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Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/chent-1.png | bin | 46084 -> 46142 bytes | |||
| -rw-r--r-- | docs/reference/chent.html | 92 | ||||
| -rw-r--r-- | docs/reference/draw_svg.chent.html | 6 | ||||
| -rw-r--r-- | docs/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/reference/pai-1.png | bin | 34451 -> 34388 bytes | |||
| -rw-r--r-- | docs/reference/pai.html | 15 | ||||
| -rw-r--r-- | docs/reference/plot.chent-1.png | bin | 46084 -> 46142 bytes | |||
| -rw-r--r-- | docs/reference/plot.chent.html | 12 | ||||
| -rw-r--r-- | docs/reference/ppp.html | 14 | ||||
| -rw-r--r-- | docs/reference/print.chent.html | 6 | ||||
| -rw-r--r-- | docs/reference/print.pai.html | 6 | ||||
| -rw-r--r-- | docs/reference/print.ppp.html | 6 |
12 files changed, 66 insertions, 97 deletions
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png Binary files differindex 36b02fa..1e8885d 100644 --- a/docs/reference/chent-1.png +++ b/docs/reference/chent-1.png diff --git a/docs/reference/chent.html b/docs/reference/chent.html index cef2061..a2bac4f 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for chemical entities with associated data — chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta name="description" content="The class is initialised with an identifier. Chemical +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for chemical entities with associated data — chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta name="description" content="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."><meta property="og:description" content="The class is initialised with an identifier. Chemical information is retrieved from the internet. Additionally, it can be @@ -11,7 +11,7 @@ generated using RDKit if RDKit and its python bindings are installed."></head><b <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -46,7 +46,7 @@ generated using RDKit if RDKit and its python bindings are installed.</p> <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> + <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> generator object</p> </div> <div class="section level2"> <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> @@ -88,7 +88,7 @@ List of information retrieved from PubChem</p></dd> <dt><code>Picture</code></dt> -<dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd> +<dd><p>Graph as a <a href="https://rdrr.io/pkg/grImport/man/Picture-class.html" class="external-link">grImport::Picture</a> object obtained using the grImport package</p></dd> <dt><code>Pict_font_size</code></dt> @@ -116,18 +116,15 @@ List of information retrieved from PubChem</p></dd> <dt><code>TPs</code></dt> -<dd><p>List of transformation products as chent objects -Add a transformation product to the internal list</p></dd> +<dd><p>List of transformation products as chent objects</p></dd> <dt><code>transformations</code></dt> -<dd><p>Data frame of observed transformations -Add a line in the internal dataframe holding observed transformations</p></dd> +<dd><p>Data frame of observed transformations</p></dd> <dt><code>soil_degradation</code></dt> -<dd><p>Dataframe of modelling DT50 values -Add a line in the internal dataframe holding modelling DT50 values</p></dd> +<dd><p>Dataframe of modelling DT50 values</p></dd> <dt><code>soil_ff</code></dt> @@ -135,8 +132,7 @@ Add a line in the internal dataframe holding modelling DT50 values</p></dd> <dt><code>soil_sorption</code></dt> -<dd><p>Dataframe of soil sorption data -Add soil sorption data</p></dd> +<dd><p>Dataframe of soil sorption data</p></dd> </dl><p></p></div> @@ -166,8 +162,7 @@ Add soil sorption data</p></dd> <li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li> </ul></div><p></p><hr><a id="method-chent-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> -<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p> -<p>Try to get chemical information from PubChem</p><div class="section"> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> <span> <span class="va">identifier</span>,</span> @@ -225,8 +220,7 @@ directory?</p></dd> </div><p></p><hr><a id="method-chent-try_pubchem"></a><div class="section"> <h3 id="method-try-pubchem-">Method <code>try_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-try-pubchem-"></a></h3> - -<div class="section"> +<p>Try to get chemical information from PubChem</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -238,8 +232,7 @@ directory?</p></dd> <dt><code>from</code></dt> -<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a> -Get chemical information from PubChem for a known PubChem CID</p></dd> +<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd> </dl><p></p></div> @@ -247,8 +240,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd> </div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section"> <h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3> - -<div class="section"> +<p>Get chemical information from PubChem for a known PubChem CID</p><div class="section"> <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -264,8 +256,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd> </div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section"> <h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3> -<p>Get chemical information from RDKit if available -Obtain information from a YAML file</p><div class="section"> +<p>Get chemical information from RDKit if available</p><div class="section"> <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -281,8 +272,7 @@ Obtain information from a YAML file</p><div class="section"> </div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section"> <h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3> - -<div class="section"> +<p>Obtain information from a YAML file</p><div class="section"> <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span> <span> repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wd"</span>, <span class="st">"local"</span>, <span class="st">"web"</span><span class="op">)</span>,</span> @@ -299,8 +289,7 @@ the web (not implemented).