From 7dadaf3fe9793afe7264125edc4e1f1ccd806dc0 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 28 Nov 2024 13:02:04 +0100
Subject: Update online docs

---
 docs/reference/chent.html | 120 +++++++++++++++++++++++++++++++++-------------
 1 file changed, 86 insertions(+), 34 deletions(-)

(limited to 'docs/reference/chent.html')

diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index a70e318..0a74440 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="">0.3.6</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</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">
@@ -166,7 +166,8 @@ Add soil sorption data</p></dd>
 <li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li>
 </ul></div><p></p><hr><a id="method-chent-new"></a><div class="section">
 <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
-<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section">
+<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p>
+<p>Try to get chemical information from PubChem</p><div class="section">
 <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
 <span>  <span class="va">identifier</span>,</span>
@@ -176,7 +177,7 @@ Add soil sorption data</p></dd>
 <span>  pubchem_from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"smiles"</span>, <span class="st">"inchikey"</span><span class="op">)</span>,</span>
 <span>  rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  chyaml <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span>  chyaml <span class="op">=</span> <span class="cn">FALSE</span></span>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
@@ -216,8 +217,7 @@ and the reticulate package?</p></dd>
 
 <dt><code>chyaml</code></dt>
 <dd><p>Should we look for a identifier.yaml file in the working
-directory?
-Try to get chemical information from PubChem</p></dd>
+directory?</p></dd>
 
 
 </dl><p></p></div>
@@ -256,8 +256,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <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
-Get chemical information from RDKit if available</p></dd>
+<dd><p>CID</p></dd>
 
 
 </dl><p></p></div>
@@ -265,8 +264,8 @@ Get chemical information from RDKit if available</p></dd>
 
 </div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section">
 <h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3>
-
-<div class="section">
+<p>Get chemical information from RDKit if available
+Obtain information from a YAML file</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>
@@ -274,8 +273,7 @@ Get chemical information from RDKit if available</p></dd>
 <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>Optional template specified as a SMILES code
-Obtain information from a YAML file</p></dd>
+<dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
 
 
 </dl><p></p></div>
@@ -319,7 +317,8 @@ Add a vapour pressure</p></dd>
 <div class="section">
 <h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>p0</code></dt>
-<dd><p>The vapour pressure in Pa</p></dd>
+<dd><p>The vapour pressure in Pa
+Add a water solubility</p></dd>
 
 
 <dt><code>T</code></dt>
@@ -335,8 +334,7 @@ Add a vapour pressure</p></dd>
 
 
 <dt><code>remark</code></dt>
-<dd><p>A remark
-Add a water solubility</p></dd>
+<dd><p>A remark</p></dd>
 
 
 </dl><p></p></div>
@@ -353,7 +351,8 @@ Add a water solubility</p></dd>
 <div class="section">
 <h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>cwsat</code></dt>
-<dd><p>The water solubility in mg/L</p></dd>
+<dd><p>The water solubility in mg/L
+Add a plant uptake factor</p></dd>
 
 
 <dt><code>T</code></dt>
@@ -361,7 +360,7 @@ Add a water solubility</p></dd>
 
 
 <dt><code>pH</code></dt>
-<dd><p>The pH value</p></dd>
+<dd><p>pH value</p></dd>
 
 
 <dt><code>source</code></dt>
@@ -373,8 +372,7 @@ Add a water solubility</p></dd>
 
 
 <dt><code>remark</code></dt>
-<dd><p>A remark
-Add a plant uptake factor</p></dd>
+<dd><p>A remark</p></dd>
 
 
 </dl><p></p></div>
@@ -429,7 +427,7 @@ Add a plant uptake factor</p></dd>
 
 
 <dt><code>smiles</code></dt>
-<dd><p>A SMILES code for defining a chent object</p></dd>
+<dd><p>Optional user provided SMILES code</p></dd>
 
 
 <dt><code>pubchem</code></dt>
@@ -480,7 +478,7 @@ result from stochiometric transformation</p></dd>
 
 
 <dt><code>pages</code></dt>
-<dd><p>The page from which the information was taken</p></dd>
+<dd><p>The pages from which the information was taken</p></dd>
 
 
 </dl><p></p></div>
@@ -615,6 +613,18 @@ the technical active ingredient</p></dd>
 <dd><p>The formation fraction(s)</p></dd>
 
 
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
 </dl><p></p></div>
 </div>
 
@@ -643,7 +653,11 @@ the technical active ingredient</p></dd>
 
 <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>Kf</code></dt>
+<p></p><div class="arguments"><dl><dt><code>soils</code></dt>
+<dd><p>Names of the soils</p></dd>
+
+
+<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>
 
@@ -656,13 +670,44 @@ or according to Freundlich</p></dd>
 <dd><p>The Freundlich exponent</p></dd>
 
 
+<dt><code>type</code></dt>
+<dd><p>The soil type</p></dd>
+
+
+<dt><code>pH_orig</code></dt>
+<dd><p>The pH stated in the study</p></dd>
+
+
+<dt><code>pH_medium</code></dt>
+<dd><p>The medium in which this pH was measured</p></dd>
+
+
+<dt><code>pH_H2O</code></dt>
+<dd><p>The pH extrapolated to pure water</p></dd>
+
+
+<dt><code>perc_OC</code></dt>
+<dd><p>The percentage of organic carbon in the soil</p></dd>
+
+
 <dt><code>perc_clay</code></dt>
 <dd><p>The percentage of clay in the soil</p></dd>
 
 
 <dt><code>CEC</code></dt>
-<dd><p>The cation exchange capacity
-Write a PDF image of the structure</p></dd>
+<dd><p>The cation exchange capacity</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
 
 
 </dl><p></p></div>
@@ -670,8 +715,8 @@ Write a PDF image of the structure</p></dd>
 
 </div><p></p><hr><a id="method-chent-pdf"></a><div class="section">
 <h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3>
-
-<div class="section">
+<p>Write a PDF image of the structure
+Write a PNG image of the structure</p><div class="section">
 <h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span>
 <span>  file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span>
@@ -691,8 +736,7 @@ Write a PDF image of the structure</p></dd>
 
 
 <dt><code>template</code></dt>
-<dd><p>A template expressed as SMILES to use in RDKit
-Write a PNG image of the structure</p></dd>
+<dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
 
 
 </dl><p></p></div>
@@ -712,9 +756,16 @@ Write a PNG image of the structure</p></dd>
 
 <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>antialias</code></dt>
-<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a>
-Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd>
+<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>
+<dd><p>The directory to write the file to</p></dd>
+
+
+<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>
@@ -722,8 +773,7 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma
 
 </div><p></p><hr><a id="method-chent-emf"></a><div class="section">
 <h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3>
-
-<div class="section">
+<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>
@@ -734,6 +784,10 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma
 <dd><p>The file to write to</p></dd>
 
 
+<dt><code>dir</code></dt>
+<dd><p>The directory to write the file to</p></dd>
+
+
 </dl><p></p></div>
 </div>
 
@@ -762,7 +816,6 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using user SMILES</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> CCCCCCCCO</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./1-octanol.yaml</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier 1-octanol </span>
@@ -779,7 +832,6 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma
 <span class="r-msg co"><span class="r-pr">#&gt;</span> PubChem:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./caffeine.yaml</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier caffeine </span>
-- 
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