Add plot example, update static docs

author: Johannes Ranke <jranke@uni-bremen.de> 2021-11-19 00:22:03 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2021-11-19 00:22:03 +0100
commit: 79123acfdd9a9b905a5b177e2b7aa0d604e52267 (patch)
tree: 010dbecd40bddb46aafb0bc6c8da8a1ced08532a
parent: 0056584e5168df75bca159ddf3469aa07457b77d (diff)
22 files changed, 1273 insertions, 347 deletions
diff --git a/R/chent.R b/R/chent.R
index d988e97..6983561 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -471,6 +471,12 @@ draw_svg.chent = function(x, width = 300, height = 150,
 #' @param x The chent object to be plotted
 #' @param ... Further arguments passed to \code{\link{grid.picture}}
 #' @export
+#' @examples
+#' caffeine <- chent$new("caffeine")
+#' print(caffeine)
+#' if (!is.null(caffeine$Picture)) {
+#'   plot(caffeine)
+#' }
 plot.chent = function(x, ...) {
   if (is.null(x$Picture)) stop("No Picture object in chent, was RDKit available during creation?")
   grid.picture(x$Picture)
diff --git a/docs/404.html b/docs/404.html
new file mode 100644
index 0000000..7bd3245
--- /dev/null
+++ b/docs/404.html
@@ -0,0 +1,145 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <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>Page not found (404) • chents</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script>
+
+
+
+
+<meta property="og:title" content="Page not found (404)" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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 data-spy="scroll" data-target="#toc">
+    <div class="container template-title-body">
+      <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" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">chents</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="index.html">
+    <span class="fas fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="reference/index.html">Reference</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="contents col-md-9">
+    <div class="page-header">
+      <h1>Page not found (404)</h1>
+    </div>
+
+Content not found. Please use links in the navbar.
+
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+
+</div>
+
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/authors.html b/docs/authors.html
index 3274797..327fe56 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -8,21 +8,29 @@
 
 <title>Authors • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="pkgdown.css" rel="stylesheet">
@@ -30,10 +38,12 @@
 
 
 
+
 <meta property="og:title" content="Authors" />
 
 
 
+
 <!-- mathjax -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -44,9 +54,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-authors">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -60,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -68,7 +79,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -76,11 +87,10 @@
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -91,6 +101,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -111,19 +122,23 @@
 </div>
 
