diff options
| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2026-07-03 11:51:32 +0200 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2026-07-03 11:51:32 +0200 |
| commit | 88027b7a70510b48bd7525ffcd536f0808d263e7 (patch) | |
| tree | 94f83bd420d494334011ff8f67a27483130fe857 /docs/reference/pai.html | |
| parent | 32caaedcc6b6b8addc9f23fce9dca4188f692fed (diff) | |
Improve description with README text
Also, read the description into the Readme to have them
in sync and update docs with roxygen 8.
Diffstat (limited to 'docs/reference/pai.html')
| -rw-r--r-- | docs/reference/pai.html | 87 |
1 files changed, 38 insertions, 49 deletions
diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 29f9368..269a1d2 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="">0.4.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</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"> @@ -56,7 +56,7 @@ the complete result of querying the BCPC compendium using </div> <div class="section level2"> <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#super-class"></a></h2> - <p><code><a href="chent.html">chents::chent</a></code> -> <code>pai</code></p> + <p><code><a href="chent.html">chent</a></code> -> <code>pai</code></p> </div> <div class="section level2"> <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> @@ -64,7 +64,7 @@ the complete result of querying the BCPC compendium using <dd><p>ISO common name of the active ingredient according to ISO 1750</p></dd> -<dt><code>bcpc</code></dt> + <dt><code>bcpc</code></dt> <dd><p>Information retrieved from the BCPC compendium available online at <pesticidecompendium.bcpc.org></p></dd> @@ -76,26 +76,25 @@ at <pesticidecompendium.bcpc.org></p></dd> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> - -<ul><li><p><a href="#method-pai-new"><code>pai$new()</code></a></p></li> +<p></p><ul><li><p><a href="#method-pai-initialize"><code>pai$new()</code></a></p></li> <li><p><a href="#method-pai-clone"><code>pai$clone()</code></a></p></li> -</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chents::chent$add_PUF()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chents::chent$add_TP()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chents::chent$add_cwsat()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chents::chent$add_p0()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chents::chent$add_soil_degradation()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chents::chent$add_soil_ff()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chents::chent$add_soil_sorption()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chents::chent$add_transformation()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chents::chent$emf()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chents::chent$get_chyaml()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chents::chent$get_pubchem()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chents::chent$get_rdkit()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chents::chent$pdf()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chents::chent$png()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li> -</ul></details></p><hr><a id="method-pai-new"></a><div class="section"> -<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chent$add_PUF()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chent$add_TP()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chent$add_cwsat()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chent$add_p0()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chent$add_soil_degradation()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chent$add_soil_ff()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chent$add_soil_sorption()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chent$add_transformation()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chent$emf()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chent$get_chyaml()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chent$get_pubchem()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chent$get_rdkit()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chent$pdf()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chent$png()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chent$try_pubchem()</code></a></span></li> +</ul></details></p><hr><a id="method-pai-initialize"></a><div class="section"> +<h3 id="pai-new-"><code>pai$new()</code><a class="anchor" aria-label="anchor" href="#pai-new-"></a></h3> <p>Create a new pai object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> @@ -110,66 +109,55 @@ at <pesticidecompendium.bcpc.org></p></dd> <span> template <span class="op">=</span> <span class="cn">NULL</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> - -<div class="section"> +</div><p></p><div class="section"> <h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> <p></p><div class="arguments"><dl><dt><code>iso</code></dt> <dd><p>The ISO common name to be used in the query of the BCPC compendium</p></dd> - -<dt><code>identifier</code></dt> + <dt><code>identifier</code></dt> <dd><p>Alternative identifier used for querying pubchem</p></dd> - -<dt><code>smiles</code></dt> + <dt><code>smiles</code></dt> <dd><p>Optional user provided SMILES code</p></dd> - -<dt><code>inchikey</code></dt> + <dt><code>inchikey</code></dt> <dd><p>Optional user provided InChI Key</p></dd> - -<dt><code>bcpc</code></dt> + <dt><code>bcpc</code></dt> <dd><p>Should the BCPC compendium be queried?</p></dd> - -<dt><code>pubchem</code></dt> + <dt><code>pubchem</code></dt> <dd><p>Should an attempt be made to retrieve chemical information from PubChem via the webchem package?</p></dd> - -<dt><code>pubchem_from</code></dt> + <dt><code>pubchem_from</code></dt> <dd><p>Possibility to select the argument that is used to query pubchem</p></dd> - -<dt><code>rdkit</code></dt> + <dt><code>rdkit</code></dt> <dd><p>Should an attempt be made to retrieve chemical information from a local rdkit installation via python and the reticulate package?</p></dd> - -<dt><code>template</code></dt> + <dt><code>template</code></dt> <dd><p>An optional SMILES code to be used as template for RDKit</p></dd> - -<dt><code>chyaml</code></dt> + <dt><code>chyaml</code></dt> <dd><p>Should we look for a identifier.yaml file in the working</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-pai-clone"></a><div class="section"> -<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +</div> + +<p></p><hr><a id="method-pai-clone"></a><div class="section"> +<h3 id="pai-clone-"><code>pai$clone()</code><a class="anchor" aria-label="anchor" href="#pai-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</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">pai</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> -</div> - -<div class="section"> +</div><p></p><div class="section"> <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> <p></p><div class="arguments"><dl><dt><code>deep</code></dt> <dd><p>Whether to make a deep clone.</p></dd> @@ -180,6 +168,7 @@ and the reticulate package?</p></dd> </div> + </div> <div class="section level2"> @@ -224,7 +213,7 @@ and the reticulate package?</p></dd> <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> [1] "1-DECANOL" "Decyl alcohol" "Decan-1-ol" "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> <span class="r-in"><span><span class="co"># }</span></span></span> |