Improve description with README text

Also, read the description into the Readme to have them in sync and update docs with roxygen 8.
author: Johannes Ranke <johannes.ranke@jrwb.de> 2026-07-03 11:51:32 +0200
committer: Johannes Ranke <johannes.ranke@jrwb.de> 2026-07-03 11:51:32 +0200
commit: 88027b7a70510b48bd7525ffcd536f0808d263e7 (patch)
tree: 94f83bd420d494334011ff8f67a27483130fe857 /docs
parent: 32caaedcc6b6b8addc9f23fce9dca4188f692fed (diff)
22 files changed, 323 insertions, 398 deletions
diff --git a/docs/404.html b/docs/404.html
index 22c2979..e909978 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="https://pkgdown.jrwb.de/chents/index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/authors.html b/docs/authors.html
index 162162f..c67c2a9 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -46,13 +46,13 @@
 
       <p>Ranke J (2026).
 <em>chents: Chemical Entities as R Objects</em>.
-R package version 0.4.1, <a href="https://pkgdown.jrwb.de/chents/">https://pkgdown.jrwb.de/chents/</a>.
+R package version 0.4.2, <a href="https://pkgdown.jrwb.de/chents/">https://pkgdown.jrwb.de/chents/</a>.
 </p>
       <pre>@Manual{,
   title = {chents: Chemical Entities as R Objects},
   author = {Johannes Ranke},
   year = {2026},
-  note = {R package version 0.4.1},
+  note = {R package version 0.4.2},
   url = {https://pkgdown.jrwb.de/chents/},
 }</pre>
     </div>
diff --git a/docs/authors.md b/docs/authors.md
index ff9ca2d..50354a2 100644
--- a/docs/authors.md
+++ b/docs/authors.md
@@ -10,12 +10,12 @@ Source:
 [`DESCRIPTION`](https://github.com/jranke/chents/blob/HEAD/DESCRIPTION)
 
 Ranke J (2026). *chents: Chemical Entities as R Objects*. R package
-version 0.4.1, <https://pkgdown.jrwb.de/chents/>.
+version 0.4.2, <https://pkgdown.jrwb.de/chents/>.
 
     @Manual{,
       title = {chents: Chemical Entities as R Objects},
       author = {Johannes Ranke},
       year = {2026},
-      note = {R package version 0.4.1},
+      note = {R package version 0.4.2},
       url = {https://pkgdown.jrwb.de/chents/},
     }
diff --git a/docs/index.html b/docs/index.html
index 2c6303f..5d7693c 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -11,8 +11,8 @@
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
 <link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
 <script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Chemical Entities as R Objects">
-<meta name="description" content="Utilities for dealing with chemical entities and associated data as R objects. If Python and RDKit (&gt; 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.">
-<meta property="og:description" content="Utilities for dealing with chemical entities and associated data as R objects. If Python and RDKit (&gt; 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.">
+<meta name="description" content="When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package chents provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. If Python and RDKit (&gt; 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.">
+<meta property="og:description" content="When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package chents provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. If Python and RDKit (&gt; 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.">
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -50,7 +50,10 @@
 <div class="page-header"><h1 id="chents">chents<a class="anchor" aria-label="anchor" href="#chents"></a>
 </h1></div>
 <p><a href="https://pkgdown.jrwb.de/chents/"><img src="https://img.shields.io/badge/docs-jrwb.de-blue.svg" alt="Online documentation"></a> <a href="https://jranke.r-universe.dev/chents" class="external-link"><img src="https://jranke.r-universe.dev/badges/chents" alt="R-Universe status"></a> <a href="https://pkgdown.jrwb.de/chents/coverage/coverage.html"><img src="https://img.shields.io/badge/coverage-jrwb.de-blue.svg" alt="Code coverage"></a></p>
-<p>When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package <strong>chents</strong> provides a way to define an R object corresponding to a chemically defined substances (“chemical entity”) and to collect related information.</p>
+<p>When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package ‘chents’ provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. If Python and ‘RDKit’ (&gt; 2015.03) are installed and configured for use with ‘reticulate’, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.</p>
+<div class="section level2">
+<h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
+</h2>
 <p>When first defining a chemical entity, some chemical information is retrieved from the <a href="https://pubchem.ncbi.nlm.nih.gov/" class="external-link">PubChem</a> website using the <a href="https://docs.ropensci.org/webchem/" class="external-link">webchem</a> package.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/chents/">chents</a></span><span class="op">)</span></span>
@@ -78,7 +81,7 @@
 <p>There is a very simple plotting method for the chemical structure.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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></code></pre></div>
-<p><img src="reference/figures/README-unnamed-chunk-4-1.png"><!-- --></p>
+<p><img src="reference/figures/README-unnamed-chunk-5-1.png"><!-- --></p>
 <p>If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the <a href="http://www.bcpcpesticidecompendium.org/" class="external-link">BCPC compendium</a> first.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">delta</span> <span class="op">&lt;-</span> <span class="va"><a href="reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Deltamethrin"</span><span class="op">)</span></span>
@@ -87,8 +90,9 @@
 <span><span class="co">#&gt; Get chemical information from RDKit using PubChem SMILES</span></span>
 <span><span class="co">#&gt; CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C</span></span>
 <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">delta</span><span class="op">)</span></span></code></pre></div>
-<p><img src="reference/figures/README-unnamed-chunk-5-1.png"><!-- --></p>
+<p><img src="reference/figures/README-unnamed-chunk-6-1.png"><!-- --></p>
 <p>Additional information can be read from a local .yaml file. This information can be leveraged e.g. by the <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html" class="external-link">PEC_soil</a> function of the ‘pfm’ package. However, this functionality is to be superseded by a dedicated package, defining data for the environmental risk assessment on chemicals, in particular on active ingredients of plant protection products.</p>
+</div>
 <div class="section level2">
 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h2>
diff --git a/docs/index.md b/docs/index.md
index 6eb0823..b8c02f3 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,9 +9,14 @@ coverage](https://img.shields.io/badge/coverage-jrwb.de-blue.svg)](https://pkgdo
 
 When working with data on chemical substances, we often need a reliable
 link between the data and the chemical identity of the substances. The R
-package **chents** provides a way to define an R object corresponding to
-a chemically defined substances (“chemical entity”) and to collect
-related information.
+package ‘chents’ provides a way to define an R object corresponding to a
+chemically defined substances, i.e. a chemical entity and to collect
+related information. If Python and ‘RDKit’ (\> 2015.03) are installed
+and configured for use with ‘reticulate’, some basic chemoinformatics
+functions like the calculation of molecular weight and plotting of
+chemical structures in R graphics are available.
+
+## Usage
 
 When first defining a chemical entity, some chemical information is
 retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website
@@ -56,7 +61,7 @@ There is a very simple plotting method for the chemical structure.
 plot(caffeine)
 ```
 
-![](reference/figures/README-unnamed-chunk-4-1.png)
+![](reference/figures/README-unnamed-chunk-5-1.png)
 
 If you have a so-called ISO common name of a pesticide active
 ingredient, you can use the ‘pai’ class derived from the ‘chent’ class,
@@ -72,7 +77,7 @@ delta <- pai$new("Deltamethrin")
 plot(delta)
 ```
 
-![](reference/figures/README-unnamed-chunk-5-1.png)
+![](reference/figures/README-unnamed-chunk-6-1.png)
 
 Additional information can be read from a local .yaml file. This
 information can be leveraged e.g. by the
diff --git a/docs/llms.txt b/docs/llms.txt
index 71e5865..c9a661b 100644
--- a/docs/llms.txt
+++ b/docs/llms.txt
@@ -9,9 +9,14 @@ coverage](https://img.shields.io/badge/coverage-jrwb.de-blue.svg)](https://pkgdo
 
 When working with data on chemical substances, we often need a reliable
 link between the data and the chemical identity of the substances. The R
-package **chents** provides a way to define an R object corresponding to
-a chemically defined substances (“chemical entity”) and to collect
-related information.
+package ‘chents’ provides a way to define an R object corresponding to a
+chemically defined substances, i.e. a chemical entity and to collect
+related information. If Python and ‘RDKit’ (\> 2015.03) are installed
+and configured for use with ‘reticulate’, some basic chemoinformatics
+functions like the calculation of molecular weight and plotting of
+chemical structures in R graphics are available.
+
+## Usage
 
 When first defining a chemical entity, some chemical information is
 retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website
@@ -56,7 +61,7 @@ There is a very simple plotting method for the chemical structure.
 plot(caffeine)
 ```
 
-![](reference/figures/README-unnamed-chunk-4-1.png)
+![](reference/figures/README-unnamed-chunk-5-1.png)
 
 If you have a so-called ISO common name of a pesticide active
 ingredient, you can use the ‘pai’ class derived from the ‘chent’ class,
@@ -72,7 +77,7 @@ delta <- pai$new("Deltamethrin")
 plot(delta)
 ```
 
-![](reference/figures/README-unnamed-chunk-5-1.png)
+![](reference/figures/README-unnamed-chunk-6-1.png)
 
 Additional information can be read from a local .yaml file. This
 information can be leveraged e.g. by the
diff --git a/docs/news/index.html b/docs/news/index.html
index 5a10ffd..2aa9c50 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index e2f241d..13ad23e 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -11,7 +11,7 @@ generated using RDKit if RDKit and its python bindings are installed."></head><b
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -46,7 +46,7 @@ generated using RDKit if RDKit and its python bindings are installed.</p>
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> generator object</p>
+    <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6Class</a> generator object</p>
     </div>
     <div class="section level2">
     <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
@@ -55,83 +55,83 @@ generated using RDKit if RDKit and its python bindings are installed.</p>
 The identifier that was used to initiate the object, with attribute 'source'</p></dd>
 
