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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-01 09:48:02 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-01 09:48:02 +0100
commit4bd4606c76dfc152547e0f5899a98494a4290d33 (patch)
tree36978d1bc83fcf56b1302181ce8367a60d6c156d /docs/reference
parent3f82707cd1e974848185b1141c69734e2573594d (diff)
Rebuild static documentation with current pkdown
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/chent-1.pngbin0 -> 34969 bytes
-rw-r--r--docs/reference/chent.html81
-rw-r--r--docs/reference/draw_svg.chent.html56
-rw-r--r--docs/reference/index.html122
-rw-r--r--docs/reference/pai.html38
-rw-r--r--docs/reference/plot.chent-1.pngbin0 -> 34969 bytes
-rw-r--r--docs/reference/plot.chent.html50
-rw-r--r--docs/reference/pp.html35
-rw-r--r--docs/reference/print.chent.html38
-rw-r--r--docs/reference/print.pai.html38
10 files changed, 313 insertions, 145 deletions
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png
new file mode 100644
index 0000000..8731cf1
--- /dev/null
+++ b/docs/reference/chent-1.png
Binary files differ
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index 15c4d10..ef683ef 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -18,19 +18,30 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="An R6 class for chemical entities with associated data — chent" />
+<meta property="og:description" content="The class is initialised with an identifier. Chemical information is retrieved from
+the internet. Additionally, it can be generated using RDKit if RDKit and its
+python bindings are installed and configured for use with PythonInR." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +60,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -75,7 +92,7 @@ the internet. Additionally, it can be generated using RDKit if RDKit and its
python bindings are installed and configured for use with PythonInR.</p>
- <pre><span class='no'>chent</span></pre>
+ <pre class="usage"><span class='no'>chent</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -83,52 +100,52 @@ python bindings are installed and configured for use with PythonInR.</p>
<h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
- <p></p>
- <p><dl class='dl-horizontal'>
-<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute &#39;source&#39;</dd></p>
- <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute &#39;source&#39;</dd></p>
- <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute &#39;source&#39;</dd></p>
- <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute &#39;source&#39;</dd></p>
- <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p>
- <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit, if installed and
-configured for use with PythonInR</dd></p>
- <p><dt><code>svg</code></dt><dd>SVG code</dd></p>
- <p><dt><code>Picture</code></dt><dd>Graph as a <code>picture</code> object obtained using grImport</dd></p>
- <p><dt><code>Pict_font_size</code></dt><dd>Font size as extracted from the intermediate PostScript file</dd></p>
- <p><dt><code>pdf_height</code></dt><dd>Height of the MediaBox in the pdf after cropping</dd></p>
- <p><dt><code>chyaml</code></dt><dd>List of information obtained from a YAML file</dd></p>
- <p><dt><code>degradation</code></dt><dd>List of degradation endpoints</dd>
-</dl></p>
+
+ <dl class='dl-horizontal'>
+<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd>
+ <dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd>
+ <dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd>
+ <dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd>
+ <dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd>
+ <dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit, if installed and
+configured for use with PythonInR</p></dd>
+ <dt><code>svg</code></dt><dd><p>SVG code</p></dd>
+ <dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
+ <dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
+ <dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
+ <dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
+ <dt><code>degradation</code></dt><dd><p>List of degradation endpoints</p></dd>
+</dl>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>Initialize Python Version 3.4.2 (default, Oct 8 2014, 10:47:48) </span>
-#&gt; <span class='message'>[GCC 4.9.1]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
-#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
+#&gt; <span class='message'>Initialize Python Version 2.7.13 (default, Nov 24 2017, 17:33:09) </span>
+#&gt; <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
+#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Loading required namespace: grConvert</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
#&gt; Identifier $identifier 1-octanol
#&gt; InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N
#&gt; SMILES string $smiles:
#&gt; user PubChem_Canonical
-#&gt; &quot;CCCCCCCCO&quot; &quot;CCCCCCCCO&quot;
+#&gt; "CCCCCCCCO" "CCCCCCCCO"
