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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-01 09:48:02 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-01 09:48:02 +0100
commit4bd4606c76dfc152547e0f5899a98494a4290d33 (patch)
tree36978d1bc83fcf56b1302181ce8367a60d6c156d /docs/reference/chent.html
parent3f82707cd1e974848185b1141c69734e2573594d (diff)
Rebuild static documentation with current pkdown
Diffstat (limited to 'docs/reference/chent.html')
-rw-r--r--docs/reference/chent.html81
1 files changed, 49 insertions, 32 deletions
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index 15c4d10..ef683ef 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -18,19 +18,30 @@
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+
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+<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" />
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@@ -49,6 +60,12 @@
<div id="navbar" class="navbar-collapse collapse">
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<li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
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+<li>
<a href="../reference/index.html">Reference</a>
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</ul>
@@ -75,7 +92,7 @@ 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>
+ <pre class="usage"><span class='no'>chent</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -83,52 +100,52 @@ python bindings are installed and configured for use with PythonInR.</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 &#39;source&#39;</dd></p>
- <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute &#39;source&#39;</dd></p>
- <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute &#39;source&#39;</dd></p>
- <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute &#39;source&#39;</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>
+
+ <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>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>
+</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'>&lt;-</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'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <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'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>Initialize Python Version 3.4.2 (default, Oct 8 2014, 10:47:48) </span>
-#&gt; <span class='message'>[GCC 4.9.1]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
-#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <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'>#&gt; &lt;chent&gt;
+#&gt; <span class='message'>Initialize Python Version 2.7.13 (default, Nov 24 2017, 17:33:09) </span>
+#&gt; <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
+#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Loading required namespace: grConvert</span></div><div class='output co'>#&gt; <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'>#&gt; &lt;chent&gt;
#&gt; Identifier $identifier 1-octanol
#&gt; InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N
#&gt; SMILES string $smiles:
#&gt; user PubChem_Canonical
-#&gt; &quot;CCCCCCCCO&quot; &quot;CCCCCCCCO&quot;
+#&gt; "CCCCCCCCO" "CCCCCCCCO"
#&gt; Molecular weight $mw: 130.2
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] &quot;957&quot; &quot;1-octanol&quot; &quot;Octan-1-ol&quot; &quot;octanol&quot;
-#&gt; [5] &quot;Octyl alcohol&quot; &quot;N-octanol&quot; &quot;Capryl alcohol&quot; &quot;n-Octyl alcohol&quot;
-#&gt; [9] &quot;111-87-5&quot; &quot;caprylic alcohol&quot;</div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <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'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
+#&gt; [1] "957" "1-octanol" "Octan-1-ol" "octanol"
+#&gt; [5] "Octyl alcohol" "N-octanol" "111-87-5" "Capryl alcohol"
+#&gt; [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'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <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'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <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'>#&gt; &lt;chent&gt;
#&gt; Identifier $identifier caffeine
#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
#&gt; SMILES string $smiles:
#&gt; PubChem_Canonical
-#&gt; &quot;CN1C=NC2=C1C(=O)N(C(=O)N2C)C&quot;
+#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
#&gt; Molecular weight $mw: 194.2
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] &quot;2519&quot; &quot;caffeine&quot;
-#&gt; [3] &quot;Guaranine&quot; &quot;1,3,7-Trimethylxanthine&quot;
-#&gt; [5] &quot;Methyltheobromine&quot; &quot;Cafeina&quot;
-#&gt; [7] &quot;Thein&quot; &quot;Koffein&quot;
-#&gt; [9] &quot;Mateina&quot; &quot;Theine&quot; </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>
+#&gt; [1] "2519" "caffeine"
+#&gt; [3] "1,3,7-Trimethylxanthine" "58-08-2"
+#&gt; [5] "Guaranine" "Thein"
+#&gt; [7] "Cafeina" "Methyltheobromine"
+#&gt; [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>
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@@ -150,7 +167,7 @@ configured for use with PythonInR</dd></p>
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- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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