aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/chent.html
blob: a70e3180ed303c1a41e1195e5d7dc9f99c1724b2 (plain) (tree)
1
2
3
4
5
6
7
8
               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                                                   
                                                                                                                                                                     
                                                                   
                                                                                    
                                                                          
 


                                                                                                                                      

                                                                

                                                                                                                         
 




                                                                                                                                                                                




                                                                                                                                                                                                     

                 
 



                                                            

                                                                     

                                                                                                                                                               

          
                                                


                                                                         
          
 
 

                                                                                        

                                                   

                                                                                                             


                                                                                     
 
 


















                                                                                                               
 

                                                       
 
 

                                                    
 
 

                         
 
 

                                                                              
 
 

                                                                            
 
 

                                                                
 
 

                                     
 
 

                                        
 
 

                                   
 
 

                                                             
 

                         

                                                          


                                     

                                                                              


                                      

                                                                           






                                                

                                      



                  

                                                                                           
 















































































































                                                                                                                                                                                                                                                                                                                                             

                                                         












                                                                                                                                                                                                                                                                                                              








                                                                                                 











                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            














                                                                                                 








                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
























                                                                                                 








                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  




























                                                                                                 













                                                                                                                                                                                    



















                                                                                                 








                                                                                                                                                                                                                                                                                                                                                                                                     















                                                                                                 















                                                                                                                                                                                               






























                                                                                                 



























                                                                                                                                                                                                 














































































                                                                                                   








                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              















                                                                                                   























                                                                                                                                                                                              

























                                                                                                   












                                                                                                                                                                                                                                                                                                                            
















                                                                                                   












                                                                                                                                                                                                                                                                                                                            








                                                                                                                                  








                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             







                                                                                                   








                                                                                                                                                                                                                                                                                                       
                                                                                                   










                                                            

                                                                                                      


                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                       
                                                                                                                                                                                                                       

                                                                                               
                                                                                     



                                                                                          







                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                      
                                                                                                                                                                                                                            












                                                                                                                      


                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                      

                   
                                                                                                   
                        
 
 
                                             
                                     

      
                                  
                                                                                                      
      
 
                   
 
 

 
 
                
 
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for chemical entities with associated data — chent • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta name="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."><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."></head><body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>


    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">

    <a class="navbar-brand me-2" href="../index.html">chents</a>

    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.6</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
      <span class="navbar-toggler-icon"></span>
    </button>

    <div id="navbar" class="collapse navbar-collapse ms-3">
      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
 <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/chents/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
      </ul></div>


  </div>
</nav><div class="container template-reference-topic">
<div class="row">
  <main id="main" class="col-md-9"><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/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
      <div class="d-none name"><code>chent.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <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 class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
    <p>An <code>R6Class</code> generator object</p>
    </div>
    <div class="section level2">
    <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></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>


<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>


<dt><code>rdkit</code></dt>
<dd><p>List of information obtained with RDKit</p></dd>


<dt><code>mol</code></dt>
<dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</p></dd>


<dt><code>svg</code></dt>
<dd><p>SVG code</p></dd>


<dt><code>Picture</code></dt>
<dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>


<dt><code>Pict_font_size</code></dt>
<dd><p>Font size as extracted from the intermediate PostScript file</p></dd>


<dt><code>pdf_height</code></dt>
<dd><p>Height of the MediaBox in the pdf after cropping</p></dd>


<dt><code>p0</code></dt>
<dd><p>Vapour pressure in Pa</p></dd>


<dt><code>cwsat</code></dt>
<dd><p>Water solubility in mg/L</p></dd>


<dt><code>PUF</code></dt>
<dd><p>Plant uptake factor</p></dd>


<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
Add a transformation product to the internal list</p></dd>


<dt><code>transformations</code></dt>
<dd><p>Data frame of observed transformations
Add a line in the internal dataframe holding observed transformations</p></dd>


<dt><code>soil_degradation</code></dt>
<dd><p>Dataframe of modelling DT50 values
Add a line in the internal dataframe holding 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
Add soil sorption data</p></dd>


</dl><p></p></div>
    </div>
    <div class="section level2">
    <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></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-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
Get chemical information from RDKit if available</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 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>template</code></dt>
<dd><p>Optional template specified as a SMILES code
Obtain information from a YAML file</p></dd>


</dl><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 class="section">
<h4 id="arguments-4">Arguments<a class="anchor" aria-label="anchor" href="#arguments-4"></a></h4>
<p></p><div class="arguments"><dl><dt><code>repo</code></dt>
<dd><p>Should the file be looked for in the current working
directory, a local git repository under <code>~/git/chyaml</code>, or from
the web (not implemented).</p></dd>


<dt><code>chyaml</code></dt>
<dd><p>The filename to be looked for
Add a vapour pressure</p></dd>


</dl><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 class="section">
<h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4>
<p></p><div class="arguments"><dl><dt><code>p0</code></dt>
<dd><p>The vapour pressure in Pa</p></dd>


<dt><code>T</code></dt>
<dd><p>Temperature</p></dd>


<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>


<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>


<dt><code>remark</code></dt>
<dd><p>A remark
Add a water solubility</p></dd>


</dl><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 class="section">
<h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4>
<p></p><div class="arguments"><dl><dt><code>cwsat</code></dt>
<dd><p>The water solubility in mg/L</p></dd>


<dt><code>T</code></dt>
<dd><p>Temperature</p></dd>


<dt><code>pH</code></dt>
<dd><p>The pH value</p></dd>


<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>


<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>


<dt><code>remark</code></dt>
<dd><p>A remark
Add a plant uptake factor</p></dd>


</dl><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 class="section">
<h4 id="arguments-7">Arguments<a class="anchor" aria-label="anchor" href="#arguments-7"></a></h4>
<p></p><div class="arguments"><dl><dt><code>PUF</code></dt>
<dd><p>The plant uptake factor, a number between 0 and 1</p></dd>


<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>


<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>


<dt><code>remark</code></dt>
<dd><p>A remark</p></dd>


</dl><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 class="section">
<h4 id="arguments-8">Arguments<a class="anchor" aria-label="anchor" href="#arguments-8"></a></h4>
<p></p><div class="arguments"><dl><dt><code>x</code></dt>
<dd><p>A chent object, or an identifier to generate a chent object</p></dd>


<dt><code>smiles</code></dt>
<dd><p>A SMILES code for defining a chent object</p></dd>


<dt><code>pubchem</code></dt>
<dd><p>Should chemical information be obtained from PubChem?</p></dd>


</dl><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 class="section">
<h4 id="arguments-9">Arguments<a class="anchor" aria-label="anchor" href="#arguments-9"></a></h4>
<p></p><div class="arguments"><dl><dt><code>study_type</code></dt>
<dd><p>A characterisation of the study type</p></dd>


<dt><code>TP_identifier</code></dt>
<dd><p>An identifier of one of the transformation products
in <code>self$TPs</code></p></dd>


<dt><code>max_occurrence</code></dt>
<dd><p>The maximum observed occurrence of the
transformation product, expressed as a fraction of the amount that would
result from stochiometric transformation</p></dd>


<dt><code>remark</code></dt>
<dd><p>A remark</p></dd>


<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>


<dt><code>pages</code></dt>
<dd><p>The page from which the information was taken</p></dd>


</dl><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 class="section">
<h4 id="arguments-10">Arguments<a class="anchor" aria-label="anchor" href="#arguments-10"></a></h4>
<p></p><div class="arguments"><dl><dt><code>soils</code></dt>
<dd><p>Names of the soils</p></dd>


<dt><code>DT50_mod</code></dt>
<dd><p>The modelling DT50 in the sense of regulatory pesticide
fate modelling</p></dd>


<dt><code>DT50_mod_ref</code></dt>
<dd><p>The normalised modelling DT50 in the sense of
regulatory pesticide fate modelling</p></dd>


<dt><code>type</code></dt>
<dd><p>The soil type</p></dd>


<dt><code>country</code></dt>
<dd><p>The country (mainly for field studies)</p></dd>


<dt><code>pH_orig</code></dt>
<dd><p>The pH stated in the study</p></dd>


<dt><code>pH_medium</code></dt>
<dd><p>The medium in which this pH was measured</p></dd>


<dt><code>pH_H2O</code></dt>
<dd><p>The pH extrapolated to pure water</p></dd>


<dt><code>perc_OC</code></dt>
<dd><p>The percentage of organic carbon in the soil</p></dd>


<dt><code>temperature</code></dt>
<dd><p>The temperature during the study in degrees Celsius</p></dd>


<dt><code>moisture</code></dt>
<dd><p>The moisture during the study</p></dd>


<dt><code>category</code></dt>
<dd><p>Is it a laboratory ('lab') or field study ('field')</p></dd>


<dt><code>formulation</code></dt>
<dd><p>Name of the formulation applied, if it was not
the technical active ingredient</p></dd>


<dt><code>model</code></dt>
<dd><p>The degradation model used for deriving <code>DT50_mod</code></p></dd>


<dt><code>chi2</code></dt>
<dd><p>The relative error as defined in FOCUS kinetics</p></dd>


<dt><code>remark</code></dt>
<dd><p>A remark</p></dd>


<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>


<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>


</dl><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 class="section">
<h4 id="arguments-11">Arguments<a class="anchor" aria-label="anchor" href="#arguments-11"></a></h4>
<p></p><div class="arguments"><dl><dt><code>target</code></dt>
<dd><p>The identifier(s) of the transformation product</p></dd>


<dt><code>soils</code></dt>
<dd><p>The soil name(s) in which the transformation was observed</p></dd>


<dt><code>ff</code></dt>
<dd><p>The formation fraction(s)</p></dd>


</dl><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 class="section">
<h4 id="arguments-12">Arguments<a class="anchor" aria-label="anchor" href="#arguments-12"></a></h4>
<p></p><div class="arguments"><dl><dt><code>Kf</code></dt>
<dd><p>The sorption constant in L/kg, either linear (then <code>N</code> is 1)
or according to Freundlich</p></dd>


<dt><code>Kfoc</code></dt>
<dd><p>The constant from above, normalised to soil organic carbon</p></dd>


<dt><code>N</code></dt>
<dd><p>The Freundlich exponent</p></dd>


<dt><code>perc_clay</code></dt>
<dd><p>The percentage of clay in the soil</p></dd>


<dt><code>CEC</code></dt>
<dd><p>The cation exchange capacity
Write a PDF image of the structure</p></dd>


</dl><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 class="section">
<h4 id="arguments-13">Arguments<a class="anchor" aria-label="anchor" href="#arguments-13"></a></h4>
<p></p><div class="arguments"><dl><dt><code>file</code></dt>
<dd><p>The file to write to</p></dd>


<dt><code>dir</code></dt>
<dd><p>The directory to write the file to</p></dd>


<dt><code>template</code></dt>
<dd><p>A template expressed as SMILES to use in RDKit
Write a PNG image of the structure</p></dd>


</dl><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 class="section">
<h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4>
<p></p><div class="arguments"><dl><dt><code>antialias</code></dt>
<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a>
Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd>


</dl><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 class="section">
<h4 id="arguments-15">Arguments<a class="anchor" aria-label="anchor" href="#arguments-15"></a></h4>
<p></p><div class="arguments"><dl><dt><code>file</code></dt>
<dd><p>The file to write to</p></dd>


</dl><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-16">Arguments<a class="anchor" aria-label="anchor" href="#arguments-16"></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 class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, 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">#&gt;</span> Trying to get chemical information from RDKit using user SMILES</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> CCCCCCCCO</span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> &lt;chent&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier 1-octanol </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        user </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "CCCCCCCCO" </span>
<span class="r-out co"><span class="r-pr">#&gt;</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">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> PubChem:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> &lt;chent&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier caffeine </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>              PubChem_Canonical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 194.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "caffeine"                "58-08-2"                </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</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>
  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
    </nav></aside></div>


    <footer><div class="pkgdown-footer-left">
  <p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown-footer-right">
  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
</div>

    </footer></div>





  </body></html>

Contact - Imprint