diff options
Diffstat (limited to 'docs')
| -rw-r--r-- | docs/404.html | 2 | ||||
| -rw-r--r-- | docs/authors.html | 6 | ||||
| -rw-r--r-- | docs/index.html | 2 | ||||
| -rw-r--r-- | docs/news/index.html | 12 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 4 | ||||
| -rw-r--r-- | docs/reference/Rplot001.png | bin | 20376 -> 20412 bytes | |||
| -rw-r--r-- | docs/reference/chent-1.png | bin | 45780 -> 46529 bytes | |||
| -rw-r--r-- | docs/reference/chent.html | 120 | ||||
| -rw-r--r-- | docs/reference/draw_svg.chent.html | 2 | ||||
| -rw-r--r-- | docs/reference/index.html | 24 | ||||
| -rw-r--r-- | docs/reference/pai-1.png | bin | 34082 -> 34451 bytes | |||
| -rw-r--r-- | docs/reference/pai.html | 73 | ||||
| -rw-r--r-- | docs/reference/plot.chent-1.png | bin | 45467 -> 46084 bytes | |||
| -rw-r--r-- | docs/reference/plot.chent.html | 3 | ||||
| -rw-r--r-- | docs/reference/ppp.html | 67 | ||||
| -rw-r--r-- | docs/reference/print.chent.html | 2 | ||||
| -rw-r--r-- | docs/reference/print.pai.html | 2 | ||||
| -rw-r--r-- | docs/reference/print.ppp.html | 78 | ||||
| -rw-r--r-- | docs/search.json | 2 | ||||
| -rw-r--r-- | docs/sitemap.xml | 1 |
20 files changed, 284 insertions, 116 deletions
diff --git a/docs/404.html b/docs/404.html index 7801234..ca1db25 100644 --- a/docs/404.html +++ b/docs/404.html @@ -20,7 +20,7 @@ <a class="navbar-brand me-2" href="https://pkgdown.jrwb.de/chents/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"> diff --git a/docs/authors.html b/docs/authors.html index 5d76736..ab6418d 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -7,7 +7,7 @@ <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"> @@ -46,13 +46,13 @@ <p>Ranke J (2024). <em>chents: Chemical Entities as R Objects</em>. -R package version 0.3.6, https://github.com/jranke/chents, <a href="https://pkgdown.jrwb.de/chents">https://pkgdown.jrwb.de/chents</a>. +R package version 0.3.7, https://github.com/jranke/chents, <a href="https://pkgdown.jrwb.de/chents">https://pkgdown.jrwb.de/chents</a>. </p> <pre>@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2024}, - note = {R package version 0.3.6, https://github.com/jranke/chents}, + note = {R package version 0.3.7, https://github.com/jranke/chents}, url = {https://pkgdown.jrwb.de/chents}, }</pre> </div> diff --git a/docs/index.html b/docs/index.html index 28915fb..179c6d9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -22,7 +22,7 @@ <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"> diff --git a/docs/news/index.html b/docs/news/index.html index 68cf526..674e324 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -7,7 +7,7 @@ <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"> @@ -33,10 +33,16 @@ </div> <div class="section level2"> +<h2 class="pkg-version" data-toc-text="0.3.7" id="version-037">version 0.3.7<a class="anchor" aria-label="anchor" href="#version-037"></a></h2> +<ul><li>R/chent.R: Do not attempt to load a chyaml file per default, as the format of such a file and the resulting chyaml list object is not documented and would need to be inferred from its use in the pfm package.</li> +</ul></div> + <div class="section level2"> <h2 class="pkg-version" data-toc-text="0.3.6" id="version-036">version 0.3.6<a class="anchor" aria-label="anchor" href="#version-036"></a></h2> <ul><li>R/chent.R: Set the fields <code>smiles</code>, <code>inchikey</code> and <code>mw</code> to NA if these fields are still NULL at the end of the initialization, with <code>source</code> attribute set to “user”, assuming that the initialisation was carefully done and <code>pubchem</code> and <code>rdkit</code> were skipped because the structure is not well-defined.</li> -</ul></div> - </main></div> +</ul><p>Please refer to the ChangeLog for commit messages up to November 2021, where I changed the GNUmakefile not to include commit messages in that file any more.</p> +</div> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> <footer><div class="pkgdown-footer-left"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index fc09a76..48fe8fc 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: 3.1.11 +pandoc: 2.17.1.1 pkgdown: 2.1.0 pkgdown_sha: ~ articles: {} -last_built: 2024-08-05T15:03Z +last_built: 2024-11-28T12:01Z urls: reference: https://pkgdown.jrwb.de/chents/reference article: https://pkgdown.jrwb.de/chents/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex ec5af46..0e4970e 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png Binary files differindex 9049a55..e763f8e 100644 --- a/docs/reference/chent-1.png +++ b/docs/reference/chent-1.png diff --git a/docs/reference/chent.html b/docs/reference/chent.html index a70e318..0a74440 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"> @@ -166,7 +166,8 @@ Add soil sorption data</p></dd> <li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li> </ul></div><p></p><hr><a id="method-chent-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> -<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p> +<p>Try to get chemical information from PubChem</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> <span> <span class="va">identifier</span>,</span> @@ -176,7 +177,7 @@ 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 +217,7 @@ 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> @@ -256,8 +256,7 @@ 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 +264,8 @@ 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 +Obtain information from a YAML file</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 +273,7 @@ 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> @@ -319,7 +317,8 @@ Add a vapour pressure</p></dd> <div class="section"> <h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4> <p></p><div class="arguments"><dl><dt><code>p0</code></dt> -<dd><p>The vapour pressure in Pa</p></dd> +<dd><p>The vapour pressure in Pa +Add a water solubility</p></dd> <dt><code>T</code></dt> @@ -335,8 +334,7 @@ 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> @@ -353,7 +351,8 @@ Add a water solubility</p></dd> <div class="section"> <h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4> <p></p><div class="arguments"><dl><dt><code>cwsat</code></dt> -<dd><p>The water solubility in mg/L</p></dd> +<dd><p>The water solubility in mg/L +Add a plant uptake factor</p></dd> <dt><code>T</code></dt> @@ -361,7 +360,7 @@ 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 +372,7 @@ 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> @@ -429,7 +427,7 @@ 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> @@ -480,7 +478,7 @@ 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> @@ -615,6 +613,18 @@ 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> @@ -643,7 +653,11 @@ 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 +670,44 @@ 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 +715,8 @@ 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 +Write a PNG 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">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span> @@ -691,8 +736,7 @@ Write a PDF image of the structure</p></dd> <dt><code>template</code></dt> -<dd><p>A template expressed as SMILES to use in RDKit -Write a PNG image of the structure</p></dd> +<dd><p>An optional SMILES code to be used as template for RDKit</p></dd> </dl><p></p></div> @@ -712,9 +756,16 @@ Write a PNG image of the structure</p></dd> <div class="section"> <h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4> -<p></p><div class="arguments"><dl><dt><code>antialias</code></dt> -<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a> -Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd> +<p></p><div class="arguments"><dl><dt><code>file</code></dt> +<dd><p>The file to write to</p></dd> + + +<dt><code>dir</code></dt> +<dd><p>The directory to write the file to</p></dd> + + +<dt><code>antialias</code></dt> +<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a></p></dd> </dl><p></p></div> @@ -722,8 +773,7 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma </div><p></p><hr><a id="method-chent-emf"></a><div class="section"> <h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3> - -<div class="section"> +<p>Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p><div class="section"> <h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -734,6 +784,10 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma <dd><p>The file to write to</p></dd> +<dt><code>dir</code></dt> +<dd><p>The directory to write the file to</p></dd> + + </dl><p></p></div> </div> @@ -762,7 +816,6 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</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> @@ -779,7 +832,6 @@ Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/ma <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> diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 6a6741f..2545578 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -7,7 +7,7 @@ <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"> diff --git a/docs/reference/index.html b/docs/reference/index.html index 12b0201..eccf7a0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -7,7 +7,7 @@ <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"> @@ -50,6 +50,18 @@ <dd>An R6 class for chemical entities with associated data</dd> </dl><dl><dt> + <code><a href="pai.html">pai</a></code> + + </dt> + <dd>An R6 class for pesticidal active ingredients and associated data</dd> + </dl><dl><dt> + + <code><a href="ppp.html">ppp</a></code> + + </dt> + <dd>R6 class for a plant protection product with at least one active ingredient</dd> + </dl><dl><dt> + <code><a href="draw_svg.chent.html">draw_svg.chent()</a></code> </dt> @@ -68,22 +80,16 @@ <dd>Printing method for chent objects</dd> </dl><dl><dt> - <code><a href="pai.html">pai</a></code> - - </dt> - <dd>An R6 class for pesticidal active ingredients and associated data</dd> - </dl><dl><dt> - <code><a href="print.pai.html">print(<i><pai></i>)</a></code> </dt> <dd>Printing method for pai objects (pesticidal active ingredients)</dd> </dl><dl><dt> - <code><a href="ppp.html">ppp</a></code> + <code><a href="print.ppp.html">print(<i><ppp></i>)</a></code> </dt> - <dd>R6 class for a plant protection product with at least one active ingredient</dd> + <dd>Printing method for ppp objects (plant protection products)</dd> </dl></div> </main></div> diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png Binary files differindex c567bc2..951bb25 100644 --- a/docs/reference/pai-1.png +++ b/docs/reference/pai-1.png diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 96c6782..30bbbac 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -1,9 +1,13 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta name="description" content="The class is initialised with an identifier which is generally -an ISO common name. Additional chemical information is retrieved from the -internet if available."><meta property="og:description" content="The class is initialised with an identifier which is generally -an ISO common name. Additional chemical information is retrieved from the -internet if available."