From e23bd3cfdaf3211c8ed63219e23204697108cb38 Mon Sep 17 00:00:00 2001
From: Ranke Johannes <johannes.ranke@agroscope.admin.ch>
Date: Wed, 22 Oct 2025 15:50:07 +0200
Subject: Improve messages and README

Use README.rmd in order to be able to include demo code and output
in the README.
---
 docs/reference/chent.html | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

(limited to 'docs/reference/chent.html')
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index aed63b3..a2bac4f 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for chemical entities with associated data — chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta name="description" content="The class is initialised with an identifier. Chemical
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for chemical entities with associated data — chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta name="description" content="The class is initialised with an identifier. Chemical
 information is retrieved from the internet. Additionally, it can be
 generated using RDKit if RDKit and its python bindings are installed."><meta property="og:description" content="The class is initialised with an identifier. Chemical
 information is retrieved from the internet. Additionally, it can be
@@ -11,7 +11,7 @@ generated using RDKit if RDKit and its python bindings are installed."></head><b
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -46,7 +46,7 @@ generated using RDKit if RDKit and its python bindings are installed.</p>
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>An <code>R6Class</code> generator object</p>
+    <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> generator object</p>
     </div>
     <div class="section level2">
     <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
@@ -88,7 +88,7 @@ List of information retrieved from PubChem</p></dd>
 
 
 <dt><code>Picture</code></dt>
-<dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
+<dd><p>Graph as a <a href="https://rdrr.io/pkg/grImport/man/Picture-class.html" class="external-link">grImport::Picture</a> object obtained using the grImport package</p></dd>
 
 
 <dt><code>Pict_font_size</code></dt>
@@ -792,14 +792,14 @@ or according to Freundlich</p></dd>
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> PubChem:</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem 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-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier caffeine </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>              PubChem_Canonical </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>                        PubChem </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 194.2 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
@@ -815,14 +815,9 @@ or according to Freundlich</p></dd>
 <span class="r-in"><span><span class="va">oct</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (!is.na(self$mw)) {    if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {        message("RDKit mw is ", self$rdkit$mw)        message("mw is ", self$mw)    }} else {    self$mw &lt;- self$rdkit$mw    attr(self$mw, "source") &lt;- "rdkit"}:</span> argument is of length zero</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier 1-octanol </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey NA </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>        user </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "CCCCCCCCO" </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 130.2 </span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> object 'oct' not found</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -834,7 +829,7 @@ or according to Freundlich</p></dd>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
 </div>
 
     </footer></div>
-- 
cgit v1.2.3

