Make an RStudio project and improve the docs

author: Ranke Johannes <johannes.ranke@agroscope.admin.ch> 2023-11-10 18:40:34 +0100
committer: Ranke Johannes <johannes.ranke@agroscope.admin.ch> 2023-11-10 19:21:11 +0100
commit: 816de01ce642c1c3d633ffb1cbcf960036d27114 (patch)
tree: cf732b6e18bcc0864b481f804a1cb0b16bdd7d4d /docs/reference
parent: 67384ac3c7c0b888d67d06473f81e46d520a7dd3 (diff)
12 files changed, 863 insertions, 1264 deletions
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 377b927..d92e93f 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png
index 7229a66..acab3e6 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 941eabb..a6b8dde 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -1,69 +1,14 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
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-  <meta charset="utf-8">
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-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
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-<meta property="og:title" content="An R6 class for chemical entities with associated data — chent" />
-<meta property="og: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." />
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-
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-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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-
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+<!-- 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=1.0"><title>An R6 class for chemical entities with associated data — chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta property="og: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."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -74,361 +19,513 @@ python bindings are installed." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
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-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>An R6 class for chemical entities with associated data</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>
     </div>
 
     <div class="ref-description">
-    <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>
+    <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>
+    <p>An <code>R6Class</code> generator object</p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</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>
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <code>R6Class</code> generator object</p>
-    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
+<dt><code>inchikey</code></dt>
+<dd><p>(<code>character(1)</code>)<br>
+InChI Key, with attribute 'source'</p></dd>
+
+
+<dt><code>smiles</code></dt>
+<dd><p>(<code><a href="https://rdrr.io/r/base/character.html" class="external-link">character()</a></code>)<br>
+SMILES code(s), with attribute 'source'</p></dd>
+
+
+<dt><code>mw</code></dt>
+<dd><p>(<code>numeric(1)</code>)<br>
+Molecular weight, with attribute 'source'</p></dd>
+
+
+<dt><code>pubchem</code></dt>
+<dd><p>(<code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>)<br>
+List of information retrieved from PubChem</p></dd>
+
 
-    <p><div class="r6-fields"></p><dl>
-<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd>
+<dt><code>rdkit</code></dt>
+<dd><p>List of information obtained with RDKit</p></dd>
 
-<dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd>
 
-<dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd>
+<dt><code>mol</code></dt>
+<dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</p></dd>
 
-<dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd>
 
-<dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd>
+<dt><code>svg</code></dt>
+<dd><p>SVG code</p></dd>
 
-<dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit</p></dd>
 
-<dt><code>mol</code></dt><dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</p></dd>
+<dt><code>Picture</code></dt>
+<dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
 
-<dt><code>svg</code></dt><dd><p>SVG code</p></dd>
 
-<dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
+<dt><code>Pict_font_size</code></dt>
+<dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
 
-<dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
 
-<dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
+<dt><code>pdf_height</code></dt>
+<dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
 
-<dt><code>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd>
 
-<dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd>
+<dt><code>p0</code></dt>
+<dd><p>Vapour pressure in Pa</p></dd>
 
-<dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
 
-<dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd>
+<dt><code>cwsat</code></dt>
+<dd><p>Water solubility in mg/L</p></dd>
 
-<dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd>
 
-<dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd>
+<dt><code>PUF</code></dt>
+<dd><p>Plant uptake factor</p></dd>
 
-<dt><code>PUF</code></dt><dd><p>Plant uptake factor</p></dd>
 
-</dl><p></div></p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
+<dt><code>chyaml</code></dt>
+<dd><p>List of information obtained from a YAML file</p></dd>
 
+
+<dt><code>TPs</code></dt>
+<dd><p>List of transformation products as chent objects</p></dd>
+
+
+<dt><code>transformations</code></dt>
+<dd><p>Data frame of observed transformations</p></dd>
+
+
+<dt><code>soil_degradation</code></dt>
+<dd><p>Dataframe of modelling DT50 values</p></dd>
+
+
+<dt><code>soil_ff</code></dt>
+<dd><p>Dataframe of formation fractions</p></dd>
+
+
+<dt><code>soil_sorption</code></dt>
+<dd><p>Dataframe of soil sorption data</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
     
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
-
-<ul>
-<li><p><a href='#method-new'><code>chent$new()</code></a></p></li>
-<li><p><a href='#method-try_pubchem'><code>chent$try_pubchem()</code></a></p></li>
-<li><p><a href='#method-get_pubchem'><code>chent$get_pubchem()</code></a></p></li>
-<li><p><a href='#method-get_rdkit'><code>chent$get_rdkit()</code></a></p></li>
-<li><p><a href='#method-get_chyaml'><code>chent$get_chyaml()</code></a></p></li>
-<li><p><a href='#method-add_p0'><code>chent$add_p0()</code></a></p></li>
-<li><p><a href='#method-add_cwsat'><code>chent$add_cwsat()</code></a></p></li>
-<li><p><a href='#method-add_PUF'><code>chent$add_PUF()</code></a></p></li>
-<li><p><a href='#method-add_TP'><code>chent$add_TP()</code></a></p></li>
-<li><p><a href='#method-add_transformation'><code>chent$add_transformation()</code></a></p></li>
-<li><p><a href='#method-add_soil_degradation'><code>chent$add_soil_degradation()</code></a></p></li>
-<li><p><a href='#method-add_soil_ff'><code>chent$add_soil_ff()</code></a></p></li>
-<li><p><a href='#method-add_soil_sorption'><code>chent$add_soil_sorption()</code></a></p></li>
-<li><p><a href='#method-pdf'><code>chent$pdf()</code></a></p></li>
-<li><p><a href='#method-png'><code>chent$png()</code></a></p></li>
-<li><p><a href='#method-emf'><code>chent$emf()</code></a></p></li>
-<li><p><a href='#method-clone'><code>chent$clone()</code></a></p></li>
-</ul>
-<p><hr>
-<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
-  <span class='va'>identifier</span>,
-  smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
-  smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
-  inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  pubchem_from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"smiles"</span>, <span class='st'>"inchikey"</span><span class='op'>)</span>,
-  rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  template <span class='op'>=</span> <span class='cn'>NULL</span>,
-  chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-try_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>try_pubchem()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>try_pubchem</span><span class='op'>(</span><span class='va'>query</span>, from <span class='op'>=</span> <span class='st'>"name"</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-get_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_pubchem()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_pubchem</span><span class='op'>(</span><span class='va'>pubchem_cid</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-get_rdkit"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_rdkit()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_rdkit</span><span class='op'>(</span>template <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-get_chyaml"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_chyaml()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_chyaml</span><span class='op'>(</span>
-  repo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
-  chyaml <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/utils/URLencode.html'>URLencode</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".yaml"</span><span class='op'>)</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_p0"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_p0()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_cwsat"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_cwsat()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_cwsat</span><span class='op'>(</span><span class='va'>cwsat</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, pH <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_PUF"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_PUF()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_PUF</span><span class='op'>(</span>
-  PUF <span class='op'>=</span> <span class='fl'>0</span>,
-  source <span class='op'>=</span> <span class='st'>"focus_generic_gw_2014"</span>,
-  page <span class='op'>=</span> <span class='fl'>41</span>,
-  remark <span class='op'>=</span> <span class='st'>"Conservative default value"</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_TP"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_TP()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_TP</span><span class='op'>(</span><span class='va'>x</span>, smiles <span class='op'>=</span> <span class='cn'>NULL</span>, pubchem <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_transformation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_transformation()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_transformation</span><span class='op'>(</span>
-  <span class='va'>study_type</span>,
-  <span class='va'>TP_identifier</span>,
-  <span class='va'>max_occurrence</span>,
-  remark <span class='op'>=</span> <span class='st'>""</span>,
-  source <span class='op'>=</span> <span class='cn'>NA</span>,
-  pages <span class='op'>=</span> <span class='cn'>NA</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_soil_degradation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_degradation()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_degradation</span><span class='op'>(</span>
-  <span class='va'>soils</span>,
-  <span class='va'>DT50_mod</span>,
-  <span class='va'>DT50_mod_ref</span>,
-  type <span class='op'>=</span> <span class='cn'>NA</span>,
-  country <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
-  perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
-  temperature <span class='op'>=</span> <span class='cn'>NA</span>,
-  moisture <span class='op'>=</span> <span class='cn'>NA</span>,
-  category <span class='op'>=</span> <span class='st'>"lab"</span>,
-  formulation <span class='op'>=</span> <span class='cn'>NA</span>,
-  model <span class='op'>=</span> <span class='cn'>NA</span>,
-  chi2 <span class='op'>=</span> <span class='cn'>NA</span>,
-  remark <span class='op'>=</span> <span class='st'>""</span>,
-  <span class='va'>source</span>,
-  page <span class='op'>=</span> <span class='cn'>NA</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_soil_ff"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_ff()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_soil_sorption"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_sorption()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_sorption</span><span class='op'>(</span>
-  <span class='va'>soils</span>,
-  <span class='va'>Kf</span>,
-  <span class='va'>Kfoc</span>,
-  <span class='va'>N</span>,
-  type <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
-  perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
-  perc_clay <span class='op'>=</span> <span class='cn'>NA</span>,
