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| -rw-r--r-- | docs/reference/pai.html | 315 |
1 files changed, 129 insertions, 186 deletions
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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="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."><!-- 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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -73,44 +18,31 @@ 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">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">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> + <ul class="nav navbar-nav"><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/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/chents/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>An R6 class for pesticidal active ingredients and associated data</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small> <div class="hidden name"><code>pai.Rd</code></div> </div> @@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.</p> </div> + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object</p> + </div> + <div id="super-class"> + <h2>Super class</h2> + <p><code><a href="chent.html">chents::chent</a></code> -> <code>pai</code></p> + </div> + <div id="public-fields"> + <h2>Public fields</h2> + <p></p><div class="r6-fields"><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> - <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="super-class"><a class="anchor" href="#super-class"></a>Super class</h2> +</dl><p></p></div> + </div> + <div id="methods"> + <h2>Methods</h2> + +<div class="section"> +<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> + +<ul><li><p><a href="#method-pai-new"><code>pai$new()</code></a></p></li> +<li><p><a href="#method-pai-clone"><code>pai$clone()</code></a></p></li> +</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chents::chent$add_PUF()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chents::chent$add_TP()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chents::chent$add_cwsat()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chents::chent$add_p0()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chents::chent$add_soil_degradation()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chents::chent$add_soil_ff()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chents::chent$add_soil_sorption()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chents::chent$add_transformation()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chents::chent$emf()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chents::chent$get_chyaml()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chents::chent$get_pubchem()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chents::chent$get_rdkit()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chents::chent$pdf()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chents::chent$png()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li> +</ul></details></p><hr><a id="method-pai-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> + +<div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">iso</span>,</span> +<span> identifier <span class="op">=</span> <span class="va">iso</span>,</span> +<span> smiles <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> bcpc <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> pubchem_from <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> template <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> chyaml <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> - <p><code><a href='chent.html'>chents::chent</a></code> -> <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> +</div><p></p><hr><a id="method-pai-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">pai</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> -<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd> +<div class="section"> +<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> - -<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3> - -<ul> -<li><p><a href='#method-new'><code>pai$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='co'># On Travis, we get a certificate validation error,</span> -<span class='co'># likely because the system (xenial) is so old,</span> -<span class='co'># therefore don't run this example on Travis</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>""</span><span class='op'>)</span> <span class='op'>{</span> - -<span class='va'>atr</span> <span class='op'><-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</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> - -<span class='op'>}</span> -</div><div class='output co'>#> <span class='message'>BCPC:</span></div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> -#> <span class='message'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> <pai> with ISO common name $iso atrazine -#> <chent> -#> Identifier $identifier atrazine -#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N -#> SMILES string $smiles: -#> PubChem_Canonical -#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" -#> Molecular weight $mw: 215.7 -#> PubChem synonyms (up to 10): -#> [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Chromozin" -#> [6] "Aktikon" "Atrazin" "Argezin" "Atazinax" "Atranex" </div></pre> +</dl><p></p></div> +</div> + +</div> + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span> +<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span> +<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">atr</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> +<span class="r-in"><span><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" class="external-link">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></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> BCPC:</span> +<span class="r-msg co"><span class="r-pr">#></span> PubChem:</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./atrazine.yaml</span> +<span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span> +<span class="r-out co"><span class="r-pr">#></span> <pai> with ISO common name $iso atrazine </span> +<span class="r-out co"><span class="r-pr">#></span> <chent></span> +<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier atrazine </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N </span> +<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> +<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 215.7 </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Aktikon" </span> +<span class="r-out co"><span class="r-pr">#></span> [6] "Atranex" "Chromozin" "Atazinax" "Atrasine" "Gesoprim" </span> +</code></pre></div> + </div> </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> + <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> + <footer><div class="copyright"> + 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