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Diffstat (limited to 'docs/reference/chent.html')
| -rw-r--r-- | docs/reference/chent.html | 81 |
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 @@ <!-- 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"> +<!-- 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> <!-- 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://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -49,6 +60,12 @@ <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> @@ -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 '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> + + <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'><-</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> +#> <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> #> Identifier $identifier 1-octanol #> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N #> SMILES string $smiles: #> user PubChem_Canonical -#> "CCCCCCCCO" "CCCCCCCCO" +#> "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> +#> [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> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical -#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" +#> "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> +#> [1] "2519" "caffeine" +#> [3] "1,3,7-Trimethylxanthine" "58-08-2" +#> [5] "Guaranine" "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> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -150,7 +167,7 @@ configured for use with PythonInR</dd></p> </div> <div class="pkgdown"> - <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> </div> </footer> |