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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-06 14:52:04 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-06 14:52:04 +0100 |
| commit | aac6606d2aee79e547f725353a42266c00ed2299 (patch) | |
| tree | e08b632e3db29ebda4faaec87cd938bb353b52cd /docs/reference | |
| parent | 6248971edad72b30f7f609a6bb2217d0b41498a0 (diff) | |
Switch to pkgdown and link to pkgdown.jrwb.de
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| -rw-r--r-- | docs/reference/chent.html | 160 | ||||
| -rw-r--r-- | docs/reference/draw_svg.chent.html | 117 | ||||
| -rw-r--r-- | docs/reference/index.html | 137 | ||||
| -rw-r--r-- | docs/reference/pai.html | 133 | ||||
| -rw-r--r-- | docs/reference/plot.chent-11.png | bin | 0 -> 12574 bytes | |||
| -rw-r--r-- | docs/reference/plot.chent.html | 128 | ||||
| -rw-r--r-- | docs/reference/pp.html | 119 | ||||
| -rw-r--r-- | docs/reference/print.chent.html | 111 | ||||
| -rw-r--r-- | docs/reference/print.pai.html | 111 |
10 files changed, 1016 insertions, 0 deletions
diff --git a/docs/reference/chent-22.png b/docs/reference/chent-22.png Binary files differnew file mode 100644 index 0000000..69b3b08 --- /dev/null +++ b/docs/reference/chent-22.png diff --git a/docs/reference/chent.html b/docs/reference/chent.html new file mode 100644 index 0000000..15c4d10 --- /dev/null +++ b/docs/reference/chent.html @@ -0,0 +1,160 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<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> +<!-- 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> + +<!-- 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"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>An R6 class for chemical entities with associated data</h1> + </div> + + + <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> + + + <pre><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> + + <p></p> + <p><dl class='dl-horizontal'> +<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute 'source'</dd></p> + <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute 'source'</dd></p> + <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute 'source'</dd></p> + <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute 'source'</dd></p> + <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p> + <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit, if installed and +configured for use with PythonInR</dd></p> + <p><dt><code>svg</code></dt><dd>SVG code</dd></p> + <p><dt><code>Picture</code></dt><dd>Graph as a <code>picture</code> object obtained using grImport</dd></p> + <p><dt><code>Pict_font_size</code></dt><dd>Font size as extracted from the intermediate PostScript file</dd></p> + <p><dt><code>pdf_height</code></dt><dd>Height of the MediaBox in the pdf after cropping</dd></p> + <p><dt><code>chyaml</code></dt><dd>List of information obtained from a YAML file</dd></p> + <p><dt><code>degradation</code></dt><dd>List of degradation endpoints</dd> +</dl></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Initialize Python Version 3.4.2 (default, Oct 8 2014, 10:47:48) </span> +#> <span class='message'>[GCC 4.9.1]</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'>print</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 $mw: 130.2 +#> PubChem synonyms (up to 10): +#> [1] "957" "1-octanol" "Octan-1-ol" "octanol" +#> [5] "Octyl alcohol" "N-octanol" "Capryl alcohol" "n-Octyl alcohol" +#> [9] "111-87-5" "caprylic alcohol"</div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<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> +#> 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] "Guaranine" "1,3,7-Trimethylxanthine" +#> [5] "Methyltheobromine" "Cafeina" +#> [7] "Thein" "Koffein" +#> [9] "Mateina" "Theine" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='chent-22.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#fields">Fields</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html new file mode 100644 index 0000000..2cc3804 --- /dev/null +++ b/docs/reference/draw_svg.chent.html @@ -0,0 +1,117 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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> + +<!-- 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"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Draw SVG graph from a chent object using RDKit</h1> + </div> + + + <p>Draw SVG graph from a chent object using RDKit</p> + + + <pre><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>, + <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fu'>paste0</span>(<span class='fu'>names</span>(<span class='no'>x</span>$<span class='no'>identifier</span>), <span class='st'>".svg"</span>), <span class='kw'>subdir</span> <span class='kw'>=</span> <span class='st'>"svg"</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>The chent object to be plotted</dd> + <dt>width</dt> + <dd>The desired width in pixels</dd> + <dt>height</dt> + <dd>The desired height in pixels</dd> + <dt>filename</dt> + <dd>The filename</dd> + <dt>subdir</dt> + <dd>The path to which the file should be written</dd> + </dl> + + + </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="#arguments">Arguments</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/index.html b/docs/reference/index.html new file mode 100644 index 0000000..e9dc7a8 --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,137 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<title>Function reference • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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> + +<!-- 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"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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-index"> + <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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9"> + <div class="page-header"> + <h1>Function reference</h1> + <h4>version 0.2-5</h4> + </div> + + <div class="contents"> + <h2 id="section-class-definitions" class="hasAnchor"><a href="#section-class-definitions" class="anchor"></a>Class definitions</h2> + <p class="section-desc"><p>R6 classes and their methods</p></p> + + + <p><a href="chent.html">An R6 class for chemical entities with associated data</a></p> + <ul> + <li><code><a href="chent.html">chent</a></code></li> + </ul> + + <p><a href="draw_svg.chent.html">Draw SVG graph from a chent object using RDKit</a></p> + <ul> + <li><code><a href="draw_svg.chent.html">draw_svg.chent</a></code></li> + </ul> + + <p><a href="plot.chent.html">Plot method for chent objects</a></p> + <ul> + <li><code><a href="plot.chent.html">plot.chent</a></code></li> + </ul> + + <p><a href="print.chent.html">Printing method for chent objects</a></p> + <ul> + <li><code><a href="print.chent.html">print.chent</a></code></li> + </ul> + + <p><a href="pai.html">An R6 class for pesticidal active ingredients and associated data</a></p> + <ul> + <li><code><a href="pai.html">pai</a></code></li> + </ul> + + <p><a href="print.pai.html">Printing method for pai objects (pesticidal active