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diff --git a/docs/reference/chent.html b/docs/reference/chent.html index ef683ef..aa367f6 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -9,32 +9,39 @@ <title>An R6 class for chemical entities with associated data — chent • chents</title> <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> +<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> <!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<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" /> <!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <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" /> + + + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<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> @@ -50,13 +57,18 @@ python bindings are installed and configured for use with PythonInR." /> <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"> + <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> - <a class="navbar-brand" href="../index.html">chents</a> + <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">0.2.6</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,8 +83,14 @@ python bindings are installed and configured for use with PythonInR." /> </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 --> @@ -80,17 +98,21 @@ python bindings are installed and configured for use with PythonInR." /> </header> - <div class="row"> +<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> <pre class="usage"><span class='no'>chent</span></pre> @@ -113,16 +135,21 @@ configured for use with PythonInR</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>degradation</code></dt><dd><p>List of degradation endpoints</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> <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, Nov 24 2017, 17:33:09) </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'>Loading required namespace: grConvert</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'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent> +#> <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'>Lade nötigen Namensraum: grConvert</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: @@ -131,9 +158,9 @@ configured for use with PythonInR</p></dd> #> Molecular weight $mw: 130.2 #> PubChem synonyms (up to 10): #> [1] "957" "1-octanol" "Octan-1-ol" "octanol" -#> [5] "Octyl alcohol" "N-octanol" "111-87-5" "Capryl alcohol" -#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<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'>print</span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <chent> +#> [5] "111-87-5" "N-octanol" "Capryl alcohol" "Octyl alcohol" +#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><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: @@ -142,10 +169,10 @@ configured for use with PythonInR</p></dd> #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] "2519" "caffeine" -#> [3] "1,3,7-Trimethylxanthine" "58-08-2" -#> [5] "Guaranine" "Thein" +#> [3] "58-08-2" "Guaranine" +#> [5] "1,3,7-Trimethylxanthine" "Thein" #> [7] "Cafeina" "Methyltheobromine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre> +#> [9] "Koffein" "Mateina" </div><div class='input'><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> @@ -167,11 +194,13 @@ configured for use with PythonInR</p></dd> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> - </footer> </div> + + </body> </html> + |