#&gt; Molecular weight $mw: 130.2
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] &quot;957&quot; &quot;1-octanol&quot; &quot;Octan-1-ol&quot; &quot;octanol&quot;
-#&gt; [5] &quot;Octyl alcohol&quot; &quot;N-octanol&quot; &quot;Capryl alcohol&quot; &quot;n-Octyl alcohol&quot;
-#&gt; [9] &quot;111-87-5&quot; &quot;caprylic alcohol&quot;</div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
+#&gt; [1] "957" "1-octanol" "Octan-1-ol" "octanol"
+#&gt; [5] "Octyl alcohol" "N-octanol" "111-87-5" "Capryl alcohol"
+#&gt; [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>caffeine</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
#&gt; Identifier $identifier caffeine
#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
#&gt; SMILES string $smiles:
#&gt; PubChem_Canonical
-#&gt; &quot;CN1C=NC2=C1C(=O)N(C(=O)N2C)C&quot;
+#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
#&gt; Molecular weight $mw: 194.2
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] &quot;2519&quot; &quot;caffeine&quot;
-#&gt; [3] &quot;Guaranine&quot; &quot;1,3,7-Trimethylxanthine&quot;
-#&gt; [5] &quot;Methyltheobromine&quot; &quot;Cafeina&quot;
-#&gt; [7] &quot;Thein&quot; &quot;Koffein&quot;
-#&gt; [9] &quot;Mateina&quot; &quot;Theine&quot; </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='chent-22.png' alt='' width='540' height='400' /></pre>
+#&gt; [1] "2519" "caffeine"
+#&gt; [3] "1,3,7-Trimethylxanthine" "58-08-2"
+#&gt; [5] "Guaranine" "Thein"
+#&gt; [7] "Cafeina" "Methyltheobromine"
+#&gt; [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -150,7 +167,7 @@ configured for use with PythonInR</dd></p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index 2cc3804..5342eca 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -18,19 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent" />
+<meta property="og:description" content="Draw SVG graph from a chent object using RDKit" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +58,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -73,22 +88,33 @@
<p>Draw SVG graph from a chent object using RDKit</p>
- <pre><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>,
+ <pre class="usage"><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>,
<span class='kw'>filename</span> <span class='kw'>=</span> <span class='fu'>paste0</span>(<span class='fu'>names</span>(<span class='no'>x</span>$<span class='no'>identifier</span>), <span class='st'>".svg"</span>), <span class='kw'>subdir</span> <span class='kw'>=</span> <span class='st'>"svg"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
- <dl class="dl-horizontal">
- <dt>x</dt>
- <dd>The chent object to be plotted</dd>
- <dt>width</dt>
- <dd>The desired width in pixels</dd>
- <dt>height</dt>
- <dd>The desired height in pixels</dd>
- <dt>filename</dt>
- <dd>The filename</dd>
- <dt>subdir</dt>
- <dd>The path to which the file should be written</dd>
- </dl>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>The chent object to be plotted</p></td>
+ </tr>
+ <tr>
+ <th>width</th>
+ <td><p>The desired width in pixels</p></td>
+ </tr>
+ <tr>
+ <th>height</th>
+ <td><p>The desired height in pixels</p></td>
+ </tr>
+ <tr>
+ <th>filename</th>
+ <td><p>The filename</p></td>
+ </tr>
+ <tr>
+ <th>subdir</th>
+ <td><p>The path to which the file should be written</p></td>
+ </tr>
+ </table>
</div>
@@ -107,7 +133,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 52967a5..29771c9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,19 +18,25 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+
+
+<meta property="og:title" content="Function reference" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +55,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -66,50 +78,72 @@
<div class="row">
<div class="col-md-9">
<div class="page-header">
- <h1>Function reference</h1>
- <h4>version&nbsp;0.2-6</h4>
+ <h1>
+ Reference
+ <small>version&nbsp;0.2-6</small>
+ </h1>
</div>
<div class="contents">
- <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2>
- <p class="section-desc"></p>
-
-
- <p><a href="chent.html">An R6 class for chemical entities with associated data</a></p>
- <ul>
- <li><code><a href="chent.html">chent</a></code></li>
- </ul>
-
- <p><a href="draw_svg.chent.html">Draw SVG graph from a chent object using RDKit</a></p>
- <ul>
- <li><code><a href="draw_svg.chent.html">draw_svg.chent</a></code></li>
- </ul>
-
- <p><a href="plot.chent.html">Plot method for chent objects</a></p>
- <ul>
- <li><code><a href="plot.chent.html">plot.chent</a></code></li>
- </ul>
-
- <p><a href="print.chent.html">Printing method for chent objects</a></p>
- <ul>
- <li><code><a href="print.chent.html">print.chent</a></code></li>
- </ul>
-
- <p><a href="pai.html">An R6 class for pesticidal active ingredients and associated data</a></p>
- <ul>
- <li><code><a href="pai.html">pai</a></code></li>
- </ul>
-
- <p><a href="print.pai.html">Printing method for pai objects (pesticidal active ingredients)</a></p>
- <ul>