ingredients)</a></p> + <ul> + <li><code><a href="print.pai.html">print.pai</a></code></li> + </ul> + + <p><a href="pp.html">R6 class for holding a product with at least one active ingredient</a></p> + <ul> + <li><code><a href="pp.html">pp</a></code></li> + </ul> + + </div> + </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="#section-class-definitions">Class definitions</a></li> + </ul> + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/pai.html b/docs/reference/pai.html new file mode 100644 index 0000000..4c143a1 --- /dev/null +++ b/docs/reference/pai.html @@ -0,0 +1,133 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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 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+ <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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>An R6 class for pesticidal active ingredients and associated data</h1> + </div> + + + <p>The class is initialised with an identifier which is generally an ISO common name. +Additional chemical information is retrieved from the internet if available.</p> + + + <pre><span class='no'>pai</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> + + <p></p> + <p><dl class='dl-horizontal'> +<dt><code>iso</code></dt><dd>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</dd></p> + <p><dt><code>alanwood</code></dt><dd>List of information retreived from www.alanwood.net/pesticides</dd> +</dl></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>atr</span> <span class='kw'><-</span> <span class='no'>pai</span>$<span class='fu'>new</span>(<span class='st'>"atrazine"</span>)</div><div class='output co'>#> <span class='message'>alanwood.net:</span></div><div class='output co'>#> <span class='message'>Querying atrazine.html</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/inchikey/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'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>atr</span>)</div><div class='output co'>#> <pai> with ISO common name $iso atrazine +#> <chent> +#> Identifier $identifier atrazine +#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N +#> SMILES string $smiles: +#> PubChem_Canonical +#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" +#> Molecular weight $mw: 215.7 +#> PubChem synonyms (up to 10): +#> [1] "2256" "atrazine" "1912-24-9" "Atranex" "Fenatrol" +#> [6] "Atred" "Oleogesaprim" "Atazinax" "Atrasine" "Chromozin" </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#fields">Fields</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/plot.chent-11.png b/docs/reference/plot.chent-11.png Binary files differnew file mode 100644 index 0000000..69b3b08 --- /dev/null +++ b/docs/reference/plot.chent-11.png diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html new file mode 100644 index 0000000..3cc23d9 --- /dev/null +++ b/docs/reference/plot.chent.html @@ -0,0 +1,128 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<title>Plot method for chent objects — plot.chent • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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> + +<!-- 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"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot method for chent objects</h1> + </div> + + + <p>Plot method for chent objects</p> + + + <pre><span class='co'># S3 method for chent</span> +<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>The chent object to be plotted</dd> + <dt>...</dt> + <dd>Further arguments passed to <code>grid.picture</code></dd> + </dl> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><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> +#> 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] "Guaranine" "1,3,7-Trimethylxanthine" +#> [5] "Methyltheobromine" "Cafeina" +#> [7] "Thein" "Koffein" +#> [9] "Mateina" "Theine" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='plot.chent-11.png' alt='' width='540' height='400' /></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="#arguments">Arguments</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/pp.html b/docs/reference/pp.html new file mode 100644 index 0000000..4569a6f --- /dev/null +++ b/docs/reference/pp.html @@ -0,0 +1,119 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<title>R6 class for holding a product with at least one active ingredient — pp • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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 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+ <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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>R6 class for holding a product with at least one active ingredient</h1> + </div> + + + <p>An R6 class for holding information about a product with at least one active ingredient</p> + + + <pre><span class='no'>pp</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> + + <p></p> + <p><dl class='dl-horizontal'> +<dt><code>name</code></dt><dd>The name of the product</dd></p> + <p><dt><code>ais</code></dt><dd>A list of active ingredients</dd></p> + <p><dt><code>concentrations</code></dt><dd>The concentration of the ais</dd></p> + <p><dt><code>concentration_units</code></dt><dd>Defaults to g/L</dd> +</dl></p> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#fields">Fields</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html new file mode 100644 index 0000000..29b215a --- /dev/null +++ b/docs/reference/print.chent.html @@ -0,0 +1,111 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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"> + +<title>Printing method for chent objects — print.chent • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" 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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"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Printing method for chent objects</h1> + </div> + + + <p>Printing method for chent objects</p> + + + <pre><span class='co'># S3 method for chent</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>The chent object to be printed</dd> + <dt>...</dt> + <dd>Further arguments for compatibility with the S3 method</dd> + </dl> + + + </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="#arguments">Arguments</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/print.pai.html 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<div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <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> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Printing method for pai objects (pesticidal active ingredients)</h1> + </div> + + + <p>Printing method for pai objects (pesticidal active ingredients)</p> + + + <pre><span class='co'># S3 method for pai</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>The chent object to be printed</dd> + <dt>...</dt> + <dd>Further arguments for compatibility with the S3 method</dd> + </dl> + + + </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="#arguments">Arguments</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> |
