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Diffstat (limited to 'docs')
-rw-r--r--docs/authors.html97
-rw-r--r--docs/index.html150
-rw-r--r--docs/jquery.sticky-kit.min.js9
-rw-r--r--docs/link.svg12
-rw-r--r--docs/pkgdown.css113
-rw-r--r--docs/pkgdown.js8
-rw-r--r--docs/reference/chent-22.pngbin0 -> 12574 bytes
-rw-r--r--docs/reference/chent.html160
-rw-r--r--docs/reference/draw_svg.chent.html117
-rw-r--r--docs/reference/index.html137
-rw-r--r--docs/reference/pai.html133
-rw-r--r--docs/reference/plot.chent-11.pngbin0 -> 12574 bytes
-rw-r--r--docs/reference/plot.chent.html128
-rw-r--r--docs/reference/pp.html119
-rw-r--r--docs/reference/print.chent.html111
-rw-r--r--docs/reference/print.pai.html111
16 files changed, 1327 insertions, 78 deletions
diff --git a/docs/authors.html b/docs/authors.html
new file mode 100644
index 0000000..9f174b2
--- /dev/null
+++ b/docs/authors.html
@@ -0,0 +1,97 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Authors • 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]>
+<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>
+ <div class="container template-authors">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="contents col-md-12">
+ <div class="page-header">
+ <h1>Authors</h1>
+ </div>
+
+ <ul class="list-unstyled">
+ <li>
+ <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
+ </p>
+ </li>
+ </ul>
+
+ </div>
+
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/index.html b/docs/index.html
index 3582067..5f8e231 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,65 +1,55 @@
<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>Home. chents 0.2-3</title>
+<!-- Generated by pkgdown: do not edit by hand --><html>
+<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=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+<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]>
+<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]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">chents 0.2-3</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
+</head>
+<body>
+ <div class="container template-home">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">chents</a>
</div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+<li>
+ <a href="reference/index.html">Reference</a>
+</li>
+ </ul>
+<ul class="nav navbar-nav navbar-right"></ul>
+</div>
+<!--/.nav-collapse -->
</div>
+<!--/.container -->
</div>
+<!--/.navbar -->
-
- <div class="container">
- <header>
-
- </header>
- <div class="row">
- <div class="span8">
- <h1>chents</h1>
-
-<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>
-
-<pre><code>This program is free software: you can redistribute it and/or modify it under
+ </header><div class="row">
+ <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>
+<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
-Foundation, either version 3 of the License, or (at your option) any later
+Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
@@ -68,37 +58,41 @@ FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details.
You should have received a copy of the GNU General Public License along with
-this program. If not, see &lt;http://www.gnu.org/licenses/&gt;
-</code></pre>
-
-<h2>Features</h2>
-
+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>
<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>
+<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>
<li>Additional information can be read from a local .yaml file</li>
</ul>
+<p>Some examples are available from the <a href="https://pkgdown.jrwb.de/chents/reference.html">Reference on github</a>.</p>
+</div>
+</div>
+ </div>
-<p>Some examples are available from the
-<a href="https://jranke.github.io/chents/reference.html">Reference on github</a>.</p>
+ <div class="col-md-3" id="sidebar">
+ <h2>License</h2>
+<p>GPL</p>
+<h2>Developers</h2>
+<ul class="list-unstyled">
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+</ul>
+</div>
+</div>
- </div>
- <div class="span3 offset1 sidebar">
- <h2>Authors</h2>
- <ul>
- <li><a href='mailto:jranke@uni-bremen.de'>Johannes Ranke</a> [aut, cre, cph]</li>
- </ul>
- </div>
+ <footer><div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
</footer>
- </div>
+</div>
+
</body>
-</html> \ No newline at end of file
+</html>
diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js
new file mode 100644
index 0000000..e2a3c6d
--- /dev/null
+++ b/docs/jquery.sticky-kit.min.js
@@ -0,0 +1,9 @@
+/*
+ Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net
+*/
+(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k));
+if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q,
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+a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize",
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diff --git a/docs/link.svg b/docs/link.svg
new file mode 100644
index 0000000..88ad827
--- /dev/null
+++ b/docs/link.svg
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 19.2.1, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+ viewBox="0 0 20 20" style="enable-background:new 0 0 20 20;" xml:space="preserve">
+<style type="text/css">
+ .st0{fill:#75AADB;}
+</style>
+<path class="st0" d="M4,11.3h1.3v1.3H4c-2,0-4-2.3-4-4.7s2.1-4.7,4-4.7h5.3c1.9,0,4,2.3,4,4.7c0,1.9-1.2,3.6-2.7,4.3v-1.5
+ C11.4,10.2,12,9.1,12,8c0-1.7-1.4-3.3-2.7-3.3H4C2.7,4.7,1.3,6.3,1.3,8S2.7,11.3,4,11.3z M16,7.3h-1.3v1.3H16c1.3,0,2.7,1.6,2.7,3.3
+ s-1.4,3.3-2.7,3.3h-5.3C9.4,15.3,8,13.7,8,12c0-1.1,0.6-2.2,1.3-2.8V7.7C7.9,8.4,6.7,10.1,6.7,12c0,2.4,2.1,4.7,4,4.7H16
