 你会看到带上小数点的数字显示有点古怪。之前小数点会被解释成为配位化合物和结晶水中间的那个分隔点。如 <code>$\ce{KCr(SO4)2.12H2O}$</code> \(\ce{KCr(SO4)2.12H2O}\) 。为了正确显示前面的例子，把这个0.5放入数学环境中即可： <code>$\ce{$0.5$H2O}$</code>

$
\ce{$0.5$H2O}
$
</p>

</div>
</div>

<div class="outline-3">
<h3 id="orgheadline2">数学环境</h3>
<div class="outline-text-3" id="text-1-2">
<p>
同样，如上所示，mathjax目前是支持ce命令里面再加入数学环境 <code>$ $</code> 的。
</p>
</div>
</div>

<div class="outline-3">
<h3 id="orgheadline3">键</h3>
<div class="outline-text-3" id="text-1-3">
<p>
<code>- = #</code> 分别表示单键，双键和三键。 \(\ce{A-A B=B C#C}\) 然后使用 \bond命令还可以加入其他一些额外的键，其中 <code>$\ce{\bond{~}}$ </code> 对应
$\ce{\bond{~}}$
，然后 <code>$\ce{\bond{~-}}$</code> 对应 \(\ce{\bond{~-}}\) ，其他类推。
</p>
</div>
</div>

<div class="outline-3">
<h3 id="orgheadline4">化学反应式</h3>
<div class="outline-text-3" id="text-1-4">
<pre>
$$
\ce{CO2 + C &lt;- 2CO}
$$
</pre>

<p>
$$
\ce{CO2 + C <- 2CO}
$$
</p>

<pre>
$$
\ce{CO2 + C -&gt;[\text{加入text命令}] 2CO}
\ce{CO2 + C -&gt;T[是支持][中文的] 2CO}
$$
</pre>

<p>
$$
\ce{CO2 + C ->[\text{加入text命令}] 2CO}
$$
</p>

<p>
$$
\ce{CO2 + C ->T[是支持][中文的] 2CO}
$$
</p>

<p>
如果不使用text命令，那么中文在latex那一边不会正常显示。上面例子第二个没有使用text命令，是因为前面加上了T，然后箭头上下文字都不需要了。
</p>
</div>
</div>

<div class="outline-3">
<h3 id="orgheadline5">上下箭头</h3>
<div class="outline-text-3" id="text-1-5">
<pre>
$$
\ce{SO4^2- + Ba^2+ -&gt; BaSO4 v ^}
$$
</pre>

<p>
$$
\ce{SO4^2- + Ba^2+ -> BaSO4 v ^}
$$
</p>

<p>
下降箭头是v，上式箭头是^，需要和前面的内容有一个空格。
</p>
</div>
</div>
</div>


<div class="outline-2">
<h2 id="orgheadline9">mathjax简介</h2>
<div class="outline-text-2" id="text-2">
<p>
网页之所以能够显示数学公式就是利用的mathjax这个javascript库，然后这里之所以能够显示一些简单的化学是因为mathjax还引入了mhchem.js这个插件。
</p>

<p>
简单的引入代码如下所示：
</p>
<pre>
&lt;script type="text/javascript">
  window.MathJax = {
    tex2jax: {
      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
      processEscapes: true
    },
        TeX: {
               extensions: ["AMSmath.js","AMSsymbols.js","noErrors.js","noUndefined.js","mhchem.js"]
             }
};
&lt;/script>

&lt;script type="text/javascript" src="http://cdn.bootcss.com/mathjax/2.6.0/MathJax.js?config=TeX-MML-AM_CHTML">&lt;/script>
</pre>

<p>
    最关键的配置就是 TeX 的 extensions 哪里要引入 mhchem.js 。
</p>
</div>
</div>


<div class="outline-2">
<h2 id="orgheadline10">参考资料</h2>
<div class="outline-text-2" id="text-3">
<ol class="org-ol">
<li><a href="https://docs.moodle.org/27/en/Chemistry_notation_using_mhchem">这个网站</a> 对于这一块内容讲解很详细。</li>
</ol>
</div>
</div>
</div>
</body>
</html>