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| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2026-03-13 13:53:10 +0100 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2026-03-13 13:53:10 +0100 |
| commit | f43f7f9dec2337c8db62f0ddb167986af59a033e (patch) | |
| tree | 394b2c37c4598e002a3f5f5bc819e6862b2d63db /docs/index.html | |
| parent | 0be378ede2f5b83c2451a57d1131288ff52685ea (diff) | |
Explain consequence of chent objects being R6 objects
Diffstat (limited to 'docs/index.html')
| -rw-r--r-- | docs/index.html | 61 |
1 files changed, 56 insertions, 5 deletions
diff --git a/docs/index.html b/docs/index.html index ec6ba42..aa6d358 100644 --- a/docs/index.html +++ b/docs/index.html @@ -54,8 +54,8 @@ <p>When first defining a chemical entity, some chemical information is retrieved from the <a href="https://pubchem.ncbi.nlm.nih.gov/" class="external-link">PubChem</a> website using the <a href="https://docs.ropensci.org/webchem/" class="external-link">webchem</a> package.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/chents/">chents</a></span><span class="op">)</span></span> -<span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span> -<span><span class="co">#> Querying PubChem for name caffeine ...</span></span> +<span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Caffeine"</span><span class="op">)</span></span> +<span><span class="co">#> Querying PubChem for name Caffeine ...</span></span> <span><span class="co">#> Get chemical information from RDKit using PubChem SMILES</span></span> <span><span class="co">#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></span></code></pre></div> <p>If Python and <a href="https://rdkit.org" class="external-link">RDKit</a> (> 2015.03) are installed and configured for use with the <a href="https://rstudio.github.io/reticulate/" class="external-link">reticulate</a> package, some additional chemical information including a 2D graph are computed.</p> @@ -63,7 +63,7 @@ <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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="co">#> <chent></span></span> -<span><span class="co">#> Identifier $identifier caffeine </span></span> +<span><span class="co">#> Identifier $identifier Caffeine </span></span> <span><span class="co">#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span></span> <span><span class="co">#> SMILES string $smiles:</span></span> <span><span class="co">#> PubChem </span></span> @@ -81,8 +81,8 @@ <p><img src="reference/figures/README-unnamed-chunk-4-1.png"><!-- --></p> <p>If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the <a href="http://www.bcpcpesticidecompendium.org/" class="external-link">BCPC compendium</a> first.</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">delta</span> <span class="op"><-</span> <span class="va"><a href="reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"deltamethrin"</span><span class="op">)</span></span> -<span><span class="co">#> Querying BCPC for deltamethrin ...</span></span> +<code class="sourceCode R"><span><span class="va">delta</span> <span class="op"><-</span> <span class="va"><a href="reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Deltamethrin"</span><span class="op">)</span></span> +<span><span class="co">#> Querying BCPC for Deltamethrin ...</span></span> <span><span class="co">#> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ...</span></span> <span><span class="co">#> Get chemical information from RDKit using PubChem SMILES</span></span> <span><span class="co">#> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C</span></span> @@ -107,6 +107,57 @@ <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>RETICULATE_PYTHON<span class="op">=</span><span class="st">"/usr/bin/python3"</span><span class="op">)</span></span></code></pre></div> </div> +<div class="section level2"> +<h2 id="using-r6-classes">Using R6 classes<a class="anchor" aria-label="anchor" href="#using-r6-classes"></a> +</h2> +<p>Note that the <code>chent</code> objects defined by this package are <a href="https://r6.r-lib.org/articles/Introduction.html" class="external-link">R6</a> classes. Therefore, if you think you make a copy by assigning them to a new name, the objects will still be connected, because only the reference is copied. For example, you can create a molecule without retrieving data from PubChem</p> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">but</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Butane"</span>, smiles <span class="op">=</span> <span class="st">"CCCC"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span><span class="co">#> Get chemical information from RDKit using user SMILES</span></span> +<span><span class="co">#> CCCC</span></span> +<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">but</span><span class="op">)</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Butane </span></span> +<span><span class="co">#> InChI Key $inchikey NA </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> user </span></span> +<span><span class="co">#> "CCCC" </span></span> +<span><span class="co">#> Molecular weight $mw: 58.1</span></span></code></pre></div> +<p>If you then assign a new name and add PubChem information to the object with the new name, the information will also be added to the original <code>chent</code> object:</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">but_pubchem</span> <span class="op"><-</span> <span class="va">but</span></span> +<span><span class="va">but_pubchem</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="op">)</span></span> +<span><span class="co">#> Querying PubChem for name Butane ...</span></span> +<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">but</span><span class="op">)</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Butane </span></span> +<span><span class="co">#> InChI Key $inchikey IJDNQMDRQITEOD-UHFFFAOYSA-N </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> user PubChem </span></span> +<span><span class="co">#> "CCCC" "CCCC" </span></span> +<span><span class="co">#> Molecular weight $mw: 58.1 </span></span> +<span><span class="co">#> PubChem synonyms (up to 10):</span></span> +<span><span class="co">#> [1] "BUTANE" "n-Butane" "106-97-8" </span></span> +<span><span class="co">#> [4] "Diethyl" "Methylethylmethane" "Butanen" </span></span> +<span><span class="co">#> [7] "Butani" "Butyl hydride" "HC 600" </span></span> +<span><span class="co">#> [10] "A 21 (lowing agent)"</span></span></code></pre></div> +<p>You can create a derived, independent object using the <code>clone()</code> method that will not be affectd by operations on the original object:</p> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">but_new</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Butane"</span>, smiles <span class="op">=</span> <span class="st">"CCCC"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span><span class="co">#> Get chemical information from RDKit using user SMILES</span></span> +<span><span class="co">#> CCCC</span></span> +<span><span class="va">but_clone</span> <span class="op"><-</span> <span class="va">but_new</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span><span class="op">)</span></span> +<span><span class="va">but_new</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="op">)</span></span> +<span><span class="co">#> Querying PubChem for name Butane ...</span></span> +<span><span class="va">but_clone</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Butane </span></span> +<span><span class="co">#> InChI Key $inchikey NA </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> user </span></span> +<span><span class="co">#> "CCCC" </span></span> +<span><span class="co">#> Molecular weight $mw: 58.1</span></span></code></pre></div> +</div> </div> </main><aside class="col-md-3"><div class="links"> <h2 data-toc-skip>Links</h2> |