+ c1.9,0,4-2.3,4-4.7S18,7.3,16,7.3z"/>
+</svg>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
new file mode 100644
index 0000000..fd7b0ba
--- /dev/null
+++ b/docs/pkgdown.css
@@ -0,0 +1,113 @@
+/* Sticker footer */
+body > .container {
+ display: flex;
+ padding-top: 60px;
+ min-height: calc(100vh);
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Section anchors ---------------------------------*/
+
+.hasAnchor {
+ margin-left: -30px;
+}
+
+a.anchor {
+ display:inline-block;
+ width: 30px;
+ height: 30px;
+ visibility: hidden;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+.hasAnchor:hover a.anchor {
+ visibility: visible;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -60px;
+}
+
+/* Sidebar --------------------------*/
+
+#sidebar {
+ margin-top: 30px;
+}
+#sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+code {
+ background-color: #f7f7f7;
+ color: #333;
+}
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+}
+
+.warning { color: red; }
+.message { font-weight: bolder; }
+.error { color: red; font-weight: bolder; }
+
+.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 {
+ background-color: #fff;
+ display: block;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
new file mode 100644
index 0000000..c8b38c4
--- /dev/null
+++ b/docs/pkgdown.js
@@ -0,0 +1,8 @@
+$(function() {
+ $("#sidebar").stick_in_parent({offset_top: 40});
+ $('body').scrollspy({
+ target: '#sidebar',
+ offset: 60
+ });
+
+});
diff --git a/docs/reference/chent-22.png b/docs/reference/chent-22.png
new file mode 100644
index 0000000..69b3b08
--- /dev/null
+++ b/docs/reference/chent-22.png
Binary files differ
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
new file mode 100644
index 0000000..15c4d10
--- /dev/null
+++ b/docs/reference/chent.html
@@ -0,0 +1,160 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>An R6 class for chemical entities with associated data — chent • 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]>
+<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>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>An R6 class for chemical entities with associated data</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='no'>chent</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <code>R6Class</code> generator object</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>
+
+
+ <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; 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; 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; <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; 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>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#format">Format</a></li>
+
+ <li><a href="#fields">Fields</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
new file mode 100644
index 0000000..2cc3804
--- /dev/null
+++ b/docs/reference/draw_svg.chent.html
@@ -0,0 +1,117 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • 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>
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+<!-- mathjax -->
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+
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+<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>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Draw SVG graph from a chent object using RDKit</h1>
+ </div>
+
+
+ <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>,
+ <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>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/index.html b/docs/reference/index.html
new file mode 100644
index 0000000..e9dc7a8
--- /dev/null
+++ b/docs/reference/index.html
@@ -0,0 +1,137 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Function reference • 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]>
+<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>
+ <div class="container template-reference-index">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9">
+ <div class="page-header">
+ <h1>Function reference</h1>
+ <h4>version&nbsp;0.2-5</h4>
+ </div>
+
+ <div class="contents">
+ <h2 id="section-class-definitions" class="hasAnchor"><a href="#section-class-definitions" class="anchor"></a>Class definitions</h2>
+ <p class="section-desc"><p>R6 classes and their methods</p></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>
+
+ </div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#section-class-definitions">Class definitions</a></li>
+ </ul>
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
new file mode 100644
index 0000000..4c143a1
--- /dev/null
+++ b/docs/reference/pai.html
@@ -0,0 +1,133 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>An R6 class for pesticidal active ingredients and associated data — pai • 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 -->
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+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+ </head>
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+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
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+
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+
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+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>An R6 class for pesticidal active ingredients and associated data</h1>
+ </div>
+
+
+ <p>The class is initialised with an identifier which is generally an ISO common name.