 
-<dt><code>inchikey</code></dt>
+    <dt><code>inchikey</code></dt>
 <dd><p>(<code>character(1)</code>)<br>
 InChI Key, with attribute 'source'</p></dd>
 
 
-<dt><code>smiles</code></dt>
+    <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>
+    <dt><code>mw</code></dt>
 <dd><p>(<code>numeric(1)</code>)<br>
 Molecular weight, with attribute 'source'</p></dd>
 
 
-<dt><code>pubchem</code></dt>
+    <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>
 
 
-<dt><code>rdkit</code></dt>
+    <dt><code>rdkit</code></dt>
 <dd><p>List of information obtained with RDKit</p></dd>
 
 
-<dt><code>mol</code></dt>
+    <dt><code>mol</code></dt>
 <dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</p></dd>
 
 
-<dt><code>svg</code></dt>
+    <dt><code>svg</code></dt>
 <dd><p>SVG code</p></dd>
 
 
-<dt><code>Picture</code></dt>
+    <dt><code>Picture</code></dt>
 <dd><p>Graph as a <a href="https://rdrr.io/pkg/grImport/man/Picture-class.html" class="external-link">grImport::Picture</a> object obtained using the grImport package</p></dd>
 
 
-<dt><code>Pict_font_size</code></dt>
+    <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>
+    <dt><code>pdf_height</code></dt>
 <dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
 
 
-<dt><code>p0</code></dt>
+    <dt><code>p0</code></dt>
 <dd><p>Vapour pressure in Pa</p></dd>
 
 
-<dt><code>cwsat</code></dt>
+    <dt><code>cwsat</code></dt>
 <dd><p>Water solubility in mg/L</p></dd>
 
 
-<dt><code>PUF</code></dt>
+    <dt><code>PUF</code></dt>
 <dd><p>Plant uptake factor</p></dd>
 
 
-<dt><code>chyaml</code></dt>
+    <dt><code>chyaml</code></dt>
 <dd><p>List of information obtained from a YAML file</p></dd>
 
 
-<dt><code>TPs</code></dt>
+    <dt><code>TPs</code></dt>
 <dd><p>List of transformation products as chent objects</p></dd>
 
 
-<dt><code>transformations</code></dt>
+    <dt><code>transformations</code></dt>
 <dd><p>Data frame of observed transformations</p></dd>
 
 
-<dt><code>soil_degradation</code></dt>
+    <dt><code>soil_degradation</code></dt>
 <dd><p>Dataframe of modelling DT50 values</p></dd>
 
 
-<dt><code>soil_ff</code></dt>
+    <dt><code>soil_ff</code></dt>
 <dd><p>Dataframe of formation fractions</p></dd>
 
 
-<dt><code>soil_sorption</code></dt>
+    <dt><code>soil_sorption</code></dt>
 <dd><p>Dataframe of soil sorption data</p></dd>
 
 
@@ -142,8 +142,7 @@ List of information retrieved from PubChem</p></dd>
 
 <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$new()</code></a></p></li>
+<p></p><ul><li><p><a href="#method-chent-initialize"><code>chent$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$get_rdkit()</code></a></p></li>
@@ -160,8 +159,8 @@ List of information retrieved from PubChem</p></dd>
 <li><p><a href="#method-chent-png"><code>chent$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>
+</ul></div><p></p><hr><a id="method-chent-initialize"></a><div class="section">
+<h3 id="chent-new-"><code>chent$new()</code><a class="anchor" aria-label="anchor" href="#chent-new-"></a></h3>
 <p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section">
 <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
@@ -174,43 +173,34 @@ List of information retrieved from PubChem</p></dd>
 <span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  chyaml <span class="op">=</span> <span class="cn">FALSE</span></span>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><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>
+      <dt><code>smiles</code></dt>
 <dd><p>Optional user provided SMILES code</p></dd>
 
-
-<dt><code>inchikey</code></dt>
+      <dt><code>inchikey</code></dt>
 <dd><p>Optional user provided InChI Key</p></dd>
 
-
-<dt><code>pubchem</code></dt>
+      <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>
+      <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>
+      <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>
+      <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>
+      <dt><code>chyaml</code></dt>
 <dd><p>Should we look for a identifier.yaml file in the working
 directory?</p></dd>
 
@@ -218,34 +208,33 @@ directory?</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>
+
+<p></p><hr><a id="method-chent-try_pubchem"></a><div class="section">
+<h3 id="chent-try-pubchem-"><code>chent$try_pubchem()</code><a class="anchor" aria-label="anchor" href="#chent-try-pubchem-"></a></h3>
 <p>Try to get chemical information from PubChem</p><div class="section">
 <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span>query <span class="op">=</span> <span class="va">self</span><span class="op">$</span><span class="va">identifier</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">
+</div><p></p><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>
+      <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></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>
+
+<p></p><hr><a id="method-chent-get_pubchem"></a><div class="section">
+<h3 id="chent-get-pubchem-"><code>chent$get_pubchem()</code><a class="anchor" aria-label="anchor" href="#chent-get-pubchem-"></a></h3>
 <p>Get chemical information from PubChem for a known PubChem CID</p><div class="section">
 <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><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>
@@ -254,14 +243,14 @@ directory?</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>
+
+<p></p><hr><a id="method-chent-get_rdkit"></a><div class="section">
+<h3 id="chent-get-rdkit-"><code>chent$get_rdkit()</code><a class="anchor" aria-label="anchor" href="#chent-get-rdkit-"></a></h3>
 <p>Get chemical information from RDKit if available</p><div class="section">
 <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><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>template</code></dt>
 <dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
@@ -270,101 +259,93 @@ directory?</p></dd>
 </dl><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>
+
+<p></p><hr><a id="method-chent-get_chyaml"></a><div class="section">
+<h3 id="chent-get-chyaml-"><code>chent$get_chyaml()</code><a class="anchor" aria-label="anchor" href="#chent-get-chyaml-"></a></h3>
 <p>Obtain information from a YAML file</p><div class="section">
 <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span>
 <span>  repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wd"</span>, <span class="st">"local"</span>, <span class="st">"web"</span><span class="op">)</span>,</span>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-4">Arguments<a class="anchor" aria-label="anchor" href="#arguments-4"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>repo</code></dt>
 <dd><p>Should the file be looked for in the current working
 directory, a local git repository under <code>~/git/chyaml</code>, or from
 the web (not implemented).</p></dd>
 
-
-<dt><code>chyaml</code></dt>
+      <dt><code>chyaml</code></dt>
 <dd><p>The filename to be looked for</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_p0"></a><div class="section">
+<h3 id="chent-add-p-"><code>chent$add_p0()</code><a class="anchor" aria-label="anchor" href="#chent-add-p-"></a></h3>
 <p>Add a vapour pressure</p><div class="section">
 <h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_p0</span><span class="op">(</span><span class="va">p0</span>, T <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>p0</code></dt>
 <dd><p>The vapour pressure in Pa</p></dd>
 
-
-<dt><code>T</code></dt>
+      <dt><code>T</code></dt>
 <dd><p>Temperature</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>page</code></dt>
+      <dt><code>page</code></dt>
 <dd><p>The page from which the information was taken</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_cwsat"></a><div class="section">
+<h3 id="chent-add-cwsat-"><code>chent$add_cwsat()</code><a class="anchor" aria-label="anchor" href="#chent-add-cwsat-"></a></h3>
 <p>Add a water solubility</p><div class="section">
 <h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>cwsat</code></dt>
 <dd><p>The water solubility in mg/L</p></dd>
 
-
-<dt><code>T</code></dt>
+      <dt><code>T</code></dt>
 <dd><p>Temperature</p></dd>
 
-
-<dt><code>pH</code></dt>
+      <dt><code>pH</code></dt>
 <dd><p>pH value</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>page</code></dt>
+      <dt><code>page</code></dt>
 <dd><p>The page from which the information was taken</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_PUF"></a><div class="section">
+<h3 id="chent-add-puf-"><code>chent$add_PUF()</code><a class="anchor" aria-label="anchor" href="#chent-add-puf-"></a></h3>
 <p>Add a plant uptake factor</p><div class="section">
 <h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span>
@@ -373,55 +354,50 @@ the web (not implemented).</p></dd>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-7">Arguments<a class="anchor" aria-label="anchor" href="#arguments-7"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>PUF</code></dt>
 <dd><p>The plant uptake factor, a number between 0 and 1</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>page</code></dt>
+      <dt><code>page</code></dt>
 <dd><p>The page from which the information was taken</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_TP"></a><div class="section">
+<h3 id="chent-add-tp-"><code>chent$add_TP()</code><a class="anchor" aria-label="anchor" href="#chent-add-tp-"></a></h3>
 <p>Add a transformation product to the internal list</p><div class="section">
 <h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-8">Arguments<a class="anchor" aria-label="anchor" href="#arguments-8"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>x</code></dt>
 <dd><p>A chent object, or an identifier to generate a chent object</p></dd>
 
-
-<dt><code>smiles</code></dt>
+      <dt><code>smiles</code></dt>
 <dd><p>Optional user provided SMILES code</p></dd>
 
-
-<dt><code>pubchem</code></dt>
+      <dt><code>pubchem</code></dt>
 <dd><p>Should chemical information be obtained from PubChem?</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_transformation"></a><div class="section">
+<h3 id="chent-add-transformation-"><code>chent$add_transformation()</code><a class="anchor" aria-label="anchor" href="#chent-add-transformation-"></a></h3>
 <p>Add a line in the internal dataframe holding observed transformations</p><div class="section">
 <h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span>
@@ -432,42 +408,37 @@ the web (not implemented).</p></dd>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-9">Arguments<a class="anchor" aria-label="anchor" href="#arguments-9"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>study_type</code></dt>
 <dd><p>A characterisation of the study type</p></dd>
 
