diff options
Diffstat (limited to 'docs/reference/pai.html')
| -rw-r--r-- | docs/reference/pai.html | 51 |
1 files changed, 32 insertions, 19 deletions
diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 443769d..25ca564 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -15,7 +15,7 @@ bcpc_query."></head><body> <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -184,23 +184,12 @@ and the reticulate package?</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span> -<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span> -<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span> -<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">atr</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">atr</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> BCPC:</span> -<span class="r-msg co"><span class="r-pr">#></span> PubChem:</span> -<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem SMILES</span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">atr</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Querying BCPC for atrazine ...</span> +<span class="r-msg co"><span class="r-pr">#></span> Querying PubChem for inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N ...</span> +<span class="r-msg co"><span class="r-pr">#></span> Get chemical information from RDKit using PubChem SMILES</span> <span class="r-msg co"><span class="r-pr">#></span> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span> -<span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <pai> with ISO common name $iso atrazine </span> <span class="r-out co"><span class="r-pr">#></span> <chent></span> <span class="r-out co"><span class="r-pr">#></span> Identifier $identifier atrazine </span> @@ -210,8 +199,32 @@ and the reticulate package?</p></dd> <span class="r-out co"><span class="r-pr">#></span> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span> <span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 215.7 </span> <span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> -<span class="r-out co"><span class="r-pr">#></span> [1] "atrazine" "1912-24-9" "Gesaprim" "Atranex" "Oleogesaprim"</span> -<span class="r-out co"><span class="r-pr">#></span> [6] "Atazinax" "Atrasine" "Chromozin" "Gesoprim" "Hungazin" </span> +<span class="r-out co"><span class="r-pr">#></span> [1] "atrazine" "1912-24-9" "Gesaprim" "Aatrex" "Atranex" </span> +<span class="r-out co"><span class="r-pr">#></span> [6] "Atrazin" "Oleogesaprim" "Atazinax" "Atrasine" "Chromozin" </span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">atr</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># We can also define pais that are not found on the BCPC site</span></span></span> +<span class="r-in"><span><span class="va">decanol</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-Decanol"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Querying BCPC for 1-Decanol ...</span> +<span class="r-msg co"><span class="r-pr">#></span> Common name 1-Decanol is not known at the BCPC compendium, trying PubChem</span> +<span class="r-msg co"><span class="r-pr">#></span> Querying PubChem for name 1-Decanol ...</span> +<span class="r-msg co"><span class="r-pr">#></span> Get chemical information from RDKit using PubChem SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCCCO</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">decanol</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <pai> without ISO common name</span> +<span class="r-out co"><span class="r-pr">#></span> <chent></span> +<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier 1-Decanol </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey MWKFXSUHUHTGQN-UHFFFAOYSA-N </span> +<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> +<span class="r-out co"><span class="r-pr">#></span> PubChem </span> +<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCCCO" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 158.3 </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "1-DECANOL" "Decan-1-ol" "Decyl alcohol" "112-30-1" </span> +<span class="r-out co"><span class="r-pr">#></span> [5] "n-Decyl alcohol" "n-Decanol" "Capric alcohol" "Nonylcarbinol" </span> +<span class="r-out co"><span class="r-pr">#></span> [9] "Antak" "Royaltac" </span> </code></pre></div> </div> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> |