></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta name="description" content="This class is derived from chent. It makes it easy +to create a chent from the ISO common name of a pesticide active +ingredient, and additionally stores the ISO name as well as +the complete result of querying the BCPC compendium using +bcpc_query."><meta property="og:description" content="This class is derived from chent. It makes it easy +to create a chent from the ISO common name of a pesticide active +ingredient, and additionally stores the ISO name as well as +the complete result of querying the BCPC compendium using +bcpc_query."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -11,7 +15,7 @@ internet if available."></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="">0.3.6</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"> @@ -38,9 +42,11 @@ internet if available."></head><body> </div> <div class="ref-description section level2"> - <p>The class is initialised with an identifier which is generally -an ISO common name. Additional chemical information is retrieved from the -internet if available.</p> + <p>This class is derived from <a href="chent.html">chent</a>. It makes it easy +to create a <a href="chent.html">chent</a> from the ISO common name of a pesticide active +ingredient, and additionally stores the ISO name as well as +the complete result of querying the BCPC compendium using +<a href="https://docs.ropensci.org/webchem/reference/bcpc_query.html" class="external-link">bcpc_query</a>.</p> </div> @@ -60,8 +66,7 @@ internet if available.</p> <dt><code>bcpc</code></dt> <dd><p>Information retrieved from the BCPC compendium available online -at <pesticidecompendium.bcpc.org> -Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd> +at <pesticidecompendium.bcpc.org></p></dd> </dl><p></p></div> @@ -91,11 +96,8 @@ Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.h <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> -<p>This class is derived from <a href="chent.html">chent</a>. It makes it easy -to create a <a href="chent.html">chent</a> from the ISO common name of a pesticide active -ingredient, and additionally stores the ISO name as well as -the complete result of querying the BCPC compendium using -<a href="https://docs.ropensci.org/webchem/reference/bcpc_query.html" class="external-link">bcpc_query</a>.</p><div class="section"> + +<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> <span> <span class="va">iso</span>,</span> @@ -107,7 +109,7 @@ the complete result of querying the BCPC compendium using <span> pubchem_from <span class="op">=</span> <span class="st">"auto"</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> @@ -122,6 +124,42 @@ BCPC compendium</p></dd> <dd><p>Alternative identifier used for querying pubchem</p></dd> +<dt><code>smiles</code></dt> +<dd><p>Optional user provided SMILES code</p></dd> + + +<dt><code>inchikey</code></dt> +<dd><p>Optional user provided InChI Key</p></dd> + + +<dt><code>bcpc</code></dt> +<dd><p>Should the BCPC compendium be queried?</p></dd> + + +<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> +<dd><p>Possibility to select the argument +that is used to query pubchem</p></dd> + + +<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> +<dd><p>An optional SMILES code to be used as template for RDKit</p></dd> + + +<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> @@ -163,7 +201,6 @@ BCPC compendium</p></dd> <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> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span> -<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./atrazine.yaml</span> <span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></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> diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png Binary files differindex c895eb3..36b02fa 100644 --- a/docs/reference/plot.chent-1.png +++ b/docs/reference/plot.chent-1.png diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index 8bbc81c..9ed70e1 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -7,7 +7,7 @@ <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"> @@ -62,7 +62,6 @@ <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 $identifier caffeine </span> diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html index 725f550..ef3933d 100644 --- a/docs/reference/ppp.html +++ b/docs/reference/ppp.html @@ -9,7 +9,7 @@ product"></head><body> <a class="navbar-brand me-2" href="../index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.6</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.7</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -72,35 +72,6 @@ product</p> Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd> -<dt><code>...</code></dt> -<dd><p>Identifiers of the active ingredients</p></dd> - - -<dt><code>concentrations</code></dt> -<dd><p>Concentrations of the active ingredients</p></dd> - - -<dt><code>concentration_units</code></dt> -<dd><p>Defaults to g/L</p></dd> - - -<dt><code>density</code></dt> -<dd><p>The density</p></dd> - - -<dt><code>density_units</code></dt> -<dd><p>Defaults to g/L -Printing method</p></dd> - - -</dl><p></p></div> - </div> - <div class="section level2"> - <h2 id="active-bindings">Active bindings<a class="anchor" aria-label="anchor" href="#active-bindings"></a></h2> - <p></p><div class="r6-active-bindings"><dl><dt><code>...