+Additional chemical information is retrieved from the internet if available.</p>
+
+
+ <pre><span class='no'>pai</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <code>R6Class</code> generator object</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>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>atr</span> <span class='kw'>&lt;-</span> <span class='no'>pai</span>$<span class='fu'>new</span>(<span class='st'>"atrazine"</span>)</div><div class='output co'>#&gt; <span class='message'>alanwood.net:</span></div><div class='output co'>#&gt; <span class='message'>Querying atrazine.html</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/inchikey/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'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>atr</span>)</div><div class='output co'>#&gt; &lt;pai&gt; with ISO common name $iso atrazine
+#&gt; &lt;chent&gt;
+#&gt; Identifier $identifier atrazine
+#&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; 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>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#format">Format</a></li>
+
+ <li><a href="#fields">Fields</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/plot.chent-11.png b/docs/reference/plot.chent-11.png
new file mode 100644
index 0000000..69b3b08
--- /dev/null
+++ b/docs/reference/plot.chent-11.png
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diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
new file mode 100644
index 0000000..3cc23d9
--- /dev/null
+++ b/docs/reference/plot.chent.html
@@ -0,0 +1,128 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Plot method for chent objects — plot.chent • chents</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<!-- Font Awesome icons -->
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+
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+ <div id="navbar" class="navbar-collapse collapse">
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+</li>
+ </ul>
+
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+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Plot method for chent objects</h1>
+ </div>
+
+
+ <p>Plot method for chent objects</p>
+
+
+ <pre><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>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><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; 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>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/pp.html b/docs/reference/pp.html
new file mode 100644
index 0000000..4569a6f
--- /dev/null
+++ b/docs/reference/pp.html
@@ -0,0 +1,119 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>R6 class for holding a product with at least one active ingredient — pp • chents</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<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 -->
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+<script src="../pkgdown.js"></script>
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>R6 class for holding a product with at least one active ingredient</h1>
+ </div>
+
+
+ <p>An R6 class for holding information about a product with at least one active ingredient</p>
+
+
+ <pre><span class='no'>pp</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <code>R6Class</code> generator object.</p>
+
+ <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>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#format">Format</a></li>
+
+ <li><a href="#fields">Fields</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
new file mode 100644
index 0000000..29b215a
--- /dev/null
+++ b/docs/reference/print.chent.html
@@ -0,0 +1,111 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Printing method for chent objects — print.chent • chents</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">chents</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Printing method for chent objects</h1>
+ </div>
+
+
+ <p>Printing method for chent objects</p>
+
+
+ <pre><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>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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+
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+</html>
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
new file mode 100644
index 0000000..d2da6b8
--- /dev/null
+++ b/docs/reference/print.pai.html
@@ -0,0 +1,111 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Printing method for pai objects (pesticidal active ingredients) — print.pai • chents</title>
+
+<!-- jquery -->
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+ <h1>Printing method for pai objects (pesticidal active ingredients)</h1>
+ </div>
+
+
+ <p>Printing method for pai objects (pesticidal active ingredients)</p>
+
+
+ <pre><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>
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+ <h2>Contents</h2>
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+ <li><a href="#arguments">Arguments</a></li>
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