diff options
Diffstat (limited to 'docs/reference/chent.html')
| -rw-r--r-- | docs/reference/chent.html | 191 |
1 files changed, 108 insertions, 83 deletions
diff --git a/docs/reference/chent.html b/docs/reference/chent.html index a70e318..aed63b3 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -11,7 +11,7 @@ generated using RDKit if RDKit and its python bindings are installed."></head><b <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="">0.3.6</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</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"> @@ -116,18 +116,15 @@ List of information retrieved from PubChem</p></dd> <dt><code>TPs</code></dt> -<dd><p>List of transformation products as chent objects -Add a transformation product to the internal list</p></dd> +<dd><p>List of transformation products as chent objects</p></dd> <dt><code>transformations</code></dt> -<dd><p>Data frame of observed transformations -Add a line in the internal dataframe holding observed transformations</p></dd> +<dd><p>Data frame of observed transformations</p></dd> <dt><code>soil_degradation</code></dt> -<dd><p>Dataframe of modelling DT50 values -Add a line in the internal dataframe holding modelling DT50 values</p></dd> +<dd><p>Dataframe of modelling DT50 values</p></dd> <dt><code>soil_ff</code></dt> @@ -135,8 +132,7 @@ Add a line in the internal dataframe holding modelling DT50 values</p></dd> <dt><code>soil_sorption</code></dt> -<dd><p>Dataframe of soil sorption data -Add soil sorption data</p></dd> +<dd><p>Dataframe of soil sorption data</p></dd> </dl><p></p></div> @@ -176,7 +172,7 @@ Add soil sorption data</p></dd> <span> pubchem_from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"smiles"</span>, <span class="st">"inchikey"</span><span class="op">)</span>,</span> <span> rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> template <span class="op">=</span> <span class="cn">NULL</span>,</span> -<span> chyaml <span class="op">=</span> <span class="cn">TRUE</span></span> +<span> chyaml <span class="op">=</span> <span class="cn">FALSE</span></span> <span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -216,8 +212,7 @@ and the reticulate package?</p></dd> <dt><code>chyaml</code></dt> <dd><p>Should we look for a identifier.yaml file in the working -directory? -Try to get chemical information from PubChem</p></dd> +directory?</p></dd> </dl><p></p></div> @@ -225,8 +220,7 @@ Try to get chemical information from PubChem</p></dd> </div><p></p><hr><a id="method-chent-try_pubchem"></a><div class="section"> <h3 id="method-try-pubchem-">Method <code>try_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-try-pubchem-"></a></h3> - -<div class="section"> +<p>Try to get chemical information from PubChem</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -238,8 +232,7 @@ Try to get chemical information from PubChem</p></dd> <dt><code>from</code></dt> -<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a> -Get chemical information from PubChem for a known PubChem CID</p></dd> +<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd> </dl><p></p></div> @@ -247,8 +240,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd> </div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section"> <h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3> - -<div class="section"> +<p>Get chemical information from PubChem for a known PubChem CID</p><div class="section"> <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -256,8 +248,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd> <div class="section"> <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> <p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt> -<dd><p>CID -Get chemical information from RDKit if available</p></dd> +<dd><p>CID</p></dd> </dl><p></p></div> @@ -265,8 +256,7 @@ Get chemical information from RDKit if available</p></dd> </div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section"> <h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3> - -<div class="section"> +<p>Get chemical information from RDKit if available</p><div class="section"> <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -274,8 +264,7 @@ Get chemical information from RDKit if available</p></dd> <div class="section"> <h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4> <p></p><div class="arguments"><dl><dt><code>template</code></dt> -<dd><p>Optional template specified as a SMILES code -Obtain information from a YAML file</p></dd> +<dd><p>An optional SMILES code to be used as template for RDKit</p></dd> </dl><p></p></div> @@ -283,8 +272,7 @@ Obtain information from a YAML file</p></dd> </div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section"> <h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3> - -<div class="section"> +<p>Obtain information from a YAML file</p><div class="section"> <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span> <span> repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wd"</span>, <span class="st">"local"</span>, <span class="st">"web"</span><span class="op">)</span>,</span> @@ -301,8 +289,7 @@ the web (not implemented).