-  CEC <span class='op'>=</span> <span class='cn'>NA</span>,
-  remark <span class='op'>=</span> <span class='st'>""</span>,
-  <span class='va'>source</span>,
-  page <span class='op'>=</span> <span class='cn'>NA</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-pdf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/pdf.html'>pdf()</a></code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>pdf</span><span class='op'>(</span>
-  file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".pdf"</span><span class='op'>)</span>,
-  dir <span class='op'>=</span> <span class='st'>"structures/pdf"</span>,
-  template <span class='op'>=</span> <span class='cn'>NULL</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-png"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/png.html'>png()</a></code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>png</span><span class='op'>(</span>
-  file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".png"</span><span class='op'>)</span>,
-  dir <span class='op'>=</span> <span class='st'>"structures/png"</span>,
-  antialias <span class='op'>=</span> <span class='st'>"gray"</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-emf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>emf()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>emf</span><span class='op'>(</span>file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".emf"</span><span class='op'>)</span>, dir <span class='op'>=</span> <span class='st'>"structures/emf"</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
-<p><div class="arguments"></p><dl>
-<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
-
-</dl><p></div></p>
-
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><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><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
-#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier 1-octanol 
-#&gt; InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;              user PubChem_Canonical 
-#&gt;       "CCCCCCCCO"       "CCCCCCCCO" 
-#&gt; Molecular weight $mw: 130.2 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "1-octanol"        "Octan-1-ol"       "octanol"          "111-87-5"        
-#&gt;  [5] "N-octanol"        "Octyl alcohol"    "Capryl alcohol"   "caprylic alcohol"
-#&gt;  [9] "n-Octyl alcohol"  "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='input'>
-<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>
-</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier caffeine 
-#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;              PubChem_Canonical 
-#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#&gt; Molecular weight $mw: 194.2 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "caffeine"                "58-08-2"                
-#&gt;  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#&gt;  [5] "Thein"                   "Methyltheobromine"      
-#&gt;  [7] "Cafeina"                 "Theine"                 
-#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre>
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-chent-new"><code>chent$new()</code></a></p></li>
+<li><p><a href="#method-chent-try_pubchem"><code>chent$try_pubchem()</code></a></p></li>
+<li><p><a href="#method-chent-get_pubchem"><code>chent$get_pubchem()</code></a></p></li>
+<li><p><a href="#method-chent-get_rdkit"><code>chent$get_rdkit()</code></a></p></li>
+<li><p><a href="#method-chent-get_chyaml"><code>chent$get_chyaml()</code></a></p></li>
+<li><p><a href="#method-chent-add_p0"><code>chent$add_p0()</code></a></p></li>
+<li><p><a href="#method-chent-add_cwsat"><code>chent$add_cwsat()</code></a></p></li>
+<li><p><a href="#method-chent-add_PUF"><code>chent$add_PUF()</code></a></p></li>
+<li><p><a href="#method-chent-add_TP"><code>chent$add_TP()</code></a></p></li>
+<li><p><a href="#method-chent-add_transformation"><code>chent$add_transformation()</code></a></p></li>
+<li><p><a href="#method-chent-add_soil_degradation"><code>chent$add_soil_degradation()</code></a></p></li>
+<li><p><a href="#method-chent-add_soil_ff"><code>chent$add_soil_ff()</code></a></p></li>
+<li><p><a href="#method-chent-add_soil_sorption"><code>chent$add_soil_sorption()</code></a></p></li>
+<li><p><a href="#method-chent-pdf"><code>chent$pdf()</code></a></p></li>
+<li><p><a href="#method-chent-png"><code>chent$png()</code></a></p></li>
+<li><p><a href="#method-chent-emf"><code>chent$emf()</code></a></p></li>
+<li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-chent-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">identifier</span>,</span>
+<span>  smiles <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  pubchem_from <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">"name"</span>, <span class="st">"smiles"</span>, <span class="st">"inchikey"</span><span class="op">)</span>,</span>
+<span>  rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  chyaml <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>identifier</code></dt>
+<dd><p>Identifier to be stored in the object</p></dd>
+
+
+<dt><code>smiles</code></dt>
+<dd><p>Optional user provided SMILES code</p></dd>
+
+
+<dt><code>inchikey</code></dt>
+<dd><p>Optional user provided InChI Key</p></dd>
+
+
+<dt><code>pubchem</code></dt>
+<dd><p>Should an attempt be made to retrieve chemical
+information from PubChem via the webchem package?</p></dd>
+
+
+<dt><code>pubchem_from</code></dt>
+<dd><p>Possibility to select the argument
+that is used to query pubchem</p></dd>
+
+
+<dt><code>rdkit</code></dt>
+<dd><p>Should an attempt be made to retrieve chemical
+information from a local rdkit installation via python
+and the reticulate package?</p></dd>
+
+
+<dt><code>template</code></dt>
+<dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
+
+
+<dt><code>chyaml</code></dt>
+<dd><p>Should we look for a identifier.yaml file in the working
+directory?
+Try to get chemical information from PubChem</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</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">
+<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">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>query</code></dt>
+<dd><p>Query string to be passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd>
+
+
+<dt><code>from</code></dt>
+<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a>
+Get chemical information from PubChem for a known PubChem CID</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section">
+<h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3>
+
+<div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+
+<div class="section">
+<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt>
+<dd><p>CID</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</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>