</code></dt> -<dd><p>Identifiers of the active ingredients</p></dd> - - </dl><p></p></div> </div> <div class="section level2"> @@ -110,7 +81,6 @@ Printing method</p></dd> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> <ul><li><p><a href="#method-ppp-new"><code>ppp$new()</code></a></p></li> -<li><p><a href="#method-ppp-print"><code>ppp$print()</code></a></p></li> <li><p><a href="#method-ppp-clone"><code>ppp$clone()</code></a></p></li> </ul></div><p></p><hr><a id="method-ppp-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> @@ -127,25 +97,44 @@ Printing method</p></dd> <span><span class="op">)</span></span></code></pre></div><p></p></div> </div> +<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>name</code></dt> +<dd><p>The name of the product</p></dd> -</div><p></p><hr><a id="method-ppp-print"></a><div class="section"> -<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3> -<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">ppp</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> -</div> +<dt><code>...</code></dt> +<dd><p>Identifiers of the active ingredients</p></dd> + + +<dt><code>concentrations</code></dt> +<dd><p>Concentrations of the active ingredients</p></dd> + + +<dt><code>concentration_units</code></dt> +<dd><p>Defaults to g/L</p></dd> +<dt><code>density</code></dt> +<dd><p>The density</p></dd> + + +<dt><code>density_units</code></dt> +<dd><p>Defaults to g/L</p></dd> + + +</dl><p></p></div> +</div> + </div><p></p><hr><a id="method-ppp-clone"></a><div class="section"> <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> -<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">ppp</span><span class="op">$</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"> -<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<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> diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index 8747604..9ae6ff4 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -7,7 +7,7 @@ <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"> diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index 78a2a0b..283bf76 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -7,7 +7,7 @@ <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"> diff --git a/docs/reference/print.ppp.html b/docs/reference/print.ppp.html new file mode 100644 index 0000000..a15f8cb --- /dev/null +++ b/docs/reference/print.ppp.html @@ -0,0 +1,78 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Printing method for ppp objects (plant protection products) — print.ppp • chents</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for ppp objects (plant protection products) — print.ppp"><meta name="description" content="Printing method for ppp objects (plant protection products)"><meta property="og:description" content="Printing method for ppp objects (plant protection products)"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + + <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="">0.3.7</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"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/chents/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Printing method for ppp objects (plant protection products)</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small> + <div class="d-none name"><code>print.ppp.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>Printing method for ppp objects (plant protection products)</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'ppp'</span></span> +<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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> +<dd><p>The chent object to be printed</p></dd> + + +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> +<dd><p>Further arguments for compatibility with the S3 method</p></dd> + +</dl></div> + + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> +</div> + + </footer></div> + + + + + + </body></html> + diff --git a/docs/search.json b/docs/search.json index 687833d..fd8a6c3 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2024). chents: Chemical Entities R Objects. R package version 0.3.6, https://github.com/jranke/chents, https://pkgdown.jrwb.de/chents.","code":"@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2024}, note = {R package version 0.3.6, https://github.com/jranke/chents}, url = {https://pkgdown.jrwb.de/chents}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"R package chents provides utilities working chemical entities R.","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"Chemical Entities as R Objects","text":"chemical information retrieved PubChem website using webchem package Python RDKit (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions additional chemical information computed 2D graph can plotted Additional information can read local .yaml file","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Chemical Entities as R Objects","text":"examples available reference jrwb.de.