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css
new file mode 100644
index 0000000..5a85941
--- /dev/null
+++ b/docs/bootstrap-toc.css
@@ -0,0 +1,60 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+
+/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
+
+/* All levels of nav */
+nav[data-toggle='toc'] .nav > li > a {
+  display: block;
+  padding: 4px 20px;
+  font-size: 13px;
+  font-weight: 500;
+  color: #767676;
+}
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+  padding-left: 19px;
+  color: #563d7c;
+  text-decoration: none;
+  background-color: transparent;
+  border-left: 1px solid #563d7c;
+}
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+  padding-left: 18px;
+  font-weight: bold;
+  color: #563d7c;
+  background-color: transparent;
+  border-left: 2px solid #563d7c;
+}
+
+/* Nav: second level (shown on .active) */
+nav[data-toggle='toc'] .nav .nav {
+  display: none; /* Hide by default, but at >768px, show it */
+  padding-bottom: 10px;
+}
+nav[data-toggle='toc'] .nav .nav > li > a {
+  padding-top: 1px;
+  padding-bottom: 1px;
+  padding-left: 30px;
+  font-size: 12px;
+  font-weight: normal;
+}
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+  padding-left: 29px;
+}
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+  padding-left: 28px;
+  font-weight: 500;
+}
+
+/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
+nav[data-toggle='toc'] .nav > .active > ul {
+  display: block;
+}
diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js
new file mode 100644
index 0000000..1cdd573
--- /dev/null
+++ b/docs/bootstrap-toc.js
@@ -0,0 +1,159 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+(function() {
+  'use strict';
+
+  window.Toc = {
+    helpers: {
+      // return all matching elements in the set, or their descendants
+      findOrFilter: function($el, selector) {
+        // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
+        // http://stackoverflow.com/a/12731439/358804
+        var $descendants = $el.find(selector);
+        return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
+      },
+
+      generateUniqueIdBase: function(el) {
+        var text = $(el).text();
+        var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
+        return anchor || el.tagName.toLowerCase();
+      },
+
+      generateUniqueId: function(el) {
+        var anchorBase = this.generateUniqueIdBase(el);
+        for (var i = 0; ; i++) {
+          var anchor = anchorBase;
+          if (i > 0) {
+            // add suffix
+            anchor += '-' + i;
+          }
+          // check if ID already exists
+          if (!document.getElementById(anchor)) {
+            return anchor;
+          }
+        }
+      },
+
+      generateAnchor: function(el) {
+        if (el.id) {
+          return el.id;
+        } else {
+          var anchor = this.generateUniqueId(el);
+          el.id = anchor;
+          return anchor;
+        }
+      },
+
+      createNavList: function() {
+        return $('<ul class="nav"></ul>');
+      },
+
+      createChildNavList: function($parent) {
+        var $childList = this.createNavList();
+        $parent.append($childList);
+        return $childList;
+      },
+
+      generateNavEl: function(anchor, text) {
+        var $a = $('<a></a>');
+        $a.attr('href', '#' + anchor);
+        $a.text(text);
+        var $li = $('<li></li>');
+        $li.append($a);
+        return $li;
+      },
+
+      generateNavItem: function(headingEl) {
+        var anchor = this.generateAnchor(headingEl);
+        var $heading = $(headingEl);
+        var text = $heading.data('toc-text') || $heading.text();
+        return this.generateNavEl(anchor, text);
+      },
+
+      // Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
+      getTopLevel: function($scope) {
+        for (var i = 1; i <= 6; i++) {
+          var $headings = this.findOrFilter($scope, 'h' + i);
+          if ($headings.length > 1) {
+            return i;
+          }
+        }
+
+        return 1;
+      },
+
+      // returns the elements for the top level, and the next below it
+      getHeadings: function($scope, topLevel) {
+        var topSelector = 'h' + topLevel;
+
+        var secondaryLevel = topLevel + 1;
+        var secondarySelector = 'h' + secondaryLevel;
+
+        return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+      },
+
+      getNavLevel: function(el) {
+        return parseInt(el.tagName.charAt(1), 10);
+      },
+
+      populateNav: function($topContext, topLevel, $headings) {
+        var $context = $topContext;
+        var $prevNav;
+
+        var helpers = this;
+        $headings.each(function(i, el) {
+          var $newNav = helpers.generateNavItem(el);
+          var navLevel = helpers.getNavLevel(el);
+
+          // determine the proper $context
+          if (navLevel === topLevel) {
+            // use top level
+            $context = $topContext;
+          } else if ($prevNav && $context === $topContext) {
+            // create a new level of the tree and switch to it
+            $context = helpers.createChildNavList($prevNav);
+          } // else use the current $context
+
+          $context.append($newNav);
+
+          $prevNav = $newNav;
+        });
+      },
+
+      parseOps: function(arg) {
+        var opts;
+        if (arg.jquery) {
+          opts = {
+            $nav: arg
+          };
+        } else {
+          opts = arg;
+        }
+        opts.$scope = opts.$scope || $(document.body);
+        return opts;
+      }
+    },
+
+    // accepts a jQuery object, or an options object
+    init: function(opts) {
+      opts = this.helpers.parseOps(opts);
+
+      // ensure that the data attribute is in place for styling
+      opts.$nav.attr('data-toggle', 'toc');
+
+      var $topContext = this.helpers.createChildNavList(opts.$nav);
+      var topLevel = this.helpers.getTopLevel(opts.$scope);
+      var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+      this.helpers.populateNav($topContext, topLevel, $headings);
+    }
+  };
+
+  $(function() {
+    $('nav[data-toggle="toc"]').each(function(i, el) {
+      var $nav = $(el);
+      Toc.init($nav);
+    });
+  });
+})();
diff --git a/docs/index.html b/docs/index.html
index c9bd988..5fadb0b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,23 +6,24 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 <title>Chemical Entities as R Objects • chents</title>
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
 <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
+    configured for use with reticulate, 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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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>
+<body data-spy="scroll" data-target="#toc">
     <div class="container template-home">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -35,7 +36,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -43,7 +44,7 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -53,8 +54,8 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -67,6 +68,7 @@
 <!--/.navbar -->
 
       
+
       </header><div class="row">
   <div class="contents col-md-9">
 <div id="chents" class="section level1">
@@ -91,11 +93,11 @@
 </div>
   </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <div class="links">
 <h2>Links</h2>
 <ul class="list-unstyled">
-<li>Browse source code at <br><a href="https://github.com/jranke/chents">https://github.com/jranke/chents</a>
+<li>Browse source code at <br><a href="https://github.com/jranke/chents/">https://github.com/jranke/chents/</a>
 </li>
 </ul>
 </div>
@@ -122,17 +124,20 @@
 </div>
 </div>
 
+
       <footer><div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
 </div>
 
   
 
+
   </body>
 </html>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index c03fb08..1273238 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -17,12 +17,14 @@ html, body {
   height: 100%;
 }
 
