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Chemical +information is retrieved from the internet. Additionally, it can be +generated using RDKit if RDKit and its python bindings are installed."><!-- 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"> @@ -74,361 +19,513 @@ python bindings are installed." /> </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 chemical entities with 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>chent.Rd</code></div> </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.</p> + <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.</p> </div> + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object</p> + </div> + <div id="public-fields"> + <h2>Public fields</h2> + <p></p><div class="r6-fields"><dl><dt><code>identifier</code></dt> +<dd><p>(<code>character(1)</code>)<br> +The identifier that was used to initiate the object, with attribute 'source'</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="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> +<dt><code>inchikey</code></dt> +<dd><p>(<code>character(1)</code>)<br> +InChI Key, with attribute 'source'</p></dd> + + +<dt><code>smiles</code></dt> +<dd><p>(<code><a href="https://rdrr.io/r/base/character.html" class="external-link">character()</a></code>)<br> +SMILES code(s), with attribute 'source'</p></dd> + + +<dt><code>mw</code></dt> +<dd><p>(<code>numeric(1)</code>)<br> +Molecular weight, with attribute 'source'</p></dd> + + +<dt><code>pubchem</code></dt> +<dd><p>(<code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>)<br> +List of information retrieved from PubChem</p></dd> + - <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>rdkit</code></dt> +<dd><p>List of information obtained with RDKit</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>mol</code></dt> +<dd><p><rdkit.Chem.rdchem.Mol> object</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>svg</code></dt> +<dd><p>SVG code</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>Picture</code></dt> +<dd><p>Graph as a <code>picture</code> object obtained using grImport</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>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>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>p0</code></dt> +<dd><p>Vapour pressure in Pa</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>cwsat</code></dt> +<dd><p>Water solubility in mg/L</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> -<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> +<dt><code>chyaml</code></dt> +<dd><p>List of information obtained from a YAML file</p></dd> + +<dt><code>TPs</code></dt> +<dd><p>List of transformation products as chent objects</p></dd> + + +<dt><code>transformations</code></dt> +<dd><p>Data frame of observed transformations</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> + + +</dl><p></p></div> + </div> + <div id="methods"> + <h2>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='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: -#> user PubChem_Canonical -#> "CCCCCCCCO" "CCCCCCCCO" -#> Molecular weight $mw: 130.2 -#> PubChem synonyms (up to 10): -#> [1] "1-octanol" "Octan-1-ol" "octanol" "111-87-5" -#> [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "caprylic alcohol" -#> [9] "n-Octyl alcohol" "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</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: -#> PubChem_Canonical -#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -#> Molecular weight $mw: 194.2 -#> PubChem synonyms (up to 10): -#> [1] "caffeine" "58-08-2" -#> [3] "1,3,7-Trimethylxanthine" "Guaranine" -#> [5] "Thein" "Methyltheobromine" -#> [7] "Cafeina" "Theine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</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 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-chent-new"><code>chent$new()</code></a></p></li> +<li><p><a href="#method-chent-try_pubchem"><code>chent$try_pubchem()</code></a></p></li> +<li><p><a href="#method-chent-get_pubchem"><code>chent$get_pubchem()</code></a></p></li> +<li><p><a href="#method-chent-get_rdkit"><code>chent$get_rdkit()</code></a></p></li> +<li><p><a href="#method-chent-get_chyaml"><code>chent$get_chyaml()</code></a></p></li> +<li><p><a href="#method-chent-add_p0"><code>chent$add_p0()</code></a></p></li> +<li><p><a href="#method-chent-add_cwsat"><code>chent$add_cwsat()</code></a></p></li> +<li><p><a href="#method-chent-add_PUF"><code>chent$add_PUF()</code></a></p></li> +<li><p><a href="#method-chent-add_TP"><code>chent$add_TP()</code></a></p></li> +<li><p><a href="#method-chent-add_transformation"><code>chent$add_transformation()</code></a></p></li> +<li><p><a href="#method-chent-add_soil_degradation"><code>chent$add_soil_degradation()</code></a></p></li> +<li><p><a href="#method-chent-add_soil_ff"><code>chent$add_soil_ff()</code></a></p></li> +<li><p><a href="#method-chent-add_soil_sorption"><code>chent$add_soil_sorption()</code></a></p></li> +<li><p><a href="#method-chent-pdf"><code>chent$pdf()</code></a></p></li> +<li><p><a href="#method-chent-png"><code>chent$png()</code></a></p></li> +<li><p><a href="#method-chent-emf"><code>chent$emf()</code></a></p></li> +<li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-chent-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">identifier</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> pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> pubchem_from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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>,</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> + +<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>identifier</code></dt> +<dd><p>Identifier to be stored in the object</p></dd> + + +<dt><code>smiles</code></dt> +<dd><p>Optional user provided SMILES code</p></dd> + + +<dt><code>inchikey</code></dt> +<dd><p>Optional user provided InChI Key</p></dd> + + +<dt><code>pubchem</code></dt> +<dd><p>Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?</p></dd> + + +<dt><code>pubchem_from</code></dt> +<dd><p>Possibility to select the argument +that is used to query pubchem</p></dd> + + +<dt><code>rdkit</code></dt> +<dd><p>Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?</p></dd> + + +<dt><code>template</code></dt> +<dd><p>An optional SMILES code to be used as template for RDKit</p></dd> + + +<dt><code>chyaml</code></dt> +<dd><p>Should we look for a identifier.yaml file in the working +directory? +Try to get chemical information from PubChem</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-chent-try_pubchem"></a><div class="section"> +<h3 id="method-try-pubchem-">Method <code>try_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-try-pubchem-"></a></h3> + +<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">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<p></p><div class="arguments"><dl><dt><code>query</code></dt> +<dd><p>Query string to be passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd> + + +<dt><code>from</code></dt> +<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a> +Get chemical information from PubChem for a known PubChem CID</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section"> +<h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3> + +<div class="section"> +<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> +<p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt> +<dd><p>CID</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section"> +<h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3> + +<div