- <li><code><a href="print.pai.html">print.pai</a></code></li>
- </ul>
-
- <p><a href="pp.html">R6 class for holding a product with at least one active ingredient</a></p>
- <ul>
- <li><code><a href="pp.html">pp</a></code></li>
- </ul>
-
+ <table class="ref-index">
+
+ <colgroup>
+ <col class="alias" />
+ <col class="title" />
+ </colgroup>
+
+ <tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2>
+ <p class="section-desc"></p>
+ </th>
+ </tr>
+ <tr>
+ <!-- -->
+ <td>
+ <p><code><a href="chent.html">chent</a></code> </p>
+ </td>
+ <td><p>An R6 class for chemical entities with associated data</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="draw_svg.chent.html">draw_svg.chent</a></code> </p>
+ </td>
+ <td><p>Draw SVG graph from a chent object using RDKit</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="plot.chent.html">plot</a></code> </p>
+ </td>
+ <td><p>Plot method for chent objects</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="print.chent.html">print</a></code> </p>
+ </td>
+ <td><p>Printing method for chent objects</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="pai.html">pai</a></code> </p>
+ </td>
+ <td><p>An R6 class for pesticidal active ingredients and associated data</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="print.pai.html">print</a></code> </p>
+ </td>
+ <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="pp.html">pp</a></code> </p>
+ </td>
+ <td><p>R6 class for holding a product with at least one active ingredient</p></td>
+ </tr>
+ </tbody>
+ </table>
</div>
</div>
@@ -127,7 +161,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 4c143a1..30a5b77 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -18,19 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai" />
+<meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name.
+Additional chemical information is retrieved from the internet if available." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +59,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -74,7 +90,7 @@
Additional chemical information is retrieved from the internet if available.</p>
- <pre><span class='no'>pai</span></pre>
+ <pre class="usage"><span class='no'>pai</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -82,11 +98,11 @@ Additional chemical information is retrieved from the internet if available.</p>
<h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
- <p></p>
- <p><dl class='dl-horizontal'>
-<dt><code>iso</code></dt><dd>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</dd></p>
- <p><dt><code>alanwood</code></dt><dd>List of information retreived from www.alanwood.net/pesticides</dd>
-</dl></p>
+
+ <dl class='dl-horizontal'>
+<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</p></dd>
+ <dt><code>alanwood</code></dt><dd><p>List of information retreived from www.alanwood.net/pesticides</p></dd>
+</dl>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -97,11 +113,11 @@ Additional chemical information is retrieved from the internet if available.</p>
#&gt; InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N
#&gt; SMILES string $smiles:
#&gt; PubChem_Canonical
-#&gt; &quot;CCNC1=NC(=NC(=N1)Cl)NC(C)C&quot;
+#&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C"
#&gt; Molecular weight $mw: 215.7
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] &quot;2256&quot; &quot;atrazine&quot; &quot;1912-24-9&quot; &quot;Atranex&quot; &quot;Fenatrol&quot;
-#&gt; [6] &quot;Atred&quot; &quot;Oleogesaprim&quot; &quot;Atazinax&quot; &quot;Atrasine&quot; &quot;Chromozin&quot; </div></pre>
+#&gt; [1] "2256" "atrazine" "1912-24-9" "Gesaprim" "Chromozin"
+#&gt; [6] "Oleogesaprim" "Aktikon" "Argezin" "Atazinax" "Atranex" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -123,7 +139,7 @@ Additional chemical information is retrieved from the internet if available.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png
new file mode 100644
index 0000000..8731cf1
--- /dev/null
+++ b/docs/reference/plot.chent-1.png
Binary files differ
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index 3cc23d9..cc3b96b 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -18,19 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Plot method for chent objects — plot.chent" />
+<meta property="og:description" content="Plot method for chent objects" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +58,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -73,16 +88,21 @@
<p>Plot method for chent objects</p>
- <pre><span class='co'># S3 method for chent</span>
+ <pre class="usage"><span class='co'># S3 method for chent</span>
<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
- <dl class="dl-horizontal">
- <dt>x</dt>
- <dd>The chent object to be plotted</dd>
- <dt>...</dt>
- <dd>Further arguments passed to <code>grid.picture</code></dd>
- </dl>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>The chent object to be plotted</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Further arguments passed to <code>grid.picture</code></p></td>