+
+<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">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section">
+<h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3>
+
+<div class="section">
+<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+<span>  chyaml <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="fu"><a href="https://rdrr.io/r/utils/URLencode.html" class="external-link">URLencode</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".yaml"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_p0"></a><div class="section">
+<h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3>
+
+<div class="section">
+<h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+
+
+</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">
+<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">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section">
+<h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3>
+
+<div class="section">
+<h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span>
+<span>  PUF <span class="op">=</span> <span class="fl">0</span>,</span>
+<span>  source <span class="op">=</span> <span class="st">"focus_generic_gw_2014"</span>,</span>
+<span>  page <span class="op">=</span> <span class="fl">41</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">"Conservative default value"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</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">
+<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">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section">
+<h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3>
+
+<div class="section">
+<h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span>
+<span>  <span class="va">study_type</span>,</span>
+<span>  <span class="va">TP_identifier</span>,</span>
+<span>  <span class="va">max_occurrence</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">""</span>,</span>
+<span>  source <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pages <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</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">
+<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">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span>
+<span>  <span class="va">soils</span>,</span>
+<span>  <span class="va">DT50_mod</span>,</span>
+<span>  <span class="va">DT50_mod_ref</span>,</span>
+<span>  type <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  country <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  temperature <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  category <span class="op">=</span> <span class="st">"lab"</span>,</span>
+<span>  formulation <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  model <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  chi2 <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">""</span>,</span>
+<span>  <span class="va">source</span>,</span>
+<span>  page <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section">
+<h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3>
+
+<div class="section">
+<h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+
+
+</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">
+<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">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span>
+<span>  <span class="va">soils</span>,</span>
+<span>  <span class="va">Kf</span>,</span>
+<span>  <span class="va">Kfoc</span>,</span>
+<span>  <span class="va">N</span>,</span>
+<span>  type <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  perc_clay <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  CEC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">""</span>,</span>
+<span>  <span class="va">source</span>,</span>
+<span>  page <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-pdf"></a><div class="section">
+<h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3>
+
+<div class="section">
+<h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span>
+<span>  dir <span class="op">=</span> <span class="st">"structures/pdf"</span>,</span>
+<span>  template <span class="op">=</span> <span class="cn">NULL</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-png"></a><div class="section">
+<h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3>
+
+<div class="section">
+<h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span>
+<span>  dir <span class="op">=</span> <span class="st">"structures/png"</span>,</span>
+<span>  antialias <span class="op">=</span> <span class="st">"gray"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-emf"></a><div class="section">
+<h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3>
+
+<div class="section">
+<h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">emf</span><span class="op">(</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">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-16">Usage<a class="anchor" aria-label="anchor" href="#usage-16"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</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-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 $mw: 130.2 </span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</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-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-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 $mw: 194.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "caffeine"                "58-08-2"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</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>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
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+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
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+  <p></p><p>Developed by Johannes Ranke.</p>
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index 1805ff1..cae8c0b 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -1,67 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="../bootstrap-toc.css">
-<script src="../bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent" />
-<meta property="og:description" content="Draw SVG graph from a chent object using RDKit" />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- 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=1.0"><title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent"><meta property="og:description" content="Draw SVG graph from a chent object using RDKit"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Draw SVG graph from a chent object using RDKit</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>draw_svg.chent.Rd</code></div>
     </div>
 