</p></dd> <dt><code>chyaml</code></dt> -<dd><p>The filename to be looked for -Add a vapour pressure</p></dd> +<dd><p>The filename to be looked for</p></dd> </dl><p></p></div> @@ -310,8 +297,7 @@ Add a vapour pressure</p></dd> </div><p></p><hr><a id="method-chent-add_p0"></a><div class="section"> <h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3> - -<div class="section"> +<p>Add a vapour pressure</p><div class="section"> <h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_p0</span><span class="op">(</span><span class="va">p0</span>, T <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -335,8 +321,7 @@ Add a vapour pressure</p></dd> <dt><code>remark</code></dt> -<dd><p>A remark -Add a water solubility</p></dd> +<dd><p>A remark</p></dd> </dl><p></p></div> @@ -344,8 +329,7 @@ Add a water solubility</p></dd> </div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section"> <h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3> - -<div class="section"> +<p>Add a water solubility</p><div class="section"> <h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -361,7 +345,7 @@ Add a water solubility</p></dd> <dt><code>pH</code></dt> -<dd><p>The pH value</p></dd> +<dd><p>pH value</p></dd> <dt><code>source</code></dt> @@ -373,8 +357,7 @@ Add a water solubility</p></dd> <dt><code>remark</code></dt> -<dd><p>A remark -Add a plant uptake factor</p></dd> +<dd><p>A remark</p></dd> </dl><p></p></div> @@ -382,8 +365,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section"> <h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3> - -<div class="section"> +<p>Add a plant uptake factor</p><div class="section"> <h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span> <span> PUF <span class="op">=</span> <span class="fl">0</span>,</span> @@ -416,8 +398,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_TP"></a><div class="section"> <h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3> - -<div class="section"> +<p>Add a transformation product to the internal list</p><div class="section"> <h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -429,7 +410,7 @@ Add a plant uptake factor</p></dd> <dt><code>smiles</code></dt> -<dd><p>A SMILES code for defining a chent object</p></dd> +<dd><p>Optional user provided SMILES code</p></dd> <dt><code>pubchem</code></dt> @@ -441,8 +422,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section"> <h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3> - -<div class="section"> +<p>Add a line in the internal dataframe holding observed transformations</p><div class="section"> <h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span> <span> <span class="va">study_type</span>,</span> @@ -480,7 +460,7 @@ result from stochiometric transformation</p></dd> <dt><code>pages</code></dt> -<dd><p>The page from which the information was taken</p></dd> +<dd><p>The pages from which the information was taken</p></dd> </dl><p></p></div> @@ -488,8 +468,7 @@ result from stochiometric transformation</p></dd> </div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section"> <h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3> - -<div class="section"> +<p>Add a line in the internal dataframe holding modelling DT50 values</p><div class="section"> <h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span> <span> <span class="va">soils</span>,</span> @@ -595,8 +574,7 @@ the technical active ingredient</p></dd> </div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section"> <h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3> - -<div class="section"> +<p>Add one or more formation fractions for degradation in soil</p><div class="section"> <h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -615,13 +593,24 @@ the technical active ingredient</p></dd> <dd><p>The formation fraction(s)</p></dd> +<dt><code>remark</code></dt> +<dd><p>A remark</p></dd> + + +<dt><code>source</code></dt> +<dd><p>An acronym specifying the source of the information</p></dd> + + +<dt><code>page</code></dt> +<dd><p>The page from which the information was taken</p></dd> + + </dl><p></p></div> </div> </div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section"> <h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3> - -<div class="section"> +<p>Add soil sorption data</p><div class="section"> <h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span> <span> <span class="va">soils</span>,</span> @@ -643,7 +632,11 @@ the technical active ingredient</p></dd> <div class="section"> <h4 id="arguments-12">Arguments<a class="anchor" aria-label="anchor" href="#arguments-12"></a></h4> -<p></p><div class="arguments"><dl><dt><code>Kf</code></dt> +<p></p><div class="arguments"><dl><dt><code>soils</code></dt> +<dd><p>Names of the soils</p></dd> + + +<dt><code>Kf</code></dt> <dd><p>The sorption constant in L/kg, either linear (then <code>N</code> is 1) or according to Freundlich</p></dd> @@ -656,13 +649,44 @@ or according to Freundlich</p></dd> <dd><p>The Freundlich exponent</p></dd> +<dt><code>type</code></dt> +<dd><p>The soil type</p></dd> + + +<dt><code>pH_orig</code></dt> +<dd><p>The pH stated in the study</p></dd> + + +<dt><code>pH_medium</code></dt> +<dd><p>The medium in which this pH was measured</p></dd> + + +<dt><code>pH_H2O</code></dt> +<dd><p>The pH extrapolated to pure water</p></dd> + + +<dt><code>perc_OC</code></dt> +<dd><p>The