-
-<dt><code>TP_identifier</code></dt>
+      <dt><code>TP_identifier</code></dt>
 <dd><p>An identifier of one of the transformation products
 in <code>self$TPs</code></p></dd>
 
-
-<dt><code>max_occurrence</code></dt>
+      <dt><code>max_occurrence</code></dt>
 <dd><p>The maximum observed occurrence of the
 transformation product, expressed as a fraction of the amount that would
 result from stochiometric transformation</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>pages</code></dt>
+      <dt><code>pages</code></dt>
 <dd><p>The pages from which the information was taken</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section">
+<h3 id="chent-add-soil-degradation-"><code>chent$add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#chent-add-soil-degradation-"></a></h3>
 <p>Add a line in the internal dataframe holding modelling DT50 values</p><div class="section">
 <h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span>
@@ -490,126 +461,104 @@ result from stochiometric transformation</p></dd>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-10">Arguments<a class="anchor" aria-label="anchor" href="#arguments-10"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>soils</code></dt>
 <dd><p>Names of the soils</p></dd>
 
-
-<dt><code>DT50_mod</code></dt>
+      <dt><code>DT50_mod</code></dt>
 <dd><p>The modelling DT50 in the sense of regulatory pesticide
 fate modelling</p></dd>
 
-
-<dt><code>DT50_mod_ref</code></dt>
+      <dt><code>DT50_mod_ref</code></dt>
 <dd><p>The normalised modelling DT50 in the sense of
 regulatory pesticide fate modelling</p></dd>
 
-
-<dt><code>type</code></dt>
+      <dt><code>type</code></dt>
 <dd><p>The soil type</p></dd>
 
-
-<dt><code>country</code></dt>
+      <dt><code>country</code></dt>
 <dd><p>The country (mainly for field studies)</p></dd>
 
-
-<dt><code>pH_orig</code></dt>
+      <dt><code>pH_orig</code></dt>
 <dd><p>The pH stated in the study</p></dd>
 
-
-<dt><code>pH_medium</code></dt>
+      <dt><code>pH_medium</code></dt>
 <dd><p>The medium in which this pH was measured</p></dd>
 
-
-<dt><code>pH_H2O</code></dt>
+      <dt><code>pH_H2O</code></dt>
 <dd><p>The pH extrapolated to pure water</p></dd>
 
-
-<dt><code>perc_OC</code></dt>
+      <dt><code>perc_OC</code></dt>
 <dd><p>The percentage of organic carbon in the soil</p></dd>
 
-
-<dt><code>temperature</code></dt>
+      <dt><code>temperature</code></dt>
 <dd><p>The temperature during the study in degrees Celsius</p></dd>
 
-
-<dt><code>moisture</code></dt>
+      <dt><code>moisture</code></dt>
 <dd><p>The moisture during the study</p></dd>
 
-
-<dt><code>category</code></dt>
+      <dt><code>category</code></dt>
 <dd><p>Is it a laboratory ('lab') or field study ('field')</p></dd>
 
-
-<dt><code>formulation</code></dt>
+      <dt><code>formulation</code></dt>
 <dd><p>Name of the formulation applied, if it was not
 the technical active ingredient</p></dd>
 
-
-<dt><code>model</code></dt>
+      <dt><code>model</code></dt>
 <dd><p>The degradation model used for deriving <code>DT50_mod</code></p></dd>
 
-
-<dt><code>chi2</code></dt>
+      <dt><code>chi2</code></dt>
 <dd><p>The relative error as defined in FOCUS kinetics</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>page</code></dt>
+      <dt><code>page</code></dt>
 <dd><p>The page from which the information was taken</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section">
+<h3 id="chent-add-soil-ff-"><code>chent$add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#chent-add-soil-ff-"></a></h3>
 <p>Add one or more formation fractions for degradation in soil</p><div class="section">
 <h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-11">Arguments<a class="anchor" aria-label="anchor" href="#arguments-11"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>target</code></dt>
 <dd><p>The identifier(s) of the transformation product</p></dd>
 
-
-<dt><code>soils</code></dt>
+      <dt><code>soils</code></dt>
 <dd><p>The soil name(s) in which the transformation was observed</p></dd>
 
-
-<dt><code>ff</code></dt>
+      <dt><code>ff</code></dt>
 <dd><p>The formation fraction(s)</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>page</code></dt>
+      <dt><code>page</code></dt>
 <dd><p>The page from which the information was taken</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section">
+<h3 id="chent-add-soil-sorption-"><code>chent$add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#chent-add-soil-sorption-"></a></h3>
 <p>Add soil sorption data</p><div class="section">
 <h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span>
@@ -628,72 +577,59 @@ the technical active ingredient</p></dd>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-12">Arguments<a class="anchor" aria-label="anchor" href="#arguments-12"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>soils</code></dt>
 <dd><p>Names of the soils</p></dd>
 
-
-<dt><code>Kf</code></dt>
+      <dt><code>Kf</code></dt>
 <dd><p>The sorption constant in L/kg, either linear (then <code>N</code> is 1)
 or according to Freundlich</p></dd>
 
-
-<dt><code>Kfoc</code></dt>
+      <dt><code>Kfoc</code></dt>
 <dd><p>The constant from above, normalised to soil organic carbon</p></dd>
 
-
-<dt><code>N</code></dt>
+      <dt><code>N</code></dt>
 <dd><p>The Freundlich exponent</p></dd>
 
-
-<dt><code>type</code></dt>
+      <dt><code>type</code></dt>
 <dd><p>The soil type</p></dd>
 
-
-<dt><code>pH_orig</code></dt>
+      <dt><code>pH_orig</code></dt>
 <dd><p>The pH stated in the study</p></dd>
 
-
-<dt><code>pH_medium</code></dt>
+      <dt><code>pH_medium</code></dt>
 <dd><p>The medium in which this pH was measured</p></dd>
 
-
-<dt><code>pH_H2O</code></dt>
+      <dt><code>pH_H2O</code></dt>
 <dd><p>The pH extrapolated to pure water</p></dd>
 
-
-<dt><code>perc_OC</code></dt>
+      <dt><code>perc_OC</code></dt>
 <dd><p>The percentage of organic carbon in the soil</p></dd>
 
-
-<dt><code>perc_clay</code></dt>
+      <dt><code>perc_clay</code></dt>
 <dd><p>The percentage of clay in the soil</p></dd>
 
-
-<dt><code>CEC</code></dt>
+      <dt><code>CEC</code></dt>
 <dd><p>The cation exchange capacity</p></dd>
 
-
-<dt><code>remark</code></dt>
+      <dt><code>remark</code></dt>
 <dd><p>A remark</p></dd>
 
-
-<dt><code>source</code></dt>
+      <dt><code>source</code></dt>
 <dd><p>An acronym specifying the source of the information</p></dd>
 
-
-<dt><code>page</code></dt>
+      <dt><code>page</code></dt>
 <dd><p>The page from which the information was taken</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-pdf"></a><div class="section">
+<h3 id="chent-pdf-"><code>chent$pdf()</code><a class="anchor" aria-label="anchor" href="#chent-pdf-"></a></h3>
 <p>Write a PDF image of the structure</p><div class="section">
 <h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span>
@@ -701,27 +637,25 @@ or according to Freundlich</p></dd>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-13">Arguments<a class="anchor" aria-label="anchor" href="#arguments-13"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>file</code></dt>
 <dd><p>The file to write to</p></dd>
 
-
-<dt><code>dir</code></dt>
+      <dt><code>dir</code></dt>
 <dd><p>The directory to write the file to</p></dd>
 
-
-<dt><code>template</code></dt>
+      <dt><code>template</code></dt>
 <dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-png"></a><div class="section">
+<h3 id="chent-png-"><code>chent$png()</code><a class="anchor" aria-label="anchor" href="#chent-png-"></a></h3>
 <p>Write a PNG image of the structure</p><div class="section">
 <h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span>
@@ -729,53 +663,48 @@ or according to Freundlich</p></dd>
 <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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>file</code></dt>
 <dd><p>The file to write to</p></dd>
 
-
-<dt><code>dir</code></dt>
+      <dt><code>dir</code></dt>
 <dd><p>The directory to write the file to</p></dd>
 
-
-<dt><code>antialias</code></dt>
+      <dt><code>antialias</code></dt>
 <dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a></p></dd>
 
 
 </dl><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>
+
+<p></p><hr><a id="method-chent-emf"></a><div class="section">
+<h3 id="chent-emf-"><code>chent$emf()</code><a class="anchor" aria-label="anchor" href="#chent-emf-"></a></h3>
 <p>Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p><div class="section">
 <h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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 class="section">
+</div><p></p><div class="section">
 <h4 id="arguments-15">Arguments<a class="anchor" aria-label="anchor" href="#arguments-15"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>file</code></dt>
 <dd><p>The file to write to</p></dd>
 
-
-<dt><code>dir</code></dt>
+      <dt><code>dir</code></dt>
 <dd><p>The directory to write the file to</p></dd>
 
 
 </dl><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>
+</div>
+
+<p></p><hr><a id="method-chent-clone"></a><div class="section">
+<h3 id="chent-clone-"><code>chent$clone()</code><a class="anchor" aria-label="anchor" href="#chent-clone-"></a></h3>
 <p>The objects of this class are cloneable with this method.</p><div class="section">
 <h4 id="usage-16">Usage<a class="anchor" aria-label="anchor" href="#usage-16"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">
+</div><p></p><div class="section">
 <h4 id="arguments-16">Arguments<a class="anchor" aria-label="anchor" href="#arguments-16"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
@@ -786,6 +715,7 @@ or according to Freundlich</p></dd>
 
 </div>
 
+
     </div>
 
     <div class="section level2">
diff --git a/docs/reference/chent.md b/docs/reference/chent.md
index 40716ce..aeaac75 100644
--- a/docs/reference/chent.md
+++ b/docs/reference/chent.md
@@ -6,7 +6,7 @@ RDKit if RDKit and its python bindings are installed.
 