@@ -117,65 +49,60 @@
     <p>Draw SVG graph from a chent object using RDKit</p>
     </div>
 
-    <pre class="usage"><span class='fu'>draw_svg.chent</span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  width <span class='op'>=</span> <span class='fl'>300</span>,
-  height <span class='op'>=</span> <span class='fl'>150</span>,
-  filename <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".svg"</span><span class='op'>)</span>,
-  subdir <span class='op'>=</span> <span class='st'>"svg"</span>
-<span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be plotted</p></td>
-    </tr>
-    <tr>
-      <th>width</th>
-      <td><p>The desired width in pixels</p></td>
-    </tr>
-    <tr>
-      <th>height</th>
-      <td><p>The desired height in pixels</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>The filename</p></td>
-    </tr>
-    <tr>
-      <th>subdir</th>
-      <td><p>The path to which the file should be written</p></td>
-    </tr>
-    </table>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">draw_svg.chent</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  width <span class="op">=</span> <span class="fl">300</span>,</span>
+<span>  height <span class="op">=</span> <span class="fl">150</span>,</span>
+<span>  filename <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".svg"</span><span class="op">)</span>,</span>
+<span>  subdir <span class="op">=</span> <span class="st">"svg"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be plotted</p></dd>
+
 
+<dt>width</dt>
+<dd><p>The desired width in pixels</p></dd>
+
+
+<dt>height</dt>
+<dd><p>The desired height in pixels</p></dd>
+
+
+<dt>filename</dt>
+<dd><p>The filename</p></dd>
+
+
+<dt>subdir</dt>
+<dd><p>The path to which the file should be written</p></dd>
+
+</dl></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 9de4a87..d9eb797 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,66 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="../bootstrap-toc.css">
-<script src="../bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- 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=1.0"><title>Function reference • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-index">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -71,136 +17,86 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="contents col-md-9">
     <div class="page-header">
       <h1>Reference</h1>
     </div>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2>
+    <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
+          <h2 id="r-class-definitions-and-methods">R6 Class definitions and methods <a href="#r-class-definitions-and-methods" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p>
         </th>
-      </tr>
-      
-      
-    </tbody><tbody>
-      
-      
-      <tr>
-        
-        <td>
+      </tr></tbody><tbody><tr><td>
           <p><code><a href="chent.html">chent</a></code> </p>
         </td>
         <td><p>An R6 class for chemical entities with associated data</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="draw_svg.chent.html">draw_svg.chent()</a></code> </p>
         </td>
         <td><p>Draw SVG graph from a chent object using RDKit</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="plot.chent.html">plot(<i>&lt;chent&gt;</i>)</a></code> </p>
         </td>
         <td><p>Plot method for chent objects</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="print.chent.html">print(<i>&lt;chent&gt;</i>)</a></code> </p>
         </td>
         <td><p>Printing method for chent objects</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="pai.html">pai</a></code> </p>
         </td>
         <td><p>An R6 class for pesticidal active ingredients and associated data</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="print.pai.html">print(<i>&lt;pai&gt;</i>)</a></code> </p>
         </td>
         <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="pp.html">pp</a></code> </p>
         </td>
         <td><p>R6 class for holding a product with at least one active ingredient</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+      </tr></tbody></table></div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
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+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
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-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png
index c235304..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 0bb3399..636007f 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -1,68 +1,13 @@
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 <!DOCTYPE html>
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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+Additional chemical information is retrieved from the internet if available."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]-->
-
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-
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
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+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -73,44 +18,31 @@ Additional chemical information is retrieved from the internet if available." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
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-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
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+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>An R6 class for pesticidal active ingredients and associated data</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>pai.Rd</code></div>
     </div>
 