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph picture object obtained using grImport Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects Add transformation product internal list transformations Data frame observed transformations Add line internal dataframe holding observed transformations soil_degradation Dataframe modelling DT50 values Add line internal dataframe holding modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data Add soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c(\"name\", \"smiles\", \"inchikey\"), rdkit = TRUE, template = NULL, chyaml = TRUE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory? Try get chemical information PubChem","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid Get chemical information PubChem known PubChem CID","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID Get chemical information RDKit available","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template Optional template specified SMILES code Obtain information YAML file","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml( repo = c(\"wd\", \"local\", \"web\"), chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked Add vapour pressure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa T Temperature source acronym specifying source information page page information taken remark remark Add water solubility","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L T Temperature pH pH value source acronym specifying source information page page information taken remark remark Add plant uptake factor","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF( PUF = 0, source = \"focus_generic_gw_2014\", page = 41, remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles SMILES code defining chent object pubchem chemical information obtained PubChem?","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = \"\", source = NA, pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_degradation( soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, temperature = NA, moisture = NA, category = \"lab\", formulation = NA, model = NA, chi2 = NA, remark = \"\", source, page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s)","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_sorption( soils, Kf, Kfoc, N, type = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, perc_clay = NA, CEC = NA, remark = \"\", source, page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent perc_clay percentage clay soil CEC cation exchange capacity Write PDF image structure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf( file = paste0(self$identifier, \".pdf\"), dir = \"structures/pdf\", template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template template expressed SMILES use RDKit Write PNG image structure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png( file = paste0(self$identifier, \".png\"), dir = \"structures/png\", antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"antialias Passed png Write EMF image structure using emf","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Trying to get chemical information from RDKit using user SMILES #> CCCCCCCCO #> Did not find chyaml file ./1-octanol.yaml print(oct) #> <chent> #> Identifier $identifier 1-octanol #> InChI Key $inchikey NA #> SMILES string $smiles: #> user #> \"CCCCCCCCO\" #> Molecular weight $mw: 130.2 if (!is.null(oct$Picture)) { plot(oct) } caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C #> Did not find chyaml file ./caffeine.yaml print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) }"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent( x, width = 300, height = 150, filename = paste0(names(x$identifier), \".svg\"), subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class initialised identifier generally ISO common name. Additional chemical information retrieved internet available.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org> Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new( iso, identifier = iso, smiles = NULL, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = \"auto\", rdkit = TRUE, template = NULL, chyaml = TRUE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# On Travis, we get a certificate validation error, # likely because the system (xenial) is so old, # therefore don't run this example on Travis if (Sys.getenv(\"TRAVIS\") == \"\") { atr <- pai$new(\"atrazine\") print(atr) if (!is.null(atr$Picture)) { plot(atr) } } #> BCPC: #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C #> Did not find chyaml file ./atrazine.yaml #> <pai> with ISO common name $iso atrazine #> <chent> #> Identifier $identifier atrazine #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CCNC1=NC(=NC(=N1)Cl)NC(C)C\" #> Molecular weight $mw: 215.7 #> PubChem synonyms (up to 10): #> [1] \"atrazine\" \"1912-24-9\" \"Gesaprim\" \"Atranex\" \"Oleogesaprim\" #> [6] \"Atazinax\" \"Atrasine\" \"Chromozin\" \"Gesoprim\" \"Hungazin\""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for class 'chent' plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C #> Did not find chyaml file ./caffeine.yaml print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) }"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L Creates new instance R6 class. ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L Printing method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"... Identifiers active ingredients","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$print() ppp$clone()","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new( name, ..., concentrations, concentration_units = \"g/L\", density = 1000, density_units = \"g/L\" )"},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$print()"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for class 'chent' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for class 'pai' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-036","dir":"Changelog","previous_headings":"","what":"version 0.3.6","title":"version 0.3.6","text":"R/chent.R: Set fields smiles, inchikey mw NA fields still NULL end initialization, source attribute set “user”, assuming initialisation carefully done pubchem rdkit skipped structure well-defined.","code":""}] +[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2024). chents: Chemical Entities R Objects. R package version 