+body {
+  position: relative;
+}
+
 body > .container {
   display: flex;
   height: 100%;
   flex-direction: column;
-
-  padding-top: 60px;
 }
 
 body > .container .row {
@@ -69,6 +71,10 @@ summary {
   margin-top: calc(-60px + 1em);
 }
 
+dd {
+  margin-left: 3em;
+}
+
 /* Section anchors ---------------------------------*/
 
 a.anchor {
@@ -102,37 +108,135 @@ a.anchor {
   margin-top: -40px;
 }
 
-/* Static header placement on mobile devices */
-@media (max-width: 767px) {
-  .navbar-fixed-top {
-    position: absolute;
-  }
-  .navbar {
-    padding: 0;
-  }
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+  position: relative;
 }
 
+.dropdown-submenu>.dropdown-menu {
+  top: 0;
+  left: 100%;
+  margin-top: -6px;
+  margin-left: -1px;
+  border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+  display: block;
+}
+
+.dropdown-submenu>a:after {
+  display: block;
+  content: " ";
+  float: right;
+  width: 0;
+  height: 0;
+  border-color: transparent;
+  border-style: solid;
+  border-width: 5px 0 5px 5px;
+  border-left-color: #cccccc;
+  margin-top: 5px;
+  margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+  border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+  float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+  left: -100%;
+  margin-left: 10px;
+  border-radius: 6px 0 6px 6px;
+}
 
 /* Sidebar --------------------------*/
 
-#sidebar {
+#pkgdown-sidebar {
   margin-top: 30px;
+  position: -webkit-sticky;
+  position: sticky;
+  top: 70px;
 }
-#sidebar h2 {
+
+#pkgdown-sidebar h2 {
   font-size: 1.5em;
   margin-top: 1em;
 }
 
-#sidebar h2:first-child {
+#pkgdown-sidebar h2:first-child {
   margin-top: 0;
 }
 
-#sidebar .list-unstyled li {
+#pkgdown-sidebar .list-unstyled li {
   margin-bottom: 0.5em;
 }
 
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+  padding: 4px 20px 4px 6px;
+  font-size: 1.5rem;
+  font-weight: 400;
+  color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+  padding-left: 5px;
+  color: inherit;
+  border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+  padding-left: 5px;
+  font-size: 1.5rem;
+  font-weight: 400;
+  color: inherit;
+  border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+  display: none; /* Hide by default, but at >768px, show it */
+  padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+  padding-left: 16px;
+  font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+  padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+  padding-left: 15px;
+  font-weight: 500;
+  font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
 .orcid {
-  height: 16px;
+  font-size: 16px;
+  color: #A6CE39;
+  /* margins are required by official ORCID trademark and display guidelines */
+  margin-left:4px;
+  margin-right:4px;
   vertical-align: middle;
 }
 
@@ -140,14 +244,14 @@ a.anchor {
 
 .ref-index th {font-weight: normal;}
 
-.ref-index td {vertical-align: top;}
+.ref-index td {vertical-align: top; min-width: 100px}
 .ref-index .icon {width: 40px;}
 .ref-index .alias {width: 40%;}
 .ref-index-icons .alias {width: calc(40% - 40px);}
 .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 th, .ref-arguments td {vertical-align: top; min-width: 100px}
 .ref-arguments .name {width: 20%;}
 .ref-arguments .desc {width: 80%;}
 
@@ -222,6 +326,19 @@ a.sourceLine:hover {
   visibility: visible;
 }
 
+/* headroom.js ------------------------ */
+
+.headroom {
+  will-change: transform;
+  transition: transform 200ms linear;
+}
+.headroom--pinned {
+  transform: translateY(0%);
+}
+.headroom--unpinned {
+  transform: translateY(-100%);
+}
+
 /* mark.js ----------------------------*/
 
 mark {
@@ -234,3 +351,17 @@ mark {
 .html-widget {
   margin-bottom: 10px;
 }
+
+/* fontawesome ------------------------ */
+
+.fab {
+    font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+  code a:link:after, code a:visited:after {
+    content: "";
+  }
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index eb7e83d..7e7048f 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -2,18 +2,11 @@
 (function($) {
   $(function() {
 
-    $("#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');
-      });
+    $('.navbar-fixed-top').headroom();
 
-    $('body').scrollspy({
-      target: '#sidebar',
-      offset: 60
+    $('body').css('padding-top', $('.navbar').height() + 10);
+    $(window).resize(function(){
+      $('body').css('padding-top', $('.navbar').height() + 10);
     });
 