 ## Format
 
-An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator
+An [R6Class](https://r6.r-lib.org/reference/R6Class.html) generator
 object
 
 ## Public fields
@@ -103,7 +103,7 @@ object
 
 ### Public methods
 
-- [`chent$new()`](#method-chent-new)
+- [`chent$new()`](#method-chent-initialize)
 
 - [`chent$try_pubchem()`](#method-chent-try_pubchem)
 
@@ -139,7 +139,7 @@ object
 
 ------------------------------------------------------------------------
 
-### Method `new()`
+### `chent$new()`
 
 Creates a new instance of this
 [R6](https://r6.r-lib.org/reference/R6Class.html) class.
@@ -195,7 +195,7 @@ Creates a new instance of this
 
 ------------------------------------------------------------------------
 
-### Method `try_pubchem()`
+### `chent$try_pubchem()`
 
 Try to get chemical information from PubChem
 
@@ -217,7 +217,7 @@ Try to get chemical information from PubChem
 
 ------------------------------------------------------------------------
 
-### Method `get_pubchem()`
+### `chent$get_pubchem()`
 
 Get chemical information from PubChem for a known PubChem CID
 
@@ -233,7 +233,7 @@ Get chemical information from PubChem for a known PubChem CID
 
 ------------------------------------------------------------------------
 
-### Method `get_rdkit()`
+### `chent$get_rdkit()`
 
 Get chemical information from RDKit if available
 
@@ -249,7 +249,7 @@ Get chemical information from RDKit if available
 
 ------------------------------------------------------------------------
 
-### Method `get_chyaml()`
+### `chent$get_chyaml()`
 
 Obtain information from a YAML file
 
@@ -274,7 +274,7 @@ Obtain information from a YAML file
 
 ------------------------------------------------------------------------
 
-### Method `add_p0()`
+### `chent$add_p0()`
 
 Add a vapour pressure
 
@@ -306,7 +306,7 @@ Add a vapour pressure
 
 ------------------------------------------------------------------------
 
-### Method `add_cwsat()`
+### `chent$add_cwsat()`
 
 Add a water solubility
 
@@ -342,7 +342,7 @@ Add a water solubility
 
 ------------------------------------------------------------------------
 
-### Method `add_PUF()`
+### `chent$add_PUF()`
 
 Add a plant uptake factor
 
@@ -375,7 +375,7 @@ Add a plant uptake factor
 
 ------------------------------------------------------------------------
 
-### Method `add_TP()`
+### `chent$add_TP()`
 
 Add a transformation product to the internal list
 
@@ -399,7 +399,7 @@ Add a transformation product to the internal list
 
 ------------------------------------------------------------------------
 
-### Method `add_transformation()`
+### `chent$add_transformation()`
 
 Add a line in the internal dataframe holding observed transformations
 
@@ -444,7 +444,7 @@ Add a line in the internal dataframe holding observed transformations
 
 ------------------------------------------------------------------------
 
-### Method `add_soil_degradation()`
+### `chent$add_soil_degradation()`
 
 Add a line in the internal dataframe holding modelling DT50 values
 
@@ -549,7 +549,7 @@ Add a line in the internal dataframe holding modelling DT50 values
 
 ------------------------------------------------------------------------
 
-### Method `add_soil_ff()`
+### `chent$add_soil_ff()`
 
 Add one or more formation fractions for degradation in soil
 
@@ -585,7 +585,7 @@ Add one or more formation fractions for degradation in soil
 
 ------------------------------------------------------------------------
 
-### Method `add_soil_sorption()`
+### `chent$add_soil_sorption()`
 
 Add soil sorption data
 
@@ -669,7 +669,7 @@ Add soil sorption data
 
 ------------------------------------------------------------------------
 
-### Method [`pdf()`](https://rdrr.io/r/grDevices/pdf.html)
+### `chent$pdf()`
 
 Write a PDF image of the structure
 
@@ -697,7 +697,7 @@ Write a PDF image of the structure
 
 ------------------------------------------------------------------------
 
-### Method [`png()`](https://rdrr.io/r/grDevices/png.html)
+### `chent$png()`
 
 Write a PNG image of the structure
 
@@ -725,7 +725,7 @@ Write a PNG image of the structure
 
 ------------------------------------------------------------------------
 
-### Method `emf()`
+### `chent$emf()`
 
 Write an EMF image of the structure using
 [emf](https://rdrr.io/pkg/devEMF/man/emf.html)
@@ -746,7 +746,7 @@ Write an EMF image of the structure using
 
 ------------------------------------------------------------------------
 
-### Method `clone()`
+### `chent$clone()`
 
 The objects of this class are cloneable with this method.
 
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index dd50cd9..8bea16c 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,7 +82,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/figures/README-unnamed-chunk-5-1.png b/docs/reference/figures/README-unnamed-chunk-5-1.png
index bf6cdb4..7e7352d 100644
--- a/docs/reference/figures/README-unnamed-chunk-5-1.png
+++ b/docs/reference/figures/README-unnamed-chunk-5-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-6-1.png b/docs/reference/figures/README-unnamed-chunk-6-1.png
new file mode 100644
index 0000000..bf6cdb4
--- /dev/null
+++ b/docs/reference/figures/README-unnamed-chunk-6-1.png
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 52b7cfb..929f683 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 29f9368..269a1d2 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -15,7 +15,7 @@ bcpc_query."></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -56,7 +56,7 @@ the complete result of querying the BCPC compendium using
     </div>
     <div class="section level2">
     <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#super-class"></a></h2>
-    <p><code><a href="chent.html">chents::chent</a></code> -&gt; <code>pai</code></p>
+    <p><code><a href="chent.html">chent</a></code> -&gt; <code>pai</code></p>
     </div>
     <div class="section level2">
     <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
@@ -64,7 +64,7 @@ the complete result of querying the BCPC compendium using
 <dd><p>ISO common name of the active ingredient according to ISO 1750</p></dd>
 
 
-<dt><code>bcpc</code></dt>
+    <dt><code>bcpc</code></dt>
 <dd><p>Information retrieved from the BCPC compendium available online
 at &lt;pesticidecompendium.bcpc.org&gt;</p></dd>
 
@@ -76,26 +76,25 @@ at &lt;pesticidecompendium.bcpc.org&gt;</p></dd>
 
 <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$new()</code></a></p></li>
+<p></p><ul><li><p><a href="#method-pai-initialize"><code>pai$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>
+</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>chent$add_PUF()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chent$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>chent$add_cwsat()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chent$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>chent$add_soil_degradation()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chent$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>chent$add_soil_sorption()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chent$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>chent$emf()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chent$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>chent$get_pubchem()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chent$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>chent$pdf()</code></a></span></li>
+  <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chent$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>chent$try_pubchem()</code></a></span></li>
+</ul></details></p><hr><a id="method-pai-initialize"></a><div class="section">
+<h3 id="pai-new-"><code>pai$new()</code><a class="anchor" aria-label="anchor" href="#pai-new-"></a></h3>
 <p>Create a new pai object</p><div class="section">
 <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
@@ -110,66 +109,55 @@ at &lt;pesticidecompendium.bcpc.org&gt;</p></dd>
 <span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  chyaml <span class="op">=</span> <span class="cn">FALSE</span></span>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
-</div>
-
-<div class="section">
+</div><p></p><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>iso</code></dt>
 <dd><p>The ISO common name to be used in the query of the
 BCPC compendium</p></dd>
 
-
-<dt><code>identifier</code></dt>
+      <dt><code>identifier</code></dt>
 <dd><p>Alternative identifier used for querying pubchem</p></dd>
 
-
-<dt><code>smiles</code></dt>
+      <dt><code>smiles</code></dt>
 <dd><p>Optional user provided SMILES code</p></dd>
 
-
-<dt><code>inchikey</code></dt>
+      <dt><code>inchikey</code></dt>
 <dd><p>Optional user provided InChI Key</p></dd>
 
-
-<dt><code>bcpc</code></dt>
+      <dt><code>bcpc</code></dt>
 <dd><p>Should the BCPC compendium be queried?</p></dd>
 
-
-<dt><code>pubchem</code></dt>
+      <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>
+      <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>
+      <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>
+      <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>
+      <dt><code>chyaml</code></dt>
 <dd><p>Should we look for a identifier.yaml file in the working</p></dd>
 
 
 </dl><p></p></div>
 </div>
 
-</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>
+</div>
+
+<p></p><hr><a id="method-pai-clone"></a><div class="section">
+<h3 id="pai-clone-"><code>pai$clone()</code><a class="anchor" aria-label="anchor" href="#pai-clone-"></a></h3>
 <p>The objects of this class are cloneable with this method.</p><div class="section">
 <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">pai</span><span class="op">$</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>
-
-<div class="section">
+</div><p></p><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>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
@@ -180,6 +168,7 @@ and the reticulate package?</p></dd>
 
 </div>
 
+
     </div>
 
     <div class="section level2">
@@ -224,7 +213,7 @@ and the reticulate package?</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span> "CCCCCCCCCCO" </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 158.3 </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] "1-DECANOL"       "Decan-1-ol"      "Decyl alcohol"   "112-30-1"       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "1-DECANOL"       "Decyl alcohol"   "Decan-1-ol"      "112-30-1"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "n-Decyl alcohol" "n-Decanol"       "Capric alcohol"  "Nonylcarbinol"  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Antak"           "Royaltac"       </span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
diff --git a/docs/reference/pai.md b/docs/reference/pai.md
index 2291653..b957cb2 100644
--- a/docs/reference/pai.md
+++ b/docs/reference/pai.md
@@ -16,8 +16,7 @@ object
 
