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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
parent3f82707cd1e974848185b1141c69734e2573594d (diff)
Rebuild static documentation with current pkdown
-rw-r--r--ChangeLog6
-rw-r--r--DESCRIPTION5
-rw-r--r--docs/authors.html20
-rw-r--r--docs/index.html26
-rw-r--r--docs/pkgdown.css129
-rw-r--r--docs/pkgdown.js88
-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
16 files changed, 550 insertions, 182 deletions
diff --git a/ChangeLog b/ChangeLog
index fcd9305..ec197d8 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+commit 3f82707cd1e974848185b1141c69734e2573594d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date: 2017-06-13 16:05:39 +0200
+
+ Make grConvert optional as it vanished on Windows
+
commit f5b36dc73e7778091a08eaed51fd9d4f8677fbc1
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-03-17 21:19:14 +0100
diff --git a/DESCRIPTION b/DESCRIPTION
index eb8cc73..05af50c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,14 +2,15 @@ Package: chents
Type: Package
Title: Chemical Entities as R Objects
Version: 0.2-6
-Date: 2017-06-13
+Date: 2018-02-27
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de"))
Description: Utilities for dealing with chemical entities and associated
data as R objects. If Python and RDKit (> 2015.03) are installed and
configured for use with 'PythonInR', some basic chemoinformatics functions
like the calculation of molecular weight and plotting of chemical
- structures in R graphics are available.
+ structures in R graphics are available. For plotting, you need
+ grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN.
Imports:
webchem,
R6,
diff --git a/docs/authors.html b/docs/authors.html
index 9f174b2..7e1fe6b 100644
--- a/docs/authors.html
+++ b/docs/authors.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="Authors" />
<!-- 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>
@@ -71,7 +83,7 @@
<ul class="list-unstyled">
<li>
- <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
+ <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder.
</p>
</li>
</ul>
@@ -87,7 +99,7 @@
</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/index.html b/docs/index.html
index 991bab9..f16ddf7 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,8 +8,16 @@
<title>Chemical Entities as R Objects • chents</title>
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- 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">
-<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- 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="Chemical Entities as R Objects">
+<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 'PythonInR', some basic chemoinformatics functions
+ like the calculation of molecular weight and plotting of chemical
+ structures in R graphics are available. For plotting, you need
+ grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN.">
+<meta name="twitter:card" content="summary">
+<!-- mathjax --><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]-->
@@ -29,6 +37,12 @@
<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>
@@ -45,7 +59,7 @@
<div class="contents col-md-9">
<div id="chents" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
-<a href="#chents" class="anchor"> </a>chents</h1></div>
+<a href="#chents" class="anchor"></a>chents</h1></div>
<p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R, made available under the GNU public license. This means:</p>
<div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software:<span class="st"> </span>you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
@@ -61,7 +75,7 @@ You should have received a copy of the GNU General Public License along with
this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">&gt;</span></code></pre></div>
<div id="features" class="section level2">
<h2 class="hasAnchor">
-<a href="#features" class="anchor"> </a>Features</h2>
+<a href="#features" class="anchor"></a>Features</h2>
<ul>
<li>Some chemical information is retrieved from the PubChem website using the webchem package</li>
<li>If PythonInR is installed and configured, and RDKit is available via PythonInR, some additional chemical information is computed and a 2D graph can be plotted</li>
@@ -77,7 +91,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
<p>GPL</p>
<h2>Developers</h2>
<ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
</ul>
</div>
</div>
@@ -88,7 +102,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
</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/pkgdown.css b/docs/pkgdown.css
index fd7b0ba..181fe63 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -34,13 +34,14 @@ img.icon {
float: right;
}
-/* Section anchors ---------------------------------*/
-
-.hasAnchor {
- margin-left: -30px;
+img {
+ max-width: 100%;
}
+/* Section anchors ---------------------------------*/
+
a.anchor {
+ margin-left: -30px;
display:inline-block;