</p></dd> <dt><code>chyaml</code></dt> -<dd><p>The filename to be looked for -Add a vapour pressure</p></dd> +<dd><p>The filename to be looked for</p></dd> </dl><p></p></div> @@ -308,8 +297,7 @@ Add a vapour pressure</p></dd> </div><p></p><hr><a id="method-chent-add_p0"></a><div class="section"> <h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3> - -<div class="section"> +<p>Add a vapour pressure</p><div class="section"> <h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_p0</span><span class="op">(</span><span class="va">p0</span>, T <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -317,8 +305,7 @@ Add a vapour pressure</p></dd> <div class="section"> <h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4> <p></p><div class="arguments"><dl><dt><code>p0</code></dt> -<dd><p>The vapour pressure in Pa -Add a water solubility</p></dd> +<dd><p>The vapour pressure in Pa</p></dd> <dt><code>T</code></dt> @@ -342,8 +329,7 @@ Add a water solubility</p></dd> </div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section"> <h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3> - -<div class="section"> +<p>Add a water solubility</p><div class="section"> <h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -351,8 +337,7 @@ Add a water solubility</p></dd> <div class="section"> <h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4> <p></p><div class="arguments"><dl><dt><code>cwsat</code></dt> -<dd><p>The water solubility in mg/L -Add a plant uptake factor</p></dd> +<dd><p>The water solubility in mg/L</p></dd> <dt><code>T</code></dt> @@ -380,8 +365,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section"> <h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3> - -<div class="section"> +<p>Add a plant uptake factor</p><div class="section"> <h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span> <span> PUF <span class="op">=</span> <span class="fl">0</span>,</span> @@ -414,8 +398,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_TP"></a><div class="section"> <h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3> - -<div class="section"> +<p>Add a transformation product to the internal list</p><div class="section"> <h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -439,8 +422,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section"> <h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3> - -<div class="section"> +<p>Add a line in the internal dataframe holding observed transformations</p><div class="section"> <h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span> <span> <span class="va">study_type</span>,</span> @@ -486,8 +468,7 @@ result from stochiometric transformation</p></dd> </div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section"> <h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3> - -<div class="section"> +<p>Add a line in the internal dataframe holding modelling DT50 values</p><div class="section"> <h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span> <span> <span class="va">soils</span>,</span> @@ -593,8 +574,7 @@ the technical active ingredient</p></dd> </div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section"> <h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3> - -<div class="section"> +<p>Add one or more formation fractions for degradation in soil</p><div class="section"> <h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -630,8 +610,7 @@ the technical active ingredient</p></dd> </div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section"> <h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3> - -<div class="section"> +<p>Add soil sorption data</p><div class="section"> <h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span> <span> <span class="va">soils</span>,</span> @@ -715,8 +694,7 @@ or according to Freundlich</p></dd> </div><p></p><hr><a id="method-chent-pdf"></a><div class="section"> <h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3> -<p>Write a PDF image of the structure -Write a PNG image of the structure</p><div class="section"> +<p>Write a PDF image of the structure</p><div class="section"> <h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span> <span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span> @@ -744,8 +722,7 @@ Write a PNG image of the structure</p><div class="section"> </div><p></p><hr><a id="method-chent-png"></a><div class="section"> <h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3> - -<div class="section"> +<p>Write a PNG image of the structure</p><div class="section"> <h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span> <span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span> @@ -815,14 +792,14 @@ Write a PNG image of the structure</p><div class="section"> <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">caffeine</span> <span class="op"><-</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">#></span> PubChem:</span> -<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem SMILES</span> <span class="r-msg co"><span class="r-pr">#></span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</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">#></span> <chent></span> <span class="r-out co"><span class="r-pr">#></span> Identifier $identifier caffeine </span> <span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span> <span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> -<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem </span> <span class="r-out co"><span class="r-pr">#></span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span> <span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 194.2 </span> <span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> @@ -838,14 +815,9 @@ Write a PNG image of the structure</p><div class="section"> <span class="r-in"><span><span class="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</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">#></span> Trying