 ## Super class
 
-[`chents::chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) -\>
-`pai`
+[`chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) -\> `pai`
 
 ## Public fields
 
@@ -34,31 +33,31 @@ object
 
 ### Public methods
 
-- [`pai$new()`](#method-pai-new)
+- [`pai$new()`](#method-pai-initialize)
 
 - [`pai$clone()`](#method-pai-clone)
 
 Inherited methods
 
-- [`chents::chent$add_PUF()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_PUF)
-- [`chents::chent$add_TP()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_TP)
-- [`chents::chent$add_cwsat()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_cwsat)
-- [`chents::chent$add_p0()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_p0)
-- [`chents::chent$add_soil_degradation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_degradation)
-- [`chents::chent$add_soil_ff()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_ff)
-- [`chents::chent$add_soil_sorption()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_sorption)
-- [`chents::chent$add_transformation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_transformation)
-- [`chents::chent$emf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-emf)
-- [`chents::chent$get_chyaml()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_chyaml)
-- [`chents::chent$get_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_pubchem)
-- [`chents::chent$get_rdkit()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_rdkit)
-- [`chents::chent$pdf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-pdf)
-- [`chents::chent$png()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-png)
-- [`chents::chent$try_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-try_pubchem)
+- [`chent$add_PUF()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_PUF)
+- [`chent$add_TP()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_TP)
+- [`chent$add_cwsat()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_cwsat)
+- [`chent$add_p0()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_p0)
+- [`chent$add_soil_degradation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_degradation)
+- [`chent$add_soil_ff()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_ff)
+- [`chent$add_soil_sorption()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_sorption)
+- [`chent$add_transformation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_transformation)
+- [`chent$emf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-emf)
+- [`chent$get_chyaml()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_chyaml)
+- [`chent$get_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_pubchem)
+- [`chent$get_rdkit()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_rdkit)
+- [`chent$pdf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-pdf)
+- [`chent$png()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-png)
+- [`chent$try_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-try_pubchem)
 
 ------------------------------------------------------------------------
 
-### Method `new()`
+### `pai$new()`
 
 Create a new pai object
 
@@ -123,7 +122,7 @@ Create a new pai object
 
 ------------------------------------------------------------------------
 
-### Method `clone()`
+### `pai$clone()`
 
 The objects of this class are cloneable with this method.
 
@@ -180,7 +179,7 @@ print(decanol)
 #> "CCCCCCCCCCO" 
 #> Molecular weight $mw: 158.3 
 #> PubChem synonyms (up to 10):
-#>  [1] "1-DECANOL"       "Decan-1-ol"      "Decyl alcohol"   "112-30-1"       
+#>  [1] "1-DECANOL"       "Decyl alcohol"   "Decan-1-ol"      "112-30-1"       
 #>  [5] "n-Decyl alcohol" "n-Decanol"       "Capric alcohol"  "Nonylcarbinol"  
 #>  [9] "Antak"           "Royaltac"       
 # }
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index c33b732..babdadc 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html
index 29ce898..fb10259 100644
--- a/docs/reference/ppp.html
+++ b/docs/reference/ppp.html
@@ -9,7 +9,7 @@ product"></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -51,23 +51,23 @@ product</p>
 <dd><p>The name of the product</p></dd>
 
 
-<dt><code>ais</code></dt>
+    <dt><code>ais</code></dt>
 <dd><p>A list of active ingredients</p></dd>
 
 
-<dt><code>concentrations</code></dt>
+    <dt><code>concentrations</code></dt>
 <dd><p>The concentration of the ais</p></dd>
 
 
-<dt><code>concentration_units</code></dt>
+    <dt><code>concentration_units</code></dt>
 <dd><p>Defaults to g/L</p></dd>
 
 
-<dt><code>density</code></dt>
+    <dt><code>density</code></dt>
 <dd><p>The density of the product</p></dd>
 
 
-<dt><code>density_units</code></dt>
+    <dt><code>density_units</code></dt>
 <dd><p>Defaults to g/L</p></dd>
 
 
@@ -78,11 +78,10 @@ product</p>
 
 <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-ppp-new"><code>ppp$new()</code></a></p></li>
+<p></p><ul><li><p><a href="#method-ppp-initialize"><code>ppp$new()</code></a></p></li>
 <li><p><a href="#method-ppp-clone"><code>ppp$clone()</code></a></p></li>
-</ul></div><p></p><hr><a id="method-ppp-new"></a><div class="section">
-<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+</ul></div><p></p><hr><a id="method-ppp-initialize"></a><div class="section">
+<h3 id="ppp-new-"><code>ppp$new()</code><a class="anchor" aria-label="anchor" href="#ppp-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/ppp.html">ppp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
@@ -93,45 +92,38 @@ product</p>
 <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>
-
-<div class="section">
+</div><p></p><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>name</code></dt>
 <dd><p>The name of the product</p></dd>
 
-
-<dt><code>...</code></dt>
+      <dt><code>...</code></dt>
 <dd><p>Identifiers of the active ingredients</p></dd>
 
-
-<dt><code>concentrations</code></dt>
+      <dt><code>concentrations</code></dt>
 <dd><p>Concentrations of the active ingredients</p></dd>
 
-
-<dt><code>concentration_units</code></dt>
+      <dt><code>concentration_units</code></dt>
 <dd><p>Defaults to g/L</p></dd>
 
-
-<dt><code>density</code></dt>
+      <dt><code>density</code></dt>
 <dd><p>The density</p></dd>
 
-
-<dt><code>density_units</code></dt>
+      <dt><code>density_units</code></dt>
 <dd><p>Defaults to g/L</p></dd>
 
 
 </dl><p></p></div>
 </div>
 
-</div><p></p><hr><a id="method-ppp-clone"></a><div class="section">
-<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+</div>
+
+<p></p><hr><a id="method-ppp-clone"></a><div class="section">
+<h3 id="ppp-clone-"><code>ppp$clone()</code><a class="anchor" aria-label="anchor" href="#ppp-clone-"></a></h3>
 <p>The objects of this class are cloneable with this method.</p><div class="section">
 <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">ppp</span><span class="op">$</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">
+</div><p></p><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>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
@@ -142,6 +134,7 @@ product</p>
 
 </div>
 
+
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/docs/reference/ppp.md b/docs/reference/ppp.md
index 77ff2b6..12293c5 100644
--- a/docs/reference/ppp.md
+++ b/docs/reference/ppp.md
@@ -37,13 +37,13 @@ object.
 
 ### Public methods
 
-- [`ppp$new()`](#method-ppp-new)
+- [`ppp$new()`](#method-ppp-initialize)
 
 - [`ppp$clone()`](#method-ppp-clone)
 
 ------------------------------------------------------------------------
 
-### Method `new()`
+### `ppp$new()`
 
 Creates a new instance of this
 [R6](https://r6.r-lib.org/reference/R6Class.html) class.
@@ -87,7 +87,7 @@ Creates a new instance of this
 
 ------------------------------------------------------------------------
 
-### Method `clone()`
+### `ppp$clone()`
 
 The objects of this class are cloneable with this method.
 