@@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.</p>
     </div>
 
 
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object</p>
+    </div>
+    <div id="super-class">
+    <h2>Super class</h2>
+    <p><code><a href="chent.html">chents::chent</a></code> -&gt; <code>pai</code></p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>iso</code></dt>
+<dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+
+
+<dt><code>bcpc</code></dt>
+<dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <code>R6Class</code> generator object</p>
-    <h2 class="hasAnchor" id="super-class"><a class="anchor" href="#super-class"></a>Super class</h2>
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
+    
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-pai-new"><code>pai$new()</code></a></p></li>
+<li><p><a href="#method-pai-clone"><code>pai$clone()</code></a></p></li>
+</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chents::chent$add_PUF()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chents::chent$add_TP()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chents::chent$add_cwsat()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chents::chent$add_p0()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chents::chent$add_soil_degradation()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chents::chent$add_soil_ff()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chents::chent$add_soil_sorption()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chents::chent$add_transformation()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chents::chent$emf()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chents::chent$get_chyaml()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chents::chent$get_pubchem()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chents::chent$get_rdkit()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chents::chent$pdf()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chents::chent$png()</code></a></span></li>
+<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$try_pubchem()</code></a></span></li>
+</ul></details></p><hr><a id="method-pai-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">iso</span>,</span>
+<span>  identifier <span class="op">=</span> <span class="va">iso</span>,</span>
+<span>  smiles <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  bcpc <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  pubchem_from <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  chyaml <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-    <p><code><a href='chent.html'>chents::chent</a></code> -&gt; <code>pai</code></p>
-    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    <p><div class="r6-fields"></p><dl>
-<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+</div><p></p><hr><a id="method-pai-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</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">pai</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
 