to get chemical information from RDKit using user SMILES</span> <span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCO</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in if (!is.na(self$mw)) { if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { message("RDKit mw is ", self$rdkit$mw) message("mw is ", self$mw) }} else { self$mw <- self$rdkit$mw attr(self$mw, "source") <- "rdkit"}:</span> argument is of length zero</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">#></span> <chent></span> -<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier 1-octanol </span> -<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey NA </span> -<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> -<span class="r-out co"><span class="r-pr">#></span> user </span> -<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCO" </span> -<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 130.2 </span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'oct' not found</span> </code></pre></div> </div> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> @@ -857,7 +829,7 @@ Write a PNG image of the structure</p><div class="section"> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 2545578..dd50cd9 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent"><meta name="description" content="Draw SVG graph from a chent object using RDKit"><meta property="og:description" content="Draw SVG graph from a chent object using RDKit"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent"><meta name="description" content="Draw SVG graph from a chent object using RDKit"><meta property="og:description" content="Draw SVG graph from a chent object using RDKit"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -82,7 +82,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/index.html b/docs/reference/index.html index eccf7a0..5112aef 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -99,7 +99,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png Binary files differindex 951bb25..802fd50 100644 --- a/docs/reference/pai-1.png +++ b/docs/reference/pai-1.png diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 30bbbac..443769d 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta name="description" content="This class is derived from chent. It makes it easy +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta name="description" content="This class is derived from chent. It makes it easy to create a chent from the ISO common name of a pesticide active ingredient, and additionally stores the ISO name as well as the complete result of querying the BCPC compendium using @@ -15,7 +15,7 @@ bcpc_query."></head><body> <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -52,7 +52,7 @@ the complete result of querying the BCPC compendium using <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> + <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> generator object</p> </div> <div class="section level2"> <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#super-class"></a></h2> @@ -96,8 +96,7 @@ at <pesticidecompendium.bcpc.org></p></dd> <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li> </ul></details></p><hr><a id="method-pai-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> - -<div class="section"> +<p>Create a new pai object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><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> <span> <span class="va">iso</span>,</span> @@ -199,7 +198,7 @@ and the reticulate package?</p></dd> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> BCPC:</span> <span class="r-msg co"><span class="r-pr">#></span> PubChem:</span> -<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem SMILES</span> <span class="r-msg co"><span class="r-pr">#></span> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span> <span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span> <span class="r-out co"><span class="r-pr">#></span> <pai> with ISO common name $iso atrazine </span> @@ -207,7 +206,7 @@ and the reticulate package?</p></dd> <span class="r-out co"><span class="r-pr">#></span> Identifier $identifier atrazine </span> <span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N </span> <span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> -<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem </span> <span class="r-out co"><span class="r-pr">#></span> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span> <span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 215.7 </span> <span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> @@ -224,7 +223,7 @@ and the reticulate package?</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png Binary files differindex 36b02fa..1e8885d 100644 --- a/docs/reference/plot.chent-1.png +++ b/docs/reference/plot.chent-1.png diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index 9ed70e1..49f54b2 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Plot method for chent objects — plot.chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot method for chent objects — plot.chent"><meta name="description" content="Plot method for chent objects"><meta property="og:description" content="Plot method for chent objects"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Plot method for chent objects — plot.chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot method for chent objects — plot.chent"><meta name="description" content="Plot method for chent objects"><meta property="og:description" content="Plot method for chent objects"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -52,7 +52,7 @@ <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> -<dd><p>Further arguments passed to <code>grid.picture</code></p></dd> +<dd><p>Further arguments passed to <a href="https://rdrr.io/pkg/grImport/man/grid.picture.html" class="external-link">grImport::grid.picture</a></p></dd> </dl></div> @@ -60,14 +60,14 @@ <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">caffeine</span> <span