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index 223c190..1d7e75a 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,7 +65,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index b59d738..29c88df 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,7 +65,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/print.ppp.html b/docs/reference/print.ppp.html
index 63f87ef..6635097 100644
--- a/docs/reference/print.ppp.html
+++ b/docs/reference/print.ppp.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
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diff --git a/docs/search.json b/docs/search.json
index cd12868..68858c4 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2026). chents: Chemical Entities R Objects. R package version 0.4.1, https://pkgdown.jrwb.de/chents/.","code":"@Manual{,   title = {chents: Chemical Entities as R Objects},   author = {Johannes Ranke},   year = {2026},   note = {R package version 0.4.1},   url = {https://pkgdown.jrwb.de/chents/}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"working data chemical substances, often need reliable link data chemical identity substances. R package chents provides way define R object corresponding chemically defined substances (“chemical entity”) collect related information. first defining chemical entity, chemical information retrieved PubChem website using webchem package. Python RDKit (> 2015.03) installed configured use reticulate package, additional chemical information including 2D graph computed. print method gives overview information collected. simple plotting method chemical structure.  -called ISO common name pesticide active ingredient, can use ‘pai’ class derived ‘chent’ class, starts querying BCPC compendium first.  Additional information can read local .yaml file. information can leveraged e.g. PEC_soil function ‘pfm’ package. However, functionality superseded dedicated package, defining data environmental risk assessment chemicals, particular active ingredients plant protection products.","code":"library(chents) caffeine <- chent$new(\"Caffeine\") #> Querying PubChem for name Caffeine ... #> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier Caffeine  #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N  #> SMILES string $smiles: #>                        PubChem  #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\"  #> Molecular weight $mw: 194.2  #> PubChem synonyms (up to 10): #>  [1] \"caffeine\"                \"58-08-2\"                 #>  [3] \"Guaranine\"               \"1,3,7-Trimethylxanthine\" #>  [5] \"Methyltheobromine\"       \"Theine\"                  #>  [7] \"Thein\"                   \"Cafeina\"                 #>  [9] \"Caffein\"                 \"Cafipel\" plot(caffeine) delta <- pai$new(\"Deltamethrin\") #> Querying BCPC for Deltamethrin ... #> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ... #> Get chemical information from RDKit using PubChem SMILES #> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C plot(delta)"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Chemical Entities as R Objects","text":"can conveniently install chents repository kindly made available R-Universe project: order profit chemoinformatics, need install RDKit python bindings. Debian type Linux distribution, just use use package Windows MacOS, happy include installation instructions share , e.g. via Pull Request.","code":"install.packages(\"chents\",   repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) sudo apt install python3-rdkit"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"configuration-of-the-python-version-to-use","dir":"","previous_headings":"","what":"Configuration of the Python version to use","title":"Chemical Entities as R Objects","text":"Debian type Linux distributions, can use following line global project specific .Rprofile file tell reticulate package use system Python version find RDKit installed system location.","code":"Sys.setenv(RETICULATE_PYTHON=\"/usr/bin/python3\")"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"using-r6-classes","dir":"","previous_headings":"","what":"Using R6 classes","title":"Chemical Entities as R Objects","text":"Note chent objects defined package R6 classes. Therefore, think make copy assigning new name, objects still connected, reference copied. example, can create molecule without retrieving data PubChem assign new name add PubChem information object new name, information also added original chent object: can create derived, independent object using clone() method affected operations original object:","code":"but <- chent$new(\"Butane\", smiles = \"CCCC\", pubchem = FALSE) #> Get chemical information from RDKit using user SMILES #> CCCC print(but) #> <chent> #> Identifier $identifier Butane  #> InChI Key $inchikey NA  #> SMILES string $smiles: #>   user  #> \"CCCC\"  #> Molecular weight $mw: 58.1 but_pubchem <- but but_pubchem$try_pubchem() #> Querying PubChem for name Butane ... print(but) #> <chent> #> Identifier $identifier Butane  #> InChI Key $inchikey IJDNQMDRQITEOD-UHFFFAOYSA-N  #> SMILES string $smiles: #>    user PubChem  #>  \"CCCC\"  \"CCCC\"  #> Molecular weight $mw: 58.1  #> PubChem synonyms (up to 10): #>  [1] \"BUTANE\"              \"n-Butane\"            \"106-97-8\"            #>  [4] \"Diethyl\"             \"Methylethylmethane\"  \"Butanen\"             #>  [7] \"Butani\"              \"Butyl hydride\"       \"HC 600\"              #> [10] \"A 21 (lowing agent)\" but_new <- chent$new(\"Butane\", smiles = \"CCCC\", pubchem = FALSE) #> Get chemical information from RDKit using user SMILES #> CCCC but_clone <- but_new$clone() but_new$try_pubchem() #> Querying PubChem for name Butane ... but_clone #> <chent> #> Identifier $identifier Butane  #> InChI Key $inchikey NA  #> SMILES string $smiles: #>   user  #> \"CCCC\"  #> Molecular weight $mw: 58.1"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6::R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph grImport::Picture object obtained using grImport package Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects transformations Data frame observed transformations soil_degradation Dataframe modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new(   identifier,   smiles = NULL,   inchikey = NULL,   pubchem = TRUE,   pubchem_from = c(\"name\", \"smiles\", \"inchikey\"),   rdkit = TRUE,   template = NULL,   chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory?","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-try-pubchem-","dir":"Reference","previous_headings":"","what":"Method try_pubchem()","title":"An R6 class for chemical entities with associated data — chent","text":"Try get chemical information PubChem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query = self$identifier, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-pubchem-","dir":"Reference","previous_headings":"","what":"Method get_pubchem()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information PubChem known PubChem CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-rdkit-","dir":"Reference","previous_headings":"","what":"Method get_rdkit()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information RDKit available","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template optional SMILES code used template RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-chyaml-","dir":"Reference","previous_headings":"","what":"Method get_chyaml()","title":"An R6 class for chemical entities with associated data — chent","text":"Obtain information YAML file","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml(   repo = c(\"wd\", \"local\", \"web\"),   chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-p-","dir":"Reference","previous_headings":"","what":"Method add_p0()","title":"An R6 class for chemical entities with associated data — chent","text":"Add vapour pressure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa T Temperature source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-cwsat-","dir":"Reference","previous_headings":"","what":"Method add_cwsat()","title":"An R6 class for chemical entities with associated data — chent","text":"Add water solubility","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L T Temperature pH pH value source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-puf-","dir":"Reference","previous_headings":"","what":"Method add_PUF()","title":"An R6 class for chemical entities with associated data — chent","text":"Add plant uptake factor","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF(   PUF = 0,   source = \"focus_generic_gw_2014\",   page = 41,   remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-tp-","dir":"Reference","previous_headings":"","what":"Method add_TP()","title":"An R6 class for chemical entities with associated data — chent","text":"Add transformation product internal list","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles Optional user provided SMILES code pubchem chemical information obtained PubChem?","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-transformation-","dir":"Reference","previous_headings":"","what":"Method add_transformation()","title":"An R6 class for chemical entities with associated data — chent","text":"Add line internal dataframe holding observed transformations","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation(   study_type,   TP_identifier,   max_occurrence,   remark = \"\",   source = NA,   pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages pages information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-soil-degradation-","dir":"Reference","previous_headings":"","what":"Method add_soil_degradation()","title":"An R6 class for chemical entities with associated data — chent","text":"Add line internal dataframe holding modelling DT50 values","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_degradation(   soils,   DT50_mod,   DT50_mod_ref,   type = NA,   country = NA,   pH_orig = NA,   pH_medium = NA,   pH_H2O = NA,   perc_OC = NA,   temperature = NA,   moisture = NA,   category = \"lab\",   formulation = NA,   model = NA,   chi2 = NA,   remark = \"\",   source,   page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-soil-ff-","dir":"Reference","previous_headings":"","what":"Method add_soil_ff()","title":"An R6 class for chemical entities with associated data — chent","text":"Add one formation fractions degradation soil","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s) remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-soil-sorption-","dir":"Reference","previous_headings":"","what":"Method add_soil_sorption()","title":"An R6 class for chemical entities with associated data — chent","text":"Add soil sorption data","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_sorption(   soils,   Kf,   Kfoc,   N,   type = NA,   pH_orig = NA,   pH_medium = NA,   pH_H2O = NA,   perc_OC = NA,   perc_clay = NA,   CEC = NA,   remark = \"\",   source,   page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent type soil type pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil perc_clay percentage clay soil CEC cation exchange capacity remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-pdf-","dir":"Reference","previous_headings":"","what":"Method pdf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PDF image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf(   file = paste0(self$identifier, \".pdf\"),   dir = \"structures/pdf\",   template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template optional SMILES code used template RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-png-","dir":"Reference","previous_headings":"","what":"Method png()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PNG image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png(   file = paste0(self$identifier, \".png\"),   dir = \"structures/png\",   antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file antialias Passed png","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-emf-","dir":"Reference","previous_headings":"","what":"Method emf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write EMF image structure using emf","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"# Don't run examples per default, as PubChem may be unavailable # \\dontrun{ caffeine <- chent$new(\"caffeine\") #> Querying PubChem for name caffeine ... #> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine  #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N  #> SMILES string $smiles: #>                        PubChem  #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\"  #> Molecular weight $mw: 194.2  #> PubChem synonyms (up to 10): #>  [1] \"caffeine\"                \"58-08-2\"                 #>  [3] \"Guaranine\"               \"1,3,7-Trimethylxanthine\" #>  [5] \"Methyltheobromine\"       \"Theine\"                  #>  [7] \"Thein\"                   \"Cafeina\"                 #>  [9] \"Caffein\"                 \"Cafipel\"                 if (!is.null(caffeine$Picture)) {   plot(caffeine) }  oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Get chemical information from RDKit