diff options
Diffstat (limited to 'docs/reference/chent.html')
| -rw-r--r-- | docs/reference/chent.html | 368 |
1 files changed, 296 insertions, 72 deletions
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><rdkit.Chem.rdchem.Mol> 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'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Initialize Python Version 2.7.13 (default, Sep 26 2018, 18:42:22) </span> -#> <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using User SMILES</span> -#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent> + <pre class="examples"><div class='input'><span class='va'>oct</span> <span class='op'><-</span> <span class='va'>chent</span><span class='op'>$</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'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using user SMILES</span> +#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <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'>#> <chent> #> Identifier $identifier 1-octanol #> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N #> SMILES string $smiles: @@ -157,12 +379,16 @@ configured for use with PythonInR</p></dd> #> "CCCCCCCCO" "CCCCCCCCO" #> Molecular weight $mw: 130.2 #> PubChem synonyms (up to 10): -#> [1] "957" "1-octanol" "Octan-1-ol" "octanol" -#> [5] "111-87-5" "N-octanol" "Capryl alcohol" "Octyl alcohol" -#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>oct</span>$<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'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> -#> <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <chent> +#> [1] "1-octanol" "Octan-1-ol" "octanol" "111-87-5" +#> [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "caprylic alcohol" +#> [9] "n-Octyl alcohol" "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</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'><-</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'>#> <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'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <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'>#> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: @@ -170,41 +396,39 @@ configured for use with PythonInR</p></dd> #> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): -#> [1] "2519" "caffeine" -#> [3] "58-08-2" "Guaranine" -#> [5] "1,3,7-Trimethylxanthine" "Thein" -#> [7] "Cafeina" "Methyltheobromine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>caffeine</span>$<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> +#> [1] "caffeine" "58-08-2" +#> [3] "1,3,7-Trimethylxanthine" "Guaranine" +#> [5] "Thein" "Methyltheobromine" +#> [7] "Cafeina" "Theine" +#> [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> + |