     $('[data-toggle="tooltip"]').tooltip();
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 1dc6ec1..e09cce3 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,6 @@
-pandoc: 2.2.1
-pkgdown: 1.3.0
+pandoc: 2.9.2.1
+pkgdown: 1.6.1
 pkgdown_sha: ~
-articles: []
+articles: {}
+last_built: 2021-11-18T23:21Z
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
new file mode 100644
index 0000000..377b927
--- /dev/null
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png
index a1798d9..7229a66 100644
--- a/docs/reference/chent-1.png
+++ b/docs/reference/chent-1.png
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index 3d0928c..941eabb 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -8,21 +8,29 @@
 
 <title>An R6 class for chemical entities with associated data — chent • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,12 +38,12 @@
 
 
 
-<meta property="og:title" content="An R6 class for chemical entities with associated data — chent" />
 
+<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" />
+python bindings are installed." />
+
 
 
 
@@ -49,9 +57,10 @@ python bindings are installed and configured for use with PythonInR." />
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -65,7 +74,7 @@ python bindings are installed and configured for use with PythonInR." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -73,7 +82,7 @@ python bindings are installed and configured for use with PythonInR." />
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -81,11 +90,10 @@ python bindings are installed and configured for use with PythonInR." />
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -96,6 +104,7 @@ python bindings are installed and configured for use with PythonInR." />
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -107,49 +116,262 @@ python bindings are installed and configured for use with PythonInR." />
     </div>
 
     <div class="ref-description">
-    
     <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>
-    
+python bindings are installed.</p>
     </div>
 
-    <pre class="usage"><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>
+    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    
-    <dl class='dl-horizontal'>
+    <p><div class="r6-fields"></p><dl>
 <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>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd>
-    <dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd>
-    <dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
-    <dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd>
-    <dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd>
-    <dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd>
-    <dt><code>PUF</code></dt><dd><p>Plant uptake factor</p></dd>
-</dl>
+
+<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</p></dd>
+
+<dt><code>mol</code></dt><dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</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>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd>
+
+<dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd>
+
+<dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
+
+<dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd>
+
+<dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd>
+
+<dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd>
+
+<dt><code>PUF</code></dt><dd><p>Plant uptake factor</p></dd>
+
+</dl><p></div></p>
+    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
+
     