using user SMILES #> CCCCCCCCO print(oct) #> <chent> #> Identifier $identifier 1-octanol  #> InChI Key $inchikey NA  #> SMILES string $smiles: #>        user  #> \"CCCCCCCCO\"  #> Molecular weight $mw: 130.2  # }"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent(   x,   width = 300,   height = 150,   filename = paste0(names(x$identifier), \".svg\"),   subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6::R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org>","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"Create new pai object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new(   iso,   identifier = iso,   smiles = NULL,   inchikey = NULL,   bcpc = TRUE,   pubchem = TRUE,   pubchem_from = \"auto\",   rdkit = TRUE,   template = NULL,   chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem smiles Optional user provided SMILES code inchikey Optional user provided InChI Key bcpc BCPC compendium queried? pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# Don't run examples per default, as PubChem may be unavailable # \\dontrun{ atr <- pai$new(\"atrazine\") #> Querying BCPC for atrazine ... #> Querying PubChem for inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N ... #> Get chemical information from RDKit using PubChem SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C print(atr) #> <pai> with ISO common name $iso atrazine  #> <chent> #> Identifier $identifier atrazine  #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N  #> SMILES string $smiles: #>                      PubChem  #> \"CCNC1=NC(=NC(=N1)Cl)NC(C)C\"  #> Molecular weight $mw: 215.7  #> PubChem synonyms (up to 10): #>  [1] \"atrazine\"     \"1912-24-9\"    \"Gesaprim\"     \"Aatrex\"       \"Atranex\"      #>  [6] \"Atrazin\"      \"Oleogesaprim\" \"Atazinax\"     \"Atrasine\"     \"Chromozin\"    if (!is.null(atr$Picture)) {   plot(atr) }  # We can also define pais that are not found on the BCPC site decanol <- pai$new(\"1-Decanol\") #> Querying BCPC for 1-Decanol ... #> Common name 1-Decanol is not known at the BCPC compendium, trying PubChem #> Querying PubChem for name 1-Decanol ... #> Get chemical information from RDKit using PubChem SMILES #> CCCCCCCCCCO print(decanol) #> <pai> without ISO common name #> <chent> #> Identifier $identifier 1-Decanol  #> InChI Key $inchikey MWKFXSUHUHTGQN-UHFFFAOYSA-N  #> SMILES string $smiles: #>       PubChem  #> \"CCCCCCCCCCO\"  #> Molecular weight $mw: 158.3  #> PubChem synonyms (up to 10): #>  [1] \"1-DECANOL\"       \"Decan-1-ol\"      \"Decyl alcohol\"   \"112-30-1\"        #>  [5] \"n-Decyl alcohol\" \"n-Decanol\"       \"Capric alcohol\"  \"Nonylcarbinol\"   #>  [9] \"Antak\"           \"Royaltac\"        # }"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for class 'chent' plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grImport::grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"# Don't run examples per default, as PubChem may be unavailable # \\dontrun{ caffeine <- chent$new(\"caffeine\") #> Querying PubChem for name caffeine ... #> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine  #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N  #> SMILES string $smiles: #>                        PubChem  #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\"  #> Molecular weight $mw: 194.2  #> PubChem synonyms (up to 10): #>  [1] \"caffeine\"                \"58-08-2\"                 #>  [3] \"Guaranine\"               \"1,3,7-Trimethylxanthine\" #>  [5] \"Methyltheobromine\"       \"Theine\"                  #>  [7] \"Thein\"                   \"Cafeina\"                 #>  [9] \"Caffein\"                 \"Cafipel\"                 if (!is.null(caffeine$Picture)) {   plot(caffeine) }  # }"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6::R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new(   name,   ...,   concentrations,   concentration_units = \"g/L\",   density = 1000,   density_units = \"g/L\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for class 'chent' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for class 'pai' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for ppp objects (plant protection products) — print.ppp","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"Printing method ppp objects (plant protection products)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"","code":"# S3 method for class 'ppp' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-041","dir":"Changelog","previous_headings":"","what":"version 0.4.1","title":"version 0.4.1","text":"Improve print method pai objects chent plot method: Pass dots argument grid.picture() documented chent plot method: Use preferred SMILES. PubChem information retrieved, now SMILES including stereochemical information","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-040","dir":"Changelog","previous_headings":"","what":"version 0.4.0","title":"version 0.4.0","text":"R/chent.R: PubChem changed names SMILES codes provide. former isomeric smiles incorporated chent objects “Pubchem_Isomeric” now simply calles SMILES, incorporated objects “PubChem”. SMILES code formerly given “canonical” now termed “connectivity SMILES” contain isotopic stereochemical specifications. chents object, now available name “PubChem_Connectivity”. breaking change, objects generated versions < 0.4.0 may produce errors used current versions.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-037","dir":"Changelog","previous_headings":"","what":"version 0.3.7","title":"version 0.3.7","text":"R/chent.R: attempt load chyaml file per default, format file resulting chyaml list object documented need inferred use pfm package.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-036","dir":"Changelog","previous_headings":"","what":"version 0.3.6","title":"version 0.3.6","text":"R/chent.R: Set fields smiles, inchikey mw NA fields still NULL end initialization, source attribute set “user”, assuming initialisation carefully done pubchem rdkit skipped structure well-defined. Please refer ChangeLog commit messages November 2021, changed GNUmakefile include commit messages file .","code":""}]
+[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2026). chents: Chemical Entities R Objects. R package version 0.4.2, https://pkgdown.jrwb.de/chents/.","code":"@Manual{,   title = {chents: Chemical Entities as R Objects},   author = {Johannes Ranke},   year = {2026},   note = {R package version 0.4.2},   url = {https://pkgdown.jrwb.de/chents/}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"working data chemical substances, often need reliable link data chemical identity substances. R package ‘chents’ provides way define R object corresponding chemically defined substances, .e. chemical entity collect related information. Python ‘RDKit’ (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions like calculation molecular weight plotting chemical structures R graphics available.","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Chemical Entities as R Objects","text":"first defining chemical entity, chemical information retrieved PubChem website using webchem package. Python RDKit (> 2015.03) installed configured use reticulate package, additional chemical information including 2D graph computed. print method gives overview information collected. simple plotting method chemical structure.  -called ISO common name pesticide active ingredient, can use ‘pai’ class derived ‘chent’ class, starts querying BCPC compendium first.  Additional information can read local .yaml file. information can leveraged e.g. PEC_soil function ‘pfm’ package. However, functionality superseded dedicated package, defining data environmental risk assessment chemicals, particular active ingredients plant protection products.","code":"library(chents) caffeine <- chent$new(\"Caffeine\") #> Querying PubChem for name Caffeine ... #> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier Caffeine  #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N  #> SMILES string $smiles: #>                        PubChem  #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\"  #> Molecular weight $mw: 194.2  #> PubChem synonyms (up to 10): #>  [1] \"caffeine\"                \"58-08-2\"                 #>  [3] \"Guaranine\"               \"1,3,7-Trimethylxanthine\" #>  [5] \"Methyltheobromine\"       \"Theine\"                  #>  [7] \"Thein\"                   \"Cafeina\"                 #>  [9] \"Caffein\"                 \"Cafipel\" plot(caffeine) delta <- pai$new(\"Deltamethrin\") #> Querying BCPC for Deltamethrin ... #> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ... #> Get chemical information from RDKit using PubChem SMILES #> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C plot(delta)"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Chemical Entities as R Objects","text":"can conveniently install chents repository kindly made available R-Universe project: order profit chemoinformatics, need install RDKit python bindings. Debian type Linux distribution, just use use package Windows MacOS, happy include installation instructions share , e.g. via Pull Request.","code":"install.packages(\"chents\",   repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) sudo apt install python3-rdkit"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"configuration-of-the-python-version-to-use","dir":"","previous_headings":"","what":"Configuration of the Python version to use","title":"Chemical Entities as R Objects","text":"Debian type Linux distributions, can use following line global project specific .Rprofile file tell reticulate package use system Python version find RDKit installed system location.","code":"Sys.setenv(RETICULATE_PYTHON=\"/usr/bin/python3\")"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"using-r6-classes","dir":"","previous_headings":"","what":"Using R6 classes","title":"Chemical Entities as R Objects","text":"Note chent objects defined package R6 classes. Therefore, think make copy assigning new name, objects still connected, reference copied. example, can create molecule without retrieving data PubChem assign new name add PubChem information object new name, information also added original chent object: can create derived, independent object using clone() method affected operations original object:","code":"but <- chent$new(\"Butane\", smiles = \"CCCC\", pubchem = FALSE) #> Get chemical information from RDKit using user SMILES #> CCCC print(but) #> <chent> #> Identifier $identifier Butane  #> InChI Key $inchikey NA  #> SMILES string $smiles: #>   user  #> \"CCCC\"  #> Molecular weight $mw: 58.1 but_pubchem <- but but_pubchem$try_pubchem() #> Querying PubChem for name Butane ... print(but) #> <chent> #> Identifier $identifier Butane  #> InChI Key $inchikey IJDNQMDRQITEOD-UHFFFAOYSA-N  #> SMILES string $smiles: #>    user PubChem  #>  \"CCCC\"  \"CCCC\"  #> Molecular weight $mw: 58.1  #> PubChem synonyms (up to 10): #>  [1] \"BUTANE\"              \"n-Butane\"            \"106-97-8\"            #>  [4] \"Diethyl\"             \"Methylethylmethane\"  \"Butanen\"             #>  [7] \"Butani\"              \"Butyl hydride\"       \"HC 600\"              #> [10] \"A 21 (lowing agent)\" but_new <- chent$new(\"Butane\", smiles = \"CCCC\", pubchem = FALSE) #> Get chemical information from RDKit using user SMILES #> CCCC but_clone <- but_new$clone() but_new$try_pubchem() #> Querying PubChem for name Butane ... but_clone #> <chent> #> Identifier $identifier Butane  #> InChI Key $inchikey NA  #> SMILES string $smiles: #>   user  #> \"CCCC\"  #> Molecular weight $mw: 58.1"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph grImport::Picture object obtained using grImport package Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects transformations Data frame observed transformations soil_degradation Dataframe modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-new-","dir":"Reference","previous_headings":"","what":"chent$new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new(   identifier,   smiles = NULL,   inchikey = NULL,   pubchem = TRUE,   pubchem_from = c(\"name\", \"smiles\", \"inchikey\"),   rdkit = TRUE,   template = NULL,   chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory?","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-try-pubchem-","dir":"Reference","previous_headings":"","what":"chent$try_pubchem()","title":"An R6 class for chemical entities with associated data — chent","text":"Try get chemical information PubChem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query = self$identifier, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-get-pubchem-","dir":"Reference","previous_headings":"","what":"chent$get_pubchem()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information PubChem known PubChem CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-get-rdkit-","dir":"Reference","previous_headings":"","what":"chent$get_rdkit()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information RDKit available","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template optional SMILES code used template RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-get-chyaml-","dir":"Reference","previous_headings":"","what":"chent$get_chyaml()","title":"An R6 class for chemical entities with associated data — chent","text":"Obtain information YAML file","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml(   repo = c(\"wd\", \"local\", \"web\"),   chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-p-","dir":"Reference","previous_headings":"","what":"chent$add_p0()","title":"An R6 class for chemical entities with associated data — chent","text":"Add vapour pressure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa T Temperature source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-cwsat-","dir":"Reference","previous_headings":"","what":"chent$add_cwsat()","title":"An R6 class for chemical entities with associated data — chent","text":"Add water solubility","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L T Temperature pH pH value source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-puf-","dir":"Reference","previous_headings":"","what":"chent$add_PUF()","title":"An R6 class for chemical entities with associated data — chent","text":"Add plant uptake factor","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF(   PUF = 0,   source = \"focus_generic_gw_2014\",   page = 41,   remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-tp-","dir":"Reference","previous_headings":"","what":"chent$add_TP()","title":"An R6 class for chemical entities with associated data — chent","text":"Add transformation product internal list","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles Optional user provided SMILES code pubchem chemical information obtained PubChem?","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-transformation-","dir":"Reference","previous_headings":"","what":"chent$add_transformation()","title":"An R6 class for chemical entities with associated data — chent","text":"Add line internal dataframe holding observed transformations","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation(   study_type,   TP_identifier,   max_occurrence,   remark = \"\",   source = NA,   pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages pages information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-soil-degradation-","dir":"Reference","previous_headings":"","what":"chent$add_soil_degradation()","title":"An R6 class for chemical entities with associated data — chent","text":"Add line internal dataframe holding modelling DT50 values","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_degradation(   soils,   DT50_mod,   DT50_mod_ref,   type = NA,   country = NA,   pH_orig = NA,   pH_medium = NA,   pH_H2O = NA,   perc_OC = NA,   temperature = NA,   moisture = NA,   category = \"lab\",   formulation = NA,   model = NA,   chi2 = NA,   remark = \"\",   source,   page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-soil-ff-","dir":"Reference","previous_headings":"","what":"chent$add_soil_ff()","title":"An R6 class for chemical entities with associated data — chent","text":"Add one formation fractions degradation soil","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s) remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-add-soil-sorption-","dir":"Reference","previous_headings":"","what":"chent$add_soil_sorption()","title":"An R6 class for chemical entities with associated data — chent","text":"Add soil sorption data","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_sorption(   soils,   Kf,   Kfoc,   N,   type = NA,   pH_orig = NA,   pH_medium = NA,   pH_H2O = NA,   perc_OC = NA,   perc_clay = NA,   CEC = NA,   remark = \"\",   source,   page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent type soil type pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil perc_clay percentage clay soil CEC cation exchange capacity remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-pdf-","dir":"Reference","previous_headings":"","what":"chent$pdf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PDF image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf(   file = paste0(self$identifier, \".pdf\"),   dir = \"structures/pdf\",   template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template optional SMILES code used template RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-png-","dir":"Reference","previous_headings":"","what":"chent$png()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PNG image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png(   file = paste0(self$identifier, \".png\"),   dir = \"structures/png\",   antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file antialias Passed png","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-emf-","dir":"Reference","previous_headings":"","what":"chent$emf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write EMF image structure using emf","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"chent-clone-","dir":"Reference","previous_headings":"","what":"chent$clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"# Don't run examples per default, as PubChem may be unavailable # \\dontrun{ caffeine <- chent$new(\"caffeine\") #> Querying PubChem for name caffeine ... #> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine  #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N  #> SMILES string $smiles: #>                        PubChem  #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\"  #> Molecular weight $mw: 194.2  #> PubChem synonyms (up to 10): #>  [1] \"caffeine\"                \"58-08-2\"                 #>  [3] \"Guaranine\"               \"1,3,7-Trimethylxanthine\" #>  [5] \"Methyltheobromine\"       \"Theine\"                  #>  [7] \"Thein\"                   \"Cafeina\"                 #>  [9] \"Caffein\"                 \"Cafipel\"                 if (!is.null(caffeine$Picture)) {   plot(caffeine) }  oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Get chemical information from RDKit using user SMILES #> CCCCCCCCO print(oct) #> <chent> #> Identifier $identifier 1-octanol  #> InChI Key $inchikey NA  #> SMILES string $smiles: #>        user  #> \"CCCCCCCCO\"  #> Molecular weight $mw: 130.2  # }"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent(   x,   width = 300,   height = 150,   filename = paste0(names(x$identifier), \".svg\"),   subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6::R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org>","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chent$add_PUF() chent$add_TP() chent$add_cwsat() chent$add_p0() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$add_transformation() chent$emf() chent$get_chyaml() chent$get_pubchem() chent$get_rdkit() chent$pdf() chent$png() chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"pai-new-","dir":"Reference","previous_headings":"","what":"pai$new()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"Create new pai object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new(   iso,   identifier = iso,   smiles = NULL,   inchikey = NULL,   bcpc = TRUE,   pubchem = TRUE,   pubchem_from = \"auto\",   rdkit = TRUE,   template = NULL,   chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem smiles Optional user provided SMILES code inchikey Optional user provided InChI Key bcpc BCPC compendium queried? pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"pai-clone-","dir":"Reference","previous_headings":"","what":"pai$clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# Don't run examples per default, as PubChem may be unavailable # \\dontrun{ atr <- pai$new(\"atrazine\") #> Querying BCPC for atrazine ... #> Querying PubChem for inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N ... #> Get chemical information from RDKit using PubChem SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C print(atr) #> <pai> with ISO common name $iso atrazine  #> <chent> #> Identifier $identifier atrazine  #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N  #> SMILES string $smiles: #>                      PubChem  #> \"CCNC1=NC(=NC(=N1)Cl)NC(C)C\"  #> Molecular weight $mw: 215.7  #> PubChem synonyms (up to 10): #>  [1] \"atrazine\"     \"1912-24-9\"    \"Gesaprim\"     \"Aatrex\"       \"Atranex\"      #>  [6] \"Atrazin\"      \"Oleogesaprim\" \"Atazinax\"     \"Atrasine\"     \"Chromozin\"    if (!is.null(atr$Picture)) {   plot(atr) }  # We can also define pais that are not found on the BCPC site decanol <- pai$new(\"1-Decanol\") #> Querying BCPC for 1-Decanol ... #> Common name 1-Decanol is not known at the BCPC compendium, trying PubChem #> Querying PubChem for name 1-Decanol ... #> Get chemical information from RDKit using PubChem SMILES #> CCCCCCCCCCO print(decanol) #> <pai> without ISO common name #> <chent> #> Identifier $identifier 1-Decanol  #> InChI Key $inchikey MWKFXSUHUHTGQN-UHFFFAOYSA-N  #> SMILES string $smiles: #>       PubChem  #> \"CCCCCCCCCCO\"  #> Molecular weight $mw: 158.3  #> PubChem synonyms (up to 10): #>  [1] \"1-DECANOL\"       \"Decyl alcohol\"   \"Decan-1-ol\"      \"112-30-1\"        #>  [5] \"n-Decyl alcohol\" \"n-Decanol\"       \"Capric alcohol\"  \"Nonylcarbinol\"   #>  [9] \"Antak\"           \"Royaltac\"        # }"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for class 'chent' plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grImport::grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"# Don't run examples per default, as PubChem may be unavailable # \\dontrun{ caffeine <- chent$new(\"caffeine\") #> Querying PubChem for name caffeine ... #> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine  #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N  #> SMILES string $smiles: #>                        PubChem  #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\"  #> Molecular weight $mw: 194.2  #> PubChem synonyms (up to 10): #>  [1] \"caffeine\"                \"58-08-2\"                 #>  [3] \"Guaranine\"               \"1,3,7-Trimethylxanthine\" #>  [5] \"Methyltheobromine\"       \"Theine\"                  #>  [7] \"Thein\"                   \"Cafeina\"                 #>  [9] \"Caffein\"                 \"Cafipel\"                 if (!is.null(caffeine$Picture)) {   plot(caffeine) }  # }"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6::R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"ppp-new-","dir":"Reference","previous_headings":"","what":"ppp$new()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new(   name,   ...,   concentrations,   concentration_units = \"g/L\",   density = 1000,   density_units = \"g/L\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"ppp-clone-","dir":"Reference","previous_headings":"","what":"ppp$clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for class 'chent' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for class 'pai' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for ppp objects (plant protection products) — print.ppp","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"Printing method ppp objects (plant protection products)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"","code":"# S3 method for class 'ppp' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-041","dir":"Changelog","previous_headings":"","what":"version 0.4.1","title":"version 0.4.1","text":"Improve print method pai objects chent plot method: Pass dots argument grid.picture() documented chent plot method: Use preferred SMILES. PubChem information retrieved, now SMILES including stereochemical information","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-040","dir":"Changelog","previous_headings":"","what":"version 0.4.0","title":"version 0.4.0","text":"R/chent.R: PubChem changed names SMILES codes provide. former isomeric smiles incorporated chent objects “Pubchem_Isomeric” now simply calles SMILES, incorporated objects “PubChem”. SMILES code formerly given “canonical” now termed “connectivity SMILES” contain isotopic stereochemical specifications. chents object, now available name “PubChem_Connectivity”. breaking change, objects generated versions < 0.4.0 may produce errors used current versions.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-037","dir":"Changelog","previous_headings":"","what":"version 0.3.7","title":"version 0.3.7","text":"R/chent.R: attempt load chyaml file per default, format file resulting chyaml list object documented need inferred use pfm package.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-036","dir":"Changelog","previous_headings":"","what":"version 0.3.6","title":"version 0.3.6","text":"R/chent.R: Set fields smiles, inchikey mw NA fields still NULL end initialization, source attribute set “user”, assuming initialisation carefully done pubchem rdkit skipped structure well-defined. Please refer ChangeLog commit messages November 2021, changed GNUmakefile include commit messages file .","code":""}]
author	Johannes Ranke <johannes.ranke@jrwb.de>	2026-07-03 11:51:32 +0200
committer	Johannes Ranke <johannes.ranke@jrwb.de>	2026-07-03 11:51:32 +0200
commit	88027b7a70510b48bd7525ffcd536f0808d263e7 (patch)
tree	94f83bd420d494334011ff8f67a27483130fe857 /docs
parent	32caaedcc6b6b8addc9f23fce9dca4188f692fed (diff)