percentage of organic carbon in the soil</p></dd> + + <dt><code>perc_clay</code></dt> <dd><p>The percentage of clay in the soil</p></dd> <dt><code>CEC</code></dt> -<dd><p>The cation exchange capacity -Write a PDF image of the structure</p></dd> +<dd><p>The cation exchange capacity</p></dd> + + +<dt><code>remark</code></dt> +<dd><p>A remark</p></dd> + + +<dt><code>source</code></dt> +<dd><p>An acronym specifying the source of the information</p></dd> + + +<dt><code>page</code></dt> +<dd><p>The page from which the information was taken</p></dd> </dl><p></p></div> @@ -670,8 +694,7 @@ Write a PDF image of the structure</p></dd> </div><p></p><hr><a id="method-chent-pdf"></a><div class="section"> <h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3> - -<div class="section"> +<p>Write a PDF image of the structure</p><div class="section"> <h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span> <span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span> @@ -691,8 +714,7 @@ Write a PDF image of the structure</p></dd> <dt><code>template</code></dt> -<dd><p>A template expressed as SMILES to use in RDKit -Write a PNG image of the structure</p></dd> +<dd><p>An optional SMILES code to be used as template for RDKit</p></dd> </dl><p></p></div> @@ -700,8 +722,7 @@ Write a PNG image of the structure</p></dd> </div><p></p><hr><a id="method-chent-png"></a><div class="section"> <h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3> - -<div class="section"> +<p>Write a PNG image of the structure</p><div class="section"> <h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span> <span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span> @@ -712,9 +733,16 @@ Write a PNG image of the structure</p></dd> <div class="section"> <h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4> -<p></p><div class="arguments"><dl><dt><code>antialias</code></dt> -<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a> -Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd> +<p></p><div class="arguments"><dl><dt><code>file</code></dt> +<dd><p>The file to write to</p></dd> + + +<dt><code>dir</code></dt> +<dd><p>The directory to write the file to</p></dd> + + +<dt><code>antialias</code></dt> +<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a></p></dd> </dl><p></p></div> @@ -722,8 +750,7 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma </div><p></p><hr><a id="method-chent-emf"></a><div class="section"> <h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3> - -<div class="section"> +<p>Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p><div class="section"> <h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">emf</span><span class="op">(</span>file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -734,6 +761,10 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma <dd><p>The file to write to</p></dd> +<dt><code>dir</code></dt> +<dd><p>The directory to write the file to</p></dd> + + </dl><p></p></div> </div> @@ -759,27 +790,10 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma <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="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using user SMILES</span> -<span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCO</span> -<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./1-octanol.yaml</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">oct</span><span class="op">)</span></span></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-octanol </span> -<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey NA </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> user </span> -<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCO" </span> -<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 130.2 </span> -<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</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">oct</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="va">caffeine</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></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_Canonical SMILES</span> <span class="r-msg co"><span class="r-pr">#></span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span> -<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./caffeine.yaml</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">caffeine</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <chent></span> <span class="r-out co"><span class="r-pr">#></span> Identifier $identifier caffeine </span> @@ -798,6 +812,17 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-plt img"><img src="chent-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using user SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCO</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">oct</span><span class="op">)</span></span></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-octanol </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey NA </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> user </span> +<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCO" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 130.2 </span> </code></pre></div> </div> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> |