+<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
+
+<ul>
+<li><p><a href='#method-new'><code>chent$new()</code></a></p></li>
+<li><p><a href='#method-try_pubchem'><code>chent$try_pubchem()</code></a></p></li>
+<li><p><a href='#method-get_pubchem'><code>chent$get_pubchem()</code></a></p></li>
+<li><p><a href='#method-get_rdkit'><code>chent$get_rdkit()</code></a></p></li>
+<li><p><a href='#method-get_chyaml'><code>chent$get_chyaml()</code></a></p></li>
+<li><p><a href='#method-add_p0'><code>chent$add_p0()</code></a></p></li>
+<li><p><a href='#method-add_cwsat'><code>chent$add_cwsat()</code></a></p></li>
+<li><p><a href='#method-add_PUF'><code>chent$add_PUF()</code></a></p></li>
+<li><p><a href='#method-add_TP'><code>chent$add_TP()</code></a></p></li>
+<li><p><a href='#method-add_transformation'><code>chent$add_transformation()</code></a></p></li>
+<li><p><a href='#method-add_soil_degradation'><code>chent$add_soil_degradation()</code></a></p></li>
+<li><p><a href='#method-add_soil_ff'><code>chent$add_soil_ff()</code></a></p></li>
+<li><p><a href='#method-add_soil_sorption'><code>chent$add_soil_sorption()</code></a></p></li>
+<li><p><a href='#method-pdf'><code>chent$pdf()</code></a></p></li>
+<li><p><a href='#method-png'><code>chent$png()</code></a></p></li>
+<li><p><a href='#method-emf'><code>chent$emf()</code></a></p></li>
+<li><p><a href='#method-clone'><code>chent$clone()</code></a></p></li>
+</ul>
+<p><hr>
+<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
+  <span class='va'>identifier</span>,
+  smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
+  smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
+  inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
+  inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
+  pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  pubchem_from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"smiles"</span>, <span class='st'>"inchikey"</span><span class='op'>)</span>,
+  rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  template <span class='op'>=</span> <span class='cn'>NULL</span>,
+  chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-try_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>try_pubchem()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>try_pubchem</span><span class='op'>(</span><span class='va'>query</span>, from <span class='op'>=</span> <span class='st'>"name"</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-get_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_pubchem()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_pubchem</span><span class='op'>(</span><span class='va'>pubchem_cid</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-get_rdkit"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_rdkit()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_rdkit</span><span class='op'>(</span>template <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-get_chyaml"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_chyaml()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_chyaml</span><span class='op'>(</span>
+  repo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"wd"</span>, <span class='st'>"local"</span>, <span class='st'>"web"</span><span class='op'>)</span>,
+  chyaml <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/utils/URLencode.html'>URLencode</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".yaml"</span><span class='op'>)</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_p0"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_p0()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_p0</span><span class='op'>(</span><span class='va'>p0</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_cwsat"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_cwsat()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_cwsat</span><span class='op'>(</span><span class='va'>cwsat</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, pH <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_PUF"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_PUF()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_PUF</span><span class='op'>(</span>
+  PUF <span class='op'>=</span> <span class='fl'>0</span>,
+  source <span class='op'>=</span> <span class='st'>"focus_generic_gw_2014"</span>,
+  page <span class='op'>=</span> <span class='fl'>41</span>,
+  remark <span class='op'>=</span> <span class='st'>"Conservative default value"</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_TP"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_TP()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_TP</span><span class='op'>(</span><span class='va'>x</span>, smiles <span class='op'>=</span> <span class='cn'>NULL</span>, pubchem <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_transformation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_transformation()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_transformation</span><span class='op'>(</span>
+  <span class='va'>study_type</span>,
+  <span class='va'>TP_identifier</span>,
+  <span class='va'>max_occurrence</span>,
+  remark <span class='op'>=</span> <span class='st'>""</span>,
+  source <span class='op'>=</span> <span class='cn'>NA</span>,
+  pages <span class='op'>=</span> <span class='cn'>NA</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_soil_degradation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_degradation()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_degradation</span><span class='op'>(</span>
+  <span class='va'>soils</span>,
+  <span class='va'>DT50_mod</span>,
+  <span class='va'>DT50_mod_ref</span>,
+  type <span class='op'>=</span> <span class='cn'>NA</span>,
+  country <span class='op'>=</span> <span class='cn'>NA</span>,
+  pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
+  pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
+  pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
+  perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
+  temperature <span class='op'>=</span> <span class='cn'>NA</span>,
+  moisture <span class='op'>=</span> <span class='cn'>NA</span>,
+  category <span class='op'>=</span> <span class='st'>"lab"</span>,
+  formulation <span class='op'>=</span> <span class='cn'>NA</span>,
+  model <span class='op'>=</span> <span class='cn'>NA</span>,
+  chi2 <span class='op'>=</span> <span class='cn'>NA</span>,
+  remark <span class='op'>=</span> <span class='st'>""</span>,
+  <span class='va'>source</span>,
+  page <span class='op'>=</span> <span class='cn'>NA</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_soil_ff"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_ff()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_ff</span><span class='op'>(</span><span class='va'>target</span>, <span class='va'>soils</span>, ff <span class='op'>=</span> <span class='fl'>1</span>, remark <span class='op'>=</span> <span class='st'>""</span>, <span class='va'>source</span>, page <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-add_soil_sorption"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_sorption()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_sorption</span><span class='op'>(</span>
+  <span class='va'>soils</span>,
+  <span class='va'>Kf</span>,
+  <span class='va'>Kfoc</span>,
+  <span class='va'>N</span>,
+  type <span class='op'>=</span> <span class='cn'>NA</span>,
+  pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
+  pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
+  pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
+  perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
+  perc_clay <span class='op'>=</span> <span class='cn'>NA</span>,
+  CEC <span class='op'>=</span> <span class='cn'>NA</span>,
+  remark <span class='op'>=</span> <span class='st'>""</span>,
+  <span class='va'>source</span>,
+  page <span class='op'>=</span> <span class='cn'>NA</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-pdf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/pdf.html'>pdf()</a></code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>pdf</span><span class='op'>(</span>
+  file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".pdf"</span><span class='op'>)</span>,
+  dir <span class='op'>=</span> <span class='st'>"structures/pdf"</span>,
+  template <span class='op'>=</span> <span class='cn'>NULL</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-png"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/png.html'>png()</a></code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>png</span><span class='op'>(</span>
+  file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".png"</span><span class='op'>)</span>,
+  dir <span class='op'>=</span> <span class='st'>"structures/png"</span>,
+  antialias <span class='op'>=</span> <span class='st'>"gray"</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-emf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>emf()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>emf</span><span class='op'>(</span>file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".emf"</span><span class='op'>)</span>, dir <span class='op'>=</span> <span class='st'>"structures/emf"</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
+<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
+<p><div class="arguments"></p><dl>
+<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
+
+</dl><p></div></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>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>Initialize Python Version 2.7.13 (default, Sep 26 2018, 18:42:22) </span>
-#&gt; <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using User SMILES</span>
-#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>oct</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
+    <pre class="examples"><div class='input'><span class='va'>oct</span> <span class='op'>&lt;-</span> <span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"1-octanol"</span>, smiles <span class='op'>=</span> <span class='st'>"CCCCCCCCO"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</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:
@@ -157,12 +379,16 @@ configured for use with PythonInR</p></dd>
 #&gt;       "CCCCCCCCO"       "CCCCCCCCO" 
 #&gt; Molecular weight $mw: 130.2 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
-#&gt;  [5] "111-87-5"         "N-octanol"        "Capryl alcohol"   "Octyl alcohol"   
-#&gt;  [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>oct</span>$<span class='no'>Picture</span>)) {
-  <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>caffeine</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
+#&gt;  [1] "1-octanol"        "Octan-1-ol"       "octanol"          "111-87-5"        
+#&gt;  [5] "N-octanol"        "Octyl alcohol"    "Capryl alcohol"   "caprylic alcohol"
+#&gt;  [9] "n-Octyl alcohol"  "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span>
+<span class='op'>}</span>
+</div><div class='input'>
+<span class='va'>caffeine</span> <span class='op'>&lt;-</span> <span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"caffeine"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</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:
@@ -170,41 +396,39 @@ configured for use with PythonInR</p></dd>
 #&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
 #&gt; Molecular weight $mw: 194.2 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "2519"                    "caffeine"               
-#&gt;  [3] "58-08-2"                 "Guaranine"              
-#&gt;  [5] "1,3,7-Trimethylxanthine" "Thein"                  
-#&gt;  [7] "Cafeina"                 "Methyltheobromine"      
-#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>caffeine</span>$<span class='no'>Picture</span>)) {
-  <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>)
-}</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre>
+#&gt;  [1] "caffeine"                "58-08-2"                
+#&gt;  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
+#&gt;  [5] "Thein"                   "Methyltheobromine"      
+#&gt;  [7] "Cafeina"                 "Theine"                 
+#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
+<span class='op'>}</span>
+</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></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 class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index 582aa0c..1805ff1 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -8,21 +8,29 @@
 