class="op"><-</span> <span class="va"><a href="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="r-msg co"><span class="r-pr">#></span> PubChem:</span> -<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem SMILES</span> <span class="r-msg co"><span class="r-pr">#></span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</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">#></span> <chent></span> <span class="r-out co"><span class="r-pr">#></span> Identifier $identifier caffeine </span> <span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span> <span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> -<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem </span> <span class="r-out co"><span class="r-pr">#></span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span> <span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 194.2 </span> <span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> @@ -91,7 +91,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html index ef3933d..98bc8e1 100644 --- a/docs/reference/ppp.html +++ b/docs/reference/ppp.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>R6 class for a plant protection product with at least one active ingredient — ppp • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="R6 class for a plant protection product with at least one active ingredient — ppp"><meta name="description" content="Contains basic information about the active ingredients in the +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>R6 class for a plant protection product with at least one active ingredient — ppp • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="R6 class for a plant protection product with at least one active ingredient — ppp"><meta name="description" content="Contains basic information about the active ingredients in the product"><meta property="og:description" content="Contains basic information about the active ingredients in the product"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -9,7 +9,7 @@ product"></head><body> <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -43,7 +43,7 @@ product</p> <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> + <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> generator object.</p> </div> <div class="section level2"> <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> @@ -68,8 +68,7 @@ product</p> <dt><code>density_units</code></dt> -<dd><p>Defaults to g/L -Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd> +<dd><p>Defaults to g/L</p></dd> </dl><p></p></div> @@ -84,8 +83,7 @@ Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.h <li><p><a href="#method-ppp-clone"><code>ppp$clone()</code></a></p></li> </ul></div><p></p><hr><a id="method-ppp-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> - -<div class="section"> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/ppp.html">ppp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> <span> <span class="va">name</span>,</span> @@ -155,7 +153,7 @@ Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.h </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index 9ae6ff4..223c190 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for chent objects — print.chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for chent objects — print.chent"><meta name="description" content="Printing method for chent objects"><meta property="og:description" content="Printing method for chent objects"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for chent objects — print.chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for chent objects — print.chent"><meta name="description" content="Printing method for chent objects"><meta property="og:description" content="Printing method for chent objects"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -65,7 +65,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index 283bf76..b59d738 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for pai objects (pesticidal active ingredients) — print.pai • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for pai objects (pesticidal active ingredients) — print.pai"><meta name="description" content="Printing method for pai objects (pesticidal active ingredients)"><meta property="og:description" content="Printing method for pai objects (pesticidal active ingredients)"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for pai objects (pesticidal active ingredients) — print.pai • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for pai objects (pesticidal active ingredients) — print.pai"><meta name="description" content="Printing method for pai objects (pesticidal active ingredients)"><meta property="og:description" content="Printing method for pai objects (pesticidal active ingredients)"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -65,7 +65,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/print.ppp.html b/docs/reference/print.ppp.html index a15f8cb..63f87ef 100644 --- a/docs/reference/print.ppp.html +++ b/docs/reference/print.ppp.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for ppp objects (plant protection products) — print.ppp • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for ppp objects (plant protection products) — print.ppp"><meta name="description" content="Printing method for ppp objects (plant protection products)"><meta property="og:description" content="Printing method for ppp objects (plant protection products)"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for ppp objects (plant protection products) — print.ppp • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for ppp objects (plant protection products) — print.ppp"><meta name="description" content="Printing method for ppp objects (plant protection products)"><meta property="og:description" content="Printing method for ppp objects (plant protection products)"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -65,7 +65,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> |