width: 30px;
height: 30px;
@@ -56,6 +57,13 @@ a.anchor {
visibility: visible;
}
+@media (max-width: 767px) {
+ .hasAnchor:hover a.anchor {
+ visibility: hidden;
+ }
+}
+
+
/* Fixes for fixed navbar --------------------------*/
.contents h1, .contents h2, .contents h3, .contents h4 {
@@ -63,6 +71,17 @@ a.anchor {
margin-top: -60px;
}
+/* Static header placement on mobile devices */
+@media (max-width: 767px) {
+ .navbar-fixed-top {
+ position: absolute;
+ }
+ .navbar {
+ padding: 0;
+ }
+}
+
+
/* Sidebar --------------------------*/
#sidebar {
@@ -81,33 +100,95 @@ a.anchor {
margin-bottom: 0.5em;
}
+.orcid {
+ height: 16px;
+ vertical-align: middle;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+.ref-index h2 {font-size: 20px;}
+
+.ref-index td {vertical-align: top;}
+.ref-index .alias {width: 40%;}
+.ref-index .title {width: 60%;}
+
+.ref-index .alias {width: 40%;}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top;}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
/* Syntax highlighting ---------------------------------------------------- */
-code {
- background-color: #f7f7f7;
- color: #333;
+pre {
+ word-wrap: normal;
+ word-break: normal;
+ border: 1px solid #eee;
}
-code a {
- color: #375f84;
+
+pre, code {
+ background-color: #f8f8f8;
+ color: #333;
}
-.warning { color: red; }
-.message { font-weight: bolder; }
-.error { color: red; font-weight: bolder; }
+pre code {
+ overflow: auto;
+ word-wrap: normal;
+ white-space: pre;
+}
-.fl,.number {color:rgb(21,20,181);}
-.fu,.functioncall {color:#264D66 ;}
-.ch,.st,.string {color:#375D81 ;}
-.kw,.keyword {color:black;}
-.argument {color:#264D66 ;}
-.co,.comment {color: #777;}
-.formalargs {color: #264D66;}
-.eqformalargs {color:#264D66;}
-.slot {font-style:italic;}
-.symbol {color:black ;}
-.prompt {color:black ;}
+pre .img {
+ margin: 5px 0;
+}
-pre img {
+pre .img img {
background-color: #fff;
display: block;
+ height: auto;
+}
+
+code a, pre a {
+ color: #375f84;
+}
+
+a.sourceLine:hover {
+ text-decoration: none;
+}
+
+.fl {color: #1514b5;}
+.fu {color: #000000;} /* function */
+.ch,.st {color: #036a07;} /* string */
+.kw {color: #264D66;} /* keyword */
+.co {color: #888888;} /* comment */
+
+.message { color: black; font-weight: bolder;}
+.error { color: orange; font-weight: bolder;}
+.warning { color: #6A0366; font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index c8b38c4..64b20df 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,8 +1,94 @@
$(function() {
- $("#sidebar").stick_in_parent({offset_top: 40});
+
+ $("#sidebar")
+ .stick_in_parent({offset_top: 40})
+ .on('sticky_kit:bottom', function(e) {
+ $(this).parent().css('position', 'static');
+ })
+ .on('sticky_kit:unbottom', function(e) {
+ $(this).parent().css('position', 'relative');
+ });
+
$('body').scrollspy({
target: '#sidebar',
offset: 60
});
+ var cur_path = paths(location.pathname);
+ $("#navbar ul li a").each(function(index, value) {
+ if (value.text == "Home")
+ return;
+ if (value.getAttribute("href") === "#")
+ return;
+
+ var path = paths(value.pathname);
+ if (is_prefix(cur_path, path)) {
+ // Add class to parent <li>, and enclosing <li> if in dropdown
+ var menu_anchor = $(value);
+ menu_anchor.parent().addClass("active");
+ menu_anchor.closest("li.dropdown").addClass("active");
+ }
+ });
});
+
+function paths(pathname) {
+ var pieces = pathname.split("/");
+ pieces.shift(); // always starts with /
+
+ var end = pieces[pieces.length - 1];
+ if (end === "index.html" || end === "")
+ pieces.pop();
+ return(pieces);
+}
+
+function is_prefix(needle, haystack) {
+ if (needle.length > haystack.lengh)
+ return(false);
+
+ for (var i = 0; i < haystack.length; i++) {
+ if (needle[i] != haystack[i])
+ return(false);
+ }
+
+ return(true);
+}
+
+/* Clipboard --------------------------*/
+
+function changeTooltipMessage(element, msg) {
+ var tooltipOriginalTitle=element.getAttribute('data-original-title');
+ element.setAttribute('data-original-title', msg);
+ $(element).tooltip('show');
+ element.setAttribute('data-original-title', tooltipOriginalTitle);
+}
+
+if(Clipboard.isSupported()) {
+ $(document).ready(function() {
+ var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+
+ $(".examples").addClass("hasCopyButton");
+
+ // Insert copy buttons:
+ $(copyButton).prependTo(".hasCopyButton");
+
+ // Initialize tooltips:
+ $('.btn-copy-ex').tooltip({container: 'body'});
+
+ // Initialize clipboard:
+ var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+ text: function(trigger) {
+ return trigger.parentNode.textContent;
+ }
+ });
+
+ clipboardBtnCopies.on('success', function(e) {
+ changeTooltipMessage(e.trigger, 'Copied!');
+ e.clearSelection();
+ });
+
+ clipboardBtnCopies.on('error', function() {
+ changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+ });
+ });
+}
+
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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