 <title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,10 +38,10 @@
 
 
 
-<meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent" />
 
+<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" />
+
 
 
 
@@ -47,9 +55,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -63,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -71,7 +80,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -79,11 +88,10 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -94,6 +102,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -105,14 +114,17 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Draw SVG graph from a chent object using RDKit</p>
-    
     </div>
 
-    <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'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste0</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>x</span>$<span class='no'>identifier</span>), <span class='st'>".svg"</span>), <span class='kw'>subdir</span> <span class='kw'>=</span> <span class='st'>"svg"</span>)</pre>
-    
+    <pre class="usage"><span class='fu'>draw_svg.chent</span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  width <span class='op'>=</span> <span class='fl'>300</span>,
+  height <span class='op'>=</span> <span class='fl'>150</span>,
+  filename <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".svg"</span><span class='op'>)</span>,
+  subdir <span class='op'>=</span> <span class='st'>"svg"</span>
+<span class='op'>)</span></pre>
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -137,31 +149,33 @@
       <td><p>The path to which the file should be written</p></td>
     </tr>
     </table>
-    
 
-  </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 class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index f08563c..9de4a87 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -8,21 +8,29 @@
 
 <title>Function reference • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,10 +38,12 @@
 
 
 
+
 <meta property="og:title" content="Function reference" />
 
 
 
+
 <!-- mathjax -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -44,9 +54,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-index">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -60,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -68,7 +79,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -76,11 +87,10 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -91,6 +101,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -114,6 +125,11 @@
           <p class="section-desc"></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -161,27 +177,30 @@
     </table>
   </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-r-class-definitions-and-methods">R6 Class definitions and methods</a></li>
-    </ul>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png
new file mode 100644
index 0000000..c235304
--- /dev/null
+++ b/docs/reference/pai-1.png
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index e240e11..e5ecb99 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -8,21 +8,29 @@
 
 <title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,11 +38,11 @@
 
 
 
-<meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai" />
 
+<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" />
+
 
 
 
@@ -48,9 +56,10 @@ Additional chemical information is retrieved from the internet if available." />
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -64,7 +73,7 @@ Additional chemical information is retrieved from the internet if available." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -72,7 +81,7 @@ Additional chemical information is retrieved from the internet if available." />
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -80,11 +89,10 @@ Additional chemical information is retrieved from the internet if available." />
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,6 +103,7 @@ Additional chemical information is retrieved from the internet if available." />
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -106,30 +115,92 @@ Additional chemical information is retrieved from the internet if available." />
     </div>
 
     <div class="ref-description">
-    
     <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>
-    
     </div>
 
-    <pre class="usage"><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>
+    <h2 class="hasAnchor" id="super-class"><a class="anchor" href="#super-class"></a>Super class</h2>
+
+    <p><code><a href='chent.html'>chents::chent</a></code> -&gt; <code>pai</code></p>
+    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
+
+    <p><div class="r6-fields"></p><dl>
+<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+
+<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+
+</dl><p></div></p>
+    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
     
-    <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>
-    
+<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
+
+<ul>
+<li><p><a href='#method-new'><code>pai$new()</code></a></p></li>
+<li><p><a href='#method-clone'><code>pai$clone()</code></a></p></li>
+</ul>
+<p><details ><summary>Inherited methods</summary>
+<ul>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-add_PUF'><code>chents::chent$add_PUF()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-add_TP'><code>chents::chent$add_TP()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-add_p0'><code>chents::chent$add_p0()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-add_transformation'><code>chents::chent$add_transformation()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-emf'><code>chents::chent$emf()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-pdf'><code>chents::chent$pdf()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-png'><code>chents::chent$png()</code></a></span></p></li>
+<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></p></li>
+</ul>
+</details>
+
+<hr>
+<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
+  <span class='va'>iso</span>,
+  identifier <span class='op'>=</span> <span class='va'>iso</span>,
+  smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
+  smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
+  inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
+  inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
+  bcpc <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  pubchem_from <span class='op'>=</span> <span class='st'>"auto"</span>,
+  rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  template <span class='op'>=</span> <span class='cn'>NULL</span>,
+  chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
+<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
+<p><div class="arguments"></p><dl>
+<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
+
+</dl><p></div></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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>atr</span>)</div><div class='output co'>#&gt; &lt;pai&gt; with ISO common name $iso atrazine 
+    <pre class="examples"><div class='input'><span class='va'>atr</span> <span class='op'>&lt;-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>BCPC:</span></div><div class='output co'>#&gt; <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</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 
@@ -138,36 +209,36 @@ Additional chemical information is retrieved from the internet if available.</p>
 #&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
 #&gt; Molecular weight $mw: 215.7 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "2256"         "atrazine"     "1912-24-9"    "Gesaprim"     "Chromozin"   
-#&gt;  [6] "Oleogesaprim" "Aktikon"      "Argezin"      "Atazinax"     "Atranex"     </div></pre>
+#&gt;  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Chromozin"   
+#&gt;  [6] "Aktikon"      "Atrazin"      "Argezin"      "Atazinax"     "Atranex"     </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span>
+<span class='op'>}</span>
+</div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></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 class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png
index a1798d9..330f0a5 100644
--- a/docs/reference/plot.chent-1.png
+++ b/docs/reference/plot.chent-1.png
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index fddd2e8..62bf38f 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -8,21 +8,29 @@
 
 <title>Plot method for chent objects — plot.chent • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,10 +38,10 @@
 
 
 
-<meta property="og:title" content="Plot method for chent objects — plot.chent" />
 
+<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" />
+
 
 
 
@@ -47,9 +55,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -63,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -71,7 +80,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -79,11 +88,10 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -94,6 +102,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -105,14 +114,12 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Plot method for chent objects</p>
-    
     </div>
 
     <pre class="usage"><span class='co'># S3 method for chent</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-    
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -125,11 +132,13 @@
       <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>
-    <pre class="examples"><div class='input'><span class='no'>caffeine</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>caffeine</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
+    <pre class="examples"><div class='input'><span class='va'>caffeine</span> <span class='op'>&lt;-</span> <span class='va'><a href='chent.html'>chent</a></span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"caffeine"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</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:
@@ -137,38 +146,39 @@
 #&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
 #&gt; Molecular weight $mw: 194.2 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "2519"                    "caffeine"               
-#&gt;  [3] "58-08-2"                 "Guaranine"              
-#&gt;  [5] "1,3,7-Trimethylxanthine" "Thein"                  
-#&gt;  [7] "Cafeina"                 "Methyltheobromine"      
-#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>caffeine</span>$<span class='no'>Picture</span>)) {
-  <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>)
-}</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></div></pre>
+#&gt;  [1] "caffeine"                "58-08-2"                
+#&gt;  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
+#&gt;  [5] "Thein"                   "Methyltheobromine"      
+#&gt;  [7] "Cafeina"                 "Theine"                 
+#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
+<span class='op'>}</span>
+</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></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="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/pp.html b/docs/reference/pp.html
index aa660cb..c4e4a01 100644
--- a/docs/reference/pp.html
+++ b/docs/reference/pp.html
@@ -8,21 +8,29 @@
 