class="section"> +<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section"> +<h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3> + +<div class="section"> +<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span> +<span> repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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>,</span> +<span> chyaml <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/URLencode.html" class="external-link">URLencode</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".yaml"</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_p0"></a><div class="section"> +<h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3> + +<div class="section"> +<h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section"> +<h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3> + +<div class="section"> +<h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section"> +<h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3> + +<div class="section"> +<h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span> +<span> PUF <span class="op">=</span> <span class="fl">0</span>,</span> +<span> source <span class="op">=</span> <span class="st">"focus_generic_gw_2014"</span>,</span> +<span> page <span class="op">=</span> <span class="fl">41</span>,</span> +<span> remark <span class="op">=</span> <span class="st">"Conservative default value"</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_TP"></a><div class="section"> +<h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3> + +<div class="section"> +<h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section"> +<h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3> + +<div class="section"> +<h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span> +<span> <span class="va">study_type</span>,</span> +<span> <span class="va">TP_identifier</span>,</span> +<span> <span class="va">max_occurrence</span>,</span> +<span> remark <span class="op">=</span> <span class="st">""</span>,</span> +<span> source <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pages <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section"> +<h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3> + +<div class="section"> +<h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span> +<span> <span class="va">soils</span>,</span> +<span> <span class="va">DT50_mod</span>,</span> +<span> <span class="va">DT50_mod_ref</span>,</span> +<span> type <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> country <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> temperature <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> category <span class="op">=</span> <span class="st">"lab"</span>,</span> +<span> formulation <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> model <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> chi2 <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> remark <span class="op">=</span> <span class="st">""</span>,</span> +<span> <span class="va">source</span>,</span> +<span> page <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section"> +<h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3> + +<div class="section"> +<h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section"> +<h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3> + +<div class="section"> +<h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span> +<span> <span class="va">soils</span>,</span> +<span> <span class="va">Kf</span>,</span> +<span> <span class="va">Kfoc</span>,</span> +<span> <span class="va">N</span>,</span> +<span> type <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> perc_clay <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> CEC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> remark <span class="op">=</span> <span class="st">""</span>,</span> +<span> <span class="va">source</span>,</span> +<span> page <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-pdf"></a><div class="section"> +<h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3> + +<div class="section"> +<h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span> +<span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span> +<span> dir <span class="op">=</span> <span class="st">"structures/pdf"</span>,</span> +<span> template <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-png"></a><div class="section"> +<h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3> + +<div class="section"> +<h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span> +<span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span> +<span> dir <span class="op">=</span> <span class="st">"structures/png"</span>,</span> +<span> antialias <span class="op">=</span> <span class="st">"gray"</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-emf"></a><div class="section"> +<h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3> + +<div class="section"> +<h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-16">Usage<a class="anchor" aria-label="anchor" href="#usage-16"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></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></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="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>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using user SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCO</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./1-octanol.yaml</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">oct</span><span class="op">)</span></span></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 1-octanol </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey </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> user </span> +<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCO" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 130.2 </span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</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">oct</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="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></span></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> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./caffeine.yaml</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">caffeine</span><span class="op">)</span></span></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 caffeine </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey RYYVLZVUVIJVGH-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> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 194.2 </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "caffeine" "58-08-2" </span> +<span class="r-out co"><span class="r-pr">#></span> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span> +<span class="r-out co"><span class="r-pr">#></span> [5] "Methyltheobromine" "Theine" </span> +<span class="r-out co"><span class="r-pr">#></span> [7] "Thein" "Cafeina" </span> +<span class="r-out co"><span class="r-pr">#></span> [9] "Koffein" "Mateina" </span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</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">caffeine</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-plt img"><img src="chent-1.png" alt="" width="700" height="433"></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"> + <p></p><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> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |