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diff --git a/docs/reference/chent.html b/docs/reference/chent.html index 3d0928c..2cedc00 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,210 +1,831 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<!-- 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"><meta name="description" content="The class is initialised with an identifier. Chemical +information is retrieved from the internet. 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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><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + -<title>An R6 class for chemical entities with associated data — chent • chents</title> + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">chents</a> -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.2</small> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> + + <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> -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> + <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> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/chents/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><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> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <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> -<meta property="og:title" content="An R6 class for chemical entities with associated data — chent" /> -<meta property="og:description" content="The class is initialised with an identifier. Chemical information is retrieved from -the internet. Additionally, it can be generated using RDKit if RDKit and its -python bindings are installed and configured for use with PythonInR." /> -<meta name="twitter:card" content="summary" /> +<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> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">chents</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span> - </span> - </div> +<dt><code>mw</code></dt> +<dd><p>(<code>numeric(1)</code>)<br> +Molecular weight, with attribute 'source'</p></dd> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/chents"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - </header> +<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> -<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> - <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 and configured for use with PythonInR.</p> - - </div> +<dt><code>rdkit</code></dt> +<dd><p>List of information obtained with RDKit</p></dd> - <pre class="usage"><span class='no'>chent</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>An <code>R6Class</code> generator object</p> - - <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> +<dt><code>mol</code></dt> +<dd><p><rdkit.Chem.rdchem.Mol> object</p></dd> + +<dt><code>svg</code></dt> +<dd><p>SVG code</p></dd> + + +<dt><code>Picture</code></dt> +<dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd> + + +<dt><code>Pict_font_size</code></dt> +<dd><p>Font size as extracted from the intermediate PostScript file</p></dd> + + +<dt><code>pdf_height</code></dt> +<dd><p>Height of the MediaBox in the pdf after cropping</p></dd> + + +<dt><code>p0</code></dt> +<dd><p>Vapour pressure in Pa</p></dd> + + +<dt><code>cwsat</code></dt> +<dd><p>Water solubility in mg/L</p></dd> + + +<dt><code>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> - <dl class='dl-horizontal'> -<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd> - <dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd> - <dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd> - <dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd> - <dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd> - <dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit, if installed and -configured for use with PythonInR</p></dd> - <dt><code>svg</code></dt><dd><p>SVG code</p></dd> - <dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd> - <dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd> - <dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd> - <dt><code>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd> - <dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd> - <dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd> - <dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd> - <dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd> - <dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd> - <dt><code>PUF</code></dt><dd><p>Plant uptake factor</p></dd> -</dl> - +<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> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Initialize Python Version 2.7.13 (default, Sep 26 2018, 18:42:22) </span> -#> <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using User SMILES</span> -#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent> -#> Identifier $identifier 1-octanol -#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N -#> SMILES string $smiles: -#> user PubChem_Canonical -#> "CCCCCCCCO" "CCCCCCCCO" -#> Molecular weight $mw: 130.2 -#> PubChem synonyms (up to 10): -#> [1] "957" "1-octanol" "Octan-1-ol" "octanol" -#> [5] "111-87-5" "N-octanol" "Capryl alcohol" "Octyl alcohol" -#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>oct</span>$<span class='no'>Picture</span>)) { - <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>oct</span>) -}</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> -#> <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <chent> -#> 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 $mw: 194.2 -#> PubChem synonyms (up to 10): -#> [1] "2519" "caffeine" -#> [3] "58-08-2" "Guaranine" -#> [5] "1,3,7-Trimethylxanthine" "Thein" -#> [7] "Cafeina" "Methyltheobromine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>caffeine</span>$<span class='no'>Picture</span>)) { - <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>) -}</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> +<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> - <li><a href="#fields">Fields</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - </div> +<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">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-16">Arguments<a class="anchor" aria-label="anchor" href="#arguments-16"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> + + +</dl><p></p></div> +</div> + </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</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> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <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> 1.3.0.</p> +<div class="pkgdown-footer-right"> + <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> |