 <title>R6 class for holding a product with at least one active ingredient — pp • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,10 +38,10 @@
 
 
 
-<meta property="og:title" content="R6 class for holding a product with at least one active ingredient — pp" />
 
+<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" />
+
 
 
 
@@ -47,9 +55,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -63,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -71,7 +80,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -79,11 +88,10 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -94,6 +102,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -105,54 +114,93 @@
     </div>
 
     <div class="ref-description">
-    
     <p>An R6 class for holding information about a product with at least one active ingredient</p>
-    
     </div>
 
-    <pre class="usage"><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>
+    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    
-    <dl class='dl-horizontal'>
+    <p><div class="r6-fields"></p><dl>
 <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>
+
+<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><p></div></p>
+    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
+
     
+<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
 
-  </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>
+<ul>
+<li><p><a href='#method-new'><code>pp$new()</code></a></p></li>
+<li><p><a href='#method-print'><code>pp$print()</code></a></p></li>
+<li><p><a href='#method-clone'><code>pp$clone()</code></a></p></li>
+</ul>
+<p><hr>
+<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
+  <span class='va'>name</span>,
+  <span class='va'>...</span>,
+  <span class='va'>concentrations</span>,
+  concentration_units <span class='op'>=</span> <span class='st'>"g/L"</span>,
+  density <span class='op'>=</span> <span class='fl'>1000</span>,
+  density_units <span class='op'>=</span> <span class='st'>"g/L"</span>
+<span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-print"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>print</span><span class='op'>(</span><span class='op'>)</span></pre><p></div></p>
+
+<p><hr>
+<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
+<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
+<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
 
-      <li><a href="#fields">Fields</a></li>
-          </ul>
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
+<p><div class="arguments"></p><dl>
+<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
 
+</dl><p></div></p>
+
+
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index 8f0dd0d..b188ed9 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -8,21 +8,29 @@
 
 <title>Printing method for chent objects — print.chent • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,10 +38,10 @@
 
 
 
-<meta property="og:title" content="Printing method for chent objects — print.chent" />
 
+<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" />
+
 
 
 
@@ -47,9 +55,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -63,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -71,7 +80,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -79,11 +88,10 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -94,6 +102,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -105,14 +114,12 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Printing method for chent objects</p>
-    
     </div>
 
     <pre class="usage"><span class='co'># S3 method for chent</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-    
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -125,31 +132,33 @@
       <td><p>Further arguments for compatibility with the S3 method</p></td>
     </tr>
     </table>
-    
 
-  </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 class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index add2687..284792f 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -8,21 +8,29 @@
 
 <title>Printing method for pai objects (pesticidal active ingredients) — print.pai • chents</title>
 
+
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -30,10 +38,10 @@
 
 
 
-<meta property="og:title" content="Printing method for pai objects (pesticidal active ingredients) — print.pai" />
 
+<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" />
+
 
 
 
@@ -47,9 +55,10 @@
 <![endif]-->
 
 
+
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -63,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
       </span>
     </div>
 
@@ -71,7 +80,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -79,11 +88,10 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://github.com/jranke/chents">
-    <span class="fa fa-github fa-lg"></span>
+  <a href="https://github.com/jranke/chents/">
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -94,6 +102,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -105,14 +114,12 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Printing method for pai objects (pesticidal active ingredients)</p>
-    
     </div>
 
     <pre class="usage"><span class='co'># S3 method for pai</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-    
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -125,31 +132,33 @@
       <td><p>Further arguments for compatibility with the S3 method</p></td>
     </tr>
     </table>
-    
 
-  </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 class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
 </div>
 
+
       <footer>
       <div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
+
       </footer>
    </div>
 
   
 
+
   </body>
 </html>
 
+
diff --git a/man/plot.chent.Rd b/man/plot.chent.Rd
index e5a8770..f2850fa 100644
--- a/man/plot.chent.Rd
+++ b/man/plot.chent.Rd
@@ -14,3 +14,10 @@
 \description{
 Plot method for chent objects
 }
+\examples{
+caffeine <- chent$new("caffeine")
+print(caffeine)
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+}
author	Johannes Ranke <jranke@uni-bremen.de>	2021-11-19 00:22:03 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2021-11-19 00:22:03 +0100
commit	79123acfdd9a9b905a5b177e2b7aa0d604e52267 (patch)
tree	010dbecd40bddb46aafb0bc6c8da8a1ced08532a
parent	0056584e5168df75bca159ddf3469aa07457b77d (diff)