+ </tr>
+ </table>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -92,14 +112,14 @@
#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
#&gt; SMILES string $smiles:
#&gt; PubChem_Canonical
-#&gt; &quot;CN1C=NC2=C1C(=O)N(C(=O)N2C)C&quot;
+#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
#&gt; Molecular weight $mw: 194.2
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] &quot;2519&quot; &quot;caffeine&quot;
-#&gt; [3] &quot;Guaranine&quot; &quot;1,3,7-Trimethylxanthine&quot;
-#&gt; [5] &quot;Methyltheobromine&quot; &quot;Cafeina&quot;
-#&gt; [7] &quot;Thein&quot; &quot;Koffein&quot;
-#&gt; [9] &quot;Mateina&quot; &quot;Theine&quot; </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='plot.chent-11.png' alt='' width='540' height='400' /></pre>
+#&gt; [1] "2519" "caffeine"
+#&gt; [3] "1,3,7-Trimethylxanthine" "58-08-2"
+#&gt; [5] "Guaranine" "Thein"
+#&gt; [7] "Cafeina" "Methyltheobromine"
+#&gt; [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -118,7 +138,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/pp.html b/docs/reference/pp.html
index 4569a6f..538b885 100644
--- a/docs/reference/pp.html
+++ b/docs/reference/pp.html
@@ -18,19 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="R6 class for holding a product with at least one active ingredient — pp" />
+<meta property="og:description" content="An R6 class for holding information about a product with at least one active ingredient" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +58,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -73,7 +88,7 @@
<p>An R6 class for holding information about a product with at least one active ingredient</p>
- <pre><span class='no'>pp</span></pre>
+ <pre class="usage"><span class='no'>pp</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -81,13 +96,13 @@
<h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
- <p></p>
- <p><dl class='dl-horizontal'>
-<dt><code>name</code></dt><dd>The name of the product</dd></p>
- <p><dt><code>ais</code></dt><dd>A list of active ingredients</dd></p>
- <p><dt><code>concentrations</code></dt><dd>The concentration of the ais</dd></p>
- <p><dt><code>concentration_units</code></dt><dd>Defaults to g/L</dd>
-</dl></p>
+
+ <dl class='dl-horizontal'>
+<dt><code>name</code></dt><dd><p>The name of the product</p></dd>
+ <dt><code>ais</code></dt><dd><p>A list of active ingredients</p></dd>
+ <dt><code>concentrations</code></dt><dd><p>The concentration of the ais</p></dd>
+ <dt><code>concentration_units</code></dt><dd><p>Defaults to g/L</p></dd>
+</dl>
</div>
@@ -109,7 +124,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index 29b215a..81fde0d 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -18,19 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Printing method for chent objects — print.chent" />
+<meta property="og:description" content="Printing method for chent objects" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +58,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -73,16 +88,21 @@
<p>Printing method for chent objects</p>
- <pre><span class='co'># S3 method for chent</span>
+ <pre class="usage"><span class='co'># S3 method for chent</span>
<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
- <dl class="dl-horizontal">
- <dt>x</dt>
- <dd>The chent object to be printed</dd>
- <dt>...</dt>
- <dd>Further arguments for compatibility with the S3 method</dd>
- </dl>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>The chent object to be printed</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Further arguments for compatibility with the S3 method</p></td>
+ </tr>
+ </table>
</div>
@@ -101,7 +121,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index d2da6b8..08966de 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -18,19 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Printing method for pai objects (pesticidal active ingredients) — print.pai" />
+<meta property="og:description" content="Printing method for pai objects (pesticidal active ingredients)" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -49,6 +58,12 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
@@ -73,16 +88,21 @@
<p>Printing method for pai objects (pesticidal active ingredients)</p>
- <pre><span class='co'># S3 method for pai</span>
+ <pre class="usage"><span class='co'># S3 method for pai</span>
<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
- <dl class="dl-horizontal">
- <dt>x</dt>
- <dd>The chent object to be printed</dd>
- <dt>...</dt>
- <dd>Further arguments for compatibility with the S3 method</dd>
- </dl>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>The chent object to be printed</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Further arguments for compatibility with the S3 method</p></td>
+ </tr>
+ </table>
</div>
@@ -101,7 +121,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>

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