-</dl><p></div></p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
-    
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
-
-<ul>
-<li><p><a href='#method-new'><code>pai$new()</code></a></p></li>
-<li><p><a href='#method-clone'><code>pai$clone()</code></a></p></li>
-</ul>
-<p><details ><summary>Inherited methods</summary>
-<ul>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-add_PUF'><code>chents::chent$add_PUF()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-add_TP'><code>chents::chent$add_TP()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-add_p0'><code>chents::chent$add_p0()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-add_transformation'><code>chents::chent$add_transformation()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-emf'><code>chents::chent$emf()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-pdf'><code>chents::chent$pdf()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-png'><code>chents::chent$png()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></p></li>
-</ul>
-</details>
-
-<hr>
-<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
-  <span class='va'>iso</span>,
-  identifier <span class='op'>=</span> <span class='va'>iso</span>,
-  smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
-  smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
-  inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  bcpc <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  pubchem_from <span class='op'>=</span> <span class='st'>"auto"</span>,
-  rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  template <span class='op'>=</span> <span class='cn'>NULL</span>,
-  chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
-<p><div class="arguments"></p><dl>
-<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
-
-</dl><p></div></p>
-
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='co'># On Travis, we get a certificate validation error,</span>
-<span class='co'># likely because the system (xenial) is so old,</span>
-<span class='co'># therefore don't run this example on Travis</span>
-<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>""</span><span class='op'>)</span> <span class='op'>{</span>
-
-<span class='va'>atr</span> <span class='op'>&lt;-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</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'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span>
-<span class='op'>}</span>
-
-<span class='op'>}</span>
-</div><div class='output co'>#&gt; <span class='message'>BCPC:</span></div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; &lt;pai&gt; with ISO common name $iso atrazine 
-#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier atrazine 
-#&gt; InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;            PubChem_Canonical 
-#&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
-#&gt; Molecular weight $mw: 215.7 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Chromozin"   
-#&gt;  [6] "Aktikon"      "Atrazin"      "Argezin"      "Atazinax"     "Atranex"     </div></pre>
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span>
+<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span>
+<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">atr</span> <span class="op">&lt;-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></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">atr</span><span class="op">)</span></span></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">atr</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">atr</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> BCPC:</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> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./atrazine.yaml</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">#&gt;</span> &lt;pai&gt; with ISO common name $iso atrazine </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 atrazine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey MXWJVTOOROXGIU-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> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 215.7 </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] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Aktikon"     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6] "Atranex"      "Chromozin"    "Atazinax"     "Atrasine"     "Gesoprim"    </span>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
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+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
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-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png
index 330f0a5..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 62bf38f..470ce79 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -1,67 +1,12 @@
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+<!-- 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=1.0"><title>Plot method for chent objects — plot.chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Plot method for chent objects — plot.chent"><meta property="og:description" content="Plot method for chent objects"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
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+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
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       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
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+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
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-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
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+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Plot method for chent objects</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>plot.chent.Rd</code></div>
     </div>
 
@@ -117,68 +49,70 @@
     <p>Plot method for chent objects</p>
     </div>
 
-    <pre class="usage"><span class='co'># S3 method for chent</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be plotted</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments passed to <code>grid.picture</code></p></td>
-    </tr>
-    </table>
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='va'>caffeine</span> <span class='op'>&lt;-</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>
-</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier caffeine 
-#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;              PubChem_Canonical 
-#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#&gt; Molecular weight $mw: 194.2 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "caffeine"                "58-08-2"                
-#&gt;  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#&gt;  [5] "Thein"                   "Methyltheobromine"      
-#&gt;  [7] "Cafeina"                 "Theine"                 
-#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></div></pre>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for chent</span></span>
+<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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be plotted</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Further arguments passed to <code>grid.picture</code></p></dd>
+
+</dl></div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</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">#&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-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 $mw: 194.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "caffeine"                "58-08-2"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</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="plot.chent-1.png" alt="" width="700" height="433"></span>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
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+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
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+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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-<![endif]-->
-
-
-
-  </head>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>R6 class for holding a product with at least one active ingredient</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>pp.Rd</code></div>
     </div>
 
@@ -118,89 +50,105 @@
     </div>
 
 
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object.</p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>name</code></dt>
+<dd><p>The name of the product</p></dd>
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <code>R6Class</code> generator object.</p>
-    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
+<dt><code>ais</code></dt>
+<dd><p>A list of active ingredients</p></dd>
 
-    <p><div class="r6-fields"></p><dl>
-<dt><code>name</code></dt><dd><p>The name of the product</p></dd>
 
-<dt><code>ais</code></dt><dd><p>A list of active ingredients</p></dd>
+<dt><code>concentrations</code></dt>
+<dd><p>The concentration of the ais</p></dd>
 
-<dt><code>concentrations</code></dt><dd><p>The concentration of the ais</p></dd>
 
