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@@ -1,65 +1,64 @@
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- <h1>An R6 class for chemical entities with associated data</h1>
- <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
- <div class="hidden name"><code>chent.Rd</code></div>
+ </ul></div>
+
+
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+</nav><div class="container template-reference-topic">
+<div class="row">
+ <main id="main" class="col-md-9"><div class="page-header">
+ <img src="" class="logo" alt=""><h1>An R6 class for chemical entities with associated data</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
+ <div class="d-none name"><code>chent.Rd</code></div>
</div>
- <div class="ref-description">
+ <div class="ref-description section level2">
<p>The class is initialised with an identifier. Chemical
information is retrieved from the internet. Additionally, it can be
generated using RDKit if RDKit and its python bindings are installed.</p>
</div>
- <div id="format">
- <h2>Format</h2>
+ <div class="section level2">
+ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An <code>R6Class</code> generator object</p>
</div>
- <div id="public-fields">
- <h2>Public fields</h2>
+ <div class="section level2">
+ <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
<p></p><div class="r6-fields"><dl><dt><code>identifier</code></dt>
<dd><p>(<code>character(1)</code>)<br>
The identifier that was used to initiate the object, with attribute 'source'</p></dd>
@@ -151,8 +150,8 @@ Add soil sorption data</p></dd>
</dl><p></p></div>
</div>
- <div id="methods">
- <h2>Methods</h2>
+ <div class="section level2">
+ <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
<div class="section">
<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
@@ -767,69 +766,48 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma
</div>
- <div id="ref-examples">
- <h2>Examples</h2>
+ <div class="section level2">
+ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using user SMILES</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> CCCCCCCCO</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./1-octanol.yaml</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in URLencode(self$identifier):</span> could not find function "URLencode"</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier 1-octanol </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> user </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "CCCCCCCCO" </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 130.2 </span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'oct' not found</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'oct' not found</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> PubChem:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./caffeine.yaml</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in URLencode(self$identifier):</span> could not find function "URLencode"</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier caffeine </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem_Canonical </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 194.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "caffeine" "58-08-2" </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "Methyltheobromine" "Theine" </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "Thein" "Cafeina" </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "Koffein" "Mateina" </span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'caffeine' not found</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="chent-1.png" alt="" width="700" height="433"></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'caffeine' not found</span>
</code></pre></div>
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