aboutsummaryrefslogblamecommitdiff
path: root/inst/web/chent.html
blob: f2adb6b520ea0fe686d2ab470a9c04a1710a19af (plain) (tree) 
f908377




























































































































































1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156




























































































































































                                                                                                                                                                                           
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
<title>chent. chents 0.2-1</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="">

<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link href="css/highlight.css" rel="stylesheet">
<link href="css/staticdocs.css" rel="stylesheet">

<!--[if lt IE 9]>
  <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->

<script type="text/x-mathjax-config">
  MathJax.Hub.Config({
    tex2jax: {
      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
      processEscapes: true
    }
  });
</script>
<script type="text/javascript"
  src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
  </head>

  <body>
    <div class="navbar">
  <div class="navbar-inner">
    <div class="container">
      <a class="brand" href="#">chents 0.2-1</a>
      <div class="nav">
        <ul class="nav">
          <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
        </ul>
      </div>
    </div>
  </div>
</div>

    <div class="container">
      <header>
        
      </header>
      
      <h1>An R6 class for chemical entities with associated data</h1>

<div class="row">
  <div class="span8">
    <h2>Usage</h2>
    <pre><div>chent</div></pre>
        
    <div class="Format">
      <h2>Format</h2>

      <p>An <code><a href='http://www.inside-r.org/packages/cran/R6/docs/R6Class'>R6Class</a></code> generator object</p>
  
    </div>

    <div class="Description">
      <h2>Description</h2>

      <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="Fields">
      <h2>Fields</h2>

      <p></p>
  
      <p><dl>
<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</dd></p>
  
      <p><dt><code>Picture</code></dt><dd>Graph as a <code><a href='http://www.inside-r.org/packages/cran/grImport/docs/picture'>picture</a></code> object obtained using grImport</dd></p>
  
      <p></dl></p>
  
    </div>
    
    <h2 id="examples">Examples</h2>
    <pre class="examples"><div class='input'>oct &lt;- chent$new(&quot;1-octanol&quot;, smiles = &quot;CCCCCCCCO&quot;)
oct$try_pubchem()
</div>
<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&amp;db=pccompound&amp;term=1-octanol</strong>
<strong class='message'>Found 1 entries in PubChem, using the first one.</strong>
<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&amp;db=pccompound&amp;ID=957</strong>
<div class='input'>print(oct)
</div>
<div class='output'>&lt;chent&gt;
Identifier $identifier 1-octanol 
InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
SMILES string $smiles CCCCCCCCO 
Molecular weight $mw: 130.2 
PubChem synonyms (first 10):
 [1] &quot;1-octanol&quot;        &quot;Octan-1-ol&quot;       &quot;octanol&quot;          &quot;N-octanol&quot;        &quot;Capryl alcohol&quot;   &quot;Octyl alcohol&quot;   
 [7] &quot;n-Octyl alcohol&quot;  &quot;caprylic alcohol&quot; &quot;Heptyl carbinol&quot;  &quot;1-Hydroxyoctane&quot; 
</div>
<div class='input'>plot(oct)
</div>
<div class='input'>caffeine &lt;- chent$new(&quot;caffeine&quot;, source = &quot;pubchem&quot;)
</div>
<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&amp;db=pccompound&amp;term=caffeine</strong>
<strong class='message'>Found 217 entries in PubChem, using the first one.</strong>
<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&amp;db=pccompound&amp;ID=1188</strong>
<div class='input'>print(caffeine)
</div>
<div class='output'>&lt;chent&gt;
Identifier $identifier caffeine 
InChI Key $inchikey LRFVTYWOQMYALW-UHFFFAOYSA-N 
SMILES string $smiles C1=NC2=C(N1)C(=O)NC(=O)N2 
Molecular weight $mw: 152.1 
PubChem synonyms (first 10):
 [1] &quot;xanthine&quot;            &quot;2,6-Dihydroxypurine&quot; &quot;69-89-6&quot;             &quot;Xanthin&quot;             &quot;2,6-dioxopurine&quot;    
 [6] &quot;Pseudoxanthine&quot;      &quot;Isoxanthine&quot;         &quot;Xanthic oxide&quot;       &quot;1H-Purine-2,6-diol&quot;  &quot;Purine-2,6-diol&quot;    
</div>
<div class='input'>caffeine$get_rdkit()
plot(caffeine)
</div>
<p><img src='chent-15.png' alt='' width='540' height='400' /></p></pre>
  </div>
  <div class="span4">
    <!-- <ul>
      <li>chent</li>
    </ul>
    <ul>
      <li>data</li>
    </ul> -->
      
        
  </div>
</div>
      
      <footer>
      <p class="pull-right"><a href="#">Back to top</a></p>
<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
      </footer>
    </div>
  </body>
</html>

Contact - Imprint