-<dt><code>concentration_units</code></dt><dd><p>Defaults to g/L</p></dd>
+<dt><code>concentration_units</code></dt>
+<dd><p>Defaults to g/L</p></dd>
 
-</dl><p></div></p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
     
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-pp-new"><code>pp$new()</code></a></p></li>
+<li><p><a href="#method-pp-print"><code>pp$print()</code></a></p></li>
+<li><p><a href="#method-pp-clone"><code>pp$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-pp-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pp.html">pp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">name</span>,</span>
+<span>  <span class="va">...</span>,</span>
+<span>  <span class="va">concentrations</span>,</span>
+<span>  concentration_units <span class="op">=</span> <span class="st">"g/L"</span>,</span>
+<span>  density <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  density_units <span class="op">=</span> <span class="st">"g/L"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-<ul>
-<li><p><a href='#method-new'><code>pp$new()</code></a></p></li>
-<li><p><a href='#method-print'><code>pp$print()</code></a></p></li>
-<li><p><a href='#method-clone'><code>pp$clone()</code></a></p></li>
-</ul>
-<p><hr>
-<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
 
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
-  <span class='va'>name</span>,
-  <span class='va'>...</span>,
-  <span class='va'>concentrations</span>,
-  concentration_units <span class='op'>=</span> <span class='st'>"g/L"</span>,
-  density <span class='op'>=</span> <span class='fl'>1000</span>,
-  density_units <span class='op'>=</span> <span class='st'>"g/L"</span>
-<span class='op'>)</span></pre><p></div></p>
+</div><p></p><hr><a id="method-pp-print"></a><div class="section">
+<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
 
-<p><hr>
-<a id="method-print"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>
+<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">pp</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>print</span><span class='op'>(</span><span class='op'>)</span></pre><p></div></p>
 
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
+</div><p></p><hr><a id="method-pp-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">pp</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
 
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
-<p><div class="arguments"></p><dl>
-<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
 
-</dl><p></div></p>
+</dl><p></p></div>
+</div>
 
+</div>
 
+    </div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index b188ed9..08497dd 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -1,67 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Printing method for chent objects — print.chent • chents</title>
-
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-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
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-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- 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=1.0"><title>Printing method for chent objects — print.chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for chent objects — print.chent"><meta property="og:description" content="Printing method for chent objects"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Printing method for chent objects</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>print.chent.Rd</code></div>
     </div>
 
@@ -117,48 +49,43 @@
     <p>Printing method for chent objects</p>
     </div>
 
-    <pre class="usage"><span class='co'># S3 method for chent</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for chent</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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be printed</p></dd>
+
 
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be printed</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments for compatibility with the S3 method</p></td>
-    </tr>
-    </table>
+<dt>...</dt>
+<dd><p>Further arguments for compatibility with the S3 method</p></dd>
 
+</dl></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
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+      </footer></div>
 
   
 
 
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-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index 284792f..3faa5f7 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -1,67 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Printing method for pai objects (pesticidal active ingredients)</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <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>print.pai.Rd</code></div>
     </div>
 
@@ -117,48 +49,43 @@
     <p>Printing method for pai objects (pesticidal active ingredients)</p>
     </div>
 
-    <pre class="usage"><span class='co'># S3 method for pai</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for pai</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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be printed</p></dd>
+
 
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be printed</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments for compatibility with the S3 method</p></td>
-    </tr>
-    </table>
+<dt>...</dt>
+<dd><p>Further arguments for compatibility with the S3 method</p></dd>
 
+</dl></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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-   </div>
+      </footer></div>
 
   
 
 
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-</html>
+  
 
+  </body></html>
author	Ranke Johannes <johannes.ranke@agroscope.admin.ch>	2023-11-10 18:40:34 +0100
committer	Ranke Johannes <johannes.ranke@agroscope.admin.ch>	2023-11-10 19:21:11 +0100
commit	816de01ce642c1c3d633ffb1cbcf960036d27114 (patch)
tree	cf732b6e18bcc0864b481f804a1cb0b16bdd7d4d /docs/reference
parent	67384ac3c7c0b888d67d06473f81e46d520a7dd3 (diff)