0.3.7, https://github.com/jranke/chents, https://pkgdown.jrwb.de/chents.","code":"@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2024}, note = {R package version 0.3.7, https://github.com/jranke/chents}, url = {https://pkgdown.jrwb.de/chents}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"R package chents provides utilities working chemical entities R.","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"Chemical Entities as R Objects","text":"chemical information retrieved PubChem website using webchem package Python RDKit (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions additional chemical information computed 2D graph can plotted Additional information can read local .yaml file","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Chemical Entities as R Objects","text":"examples available reference jrwb.de.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph picture object obtained using grImport Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects Add transformation product internal list transformations Data frame observed transformations Add line internal dataframe holding observed transformations soil_degradation Dataframe modelling DT50 values Add line internal dataframe holding modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data Add soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class. Try get chemical information PubChem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c(\"name\", \"smiles\", \"inchikey\"), rdkit = TRUE, template = NULL, chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory?","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid Get chemical information PubChem known PubChem CID","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-rdkit-","dir":"Reference","previous_headings":"","what":"Method get_rdkit()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information RDKit available Obtain information YAML file","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template optional SMILES code used template RDKit","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml( repo = c(\"wd\", \"local\", \"web\"), chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked Add vapour pressure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa Add water solubility T Temperature source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L Add plant uptake factor T Temperature pH pH value source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF( PUF = 0, source = \"focus_generic_gw_2014\", page = 41, remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles Optional user provided SMILES code pubchem chemical information obtained PubChem?","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = \"\", source = NA, pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages pages information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_degradation( soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, temperature = NA, moisture = NA, category = \"lab\", formulation = NA, model = NA, chi2 = NA, remark = \"\", source, page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s) remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_sorption( soils, Kf, Kfoc, N, type = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, perc_clay = NA, CEC = NA, remark = \"\", source, page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent type soil type pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil perc_clay percentage clay soil CEC cation exchange capacity remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-pdf-","dir":"Reference","previous_headings":"","what":"Method pdf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PDF image structure Write PNG image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf( file = paste0(self$identifier, \".pdf\"), dir = \"structures/pdf\", template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template optional SMILES code used template RDKit","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png( file = paste0(self$identifier, \".png\"), dir = \"structures/png\", antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file antialias Passed png","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-emf-","dir":"Reference","previous_headings":"","what":"Method emf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write EMF image structure using emf","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Trying to get chemical information from RDKit using user SMILES #> CCCCCCCCO print(oct) #> <chent> #> Identifier $identifier 1-octanol #> InChI Key $inchikey NA #> SMILES string $smiles: #> user #> \"CCCCCCCCO\" #> Molecular weight $mw: 130.2 if (!is.null(oct$Picture)) { plot(oct) } caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) }"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent( x, width = 300, height = 150, filename = paste0(names(x$identifier), \".svg\"), subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org>","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new( iso, identifier = iso, smiles = NULL, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = \"auto\", rdkit = TRUE, template = NULL, chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem smiles Optional user provided SMILES code inchikey Optional user provided InChI Key bcpc BCPC compendium queried? pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# On Travis, we get a certificate validation error, # likely because the system (xenial) is so old, # therefore don't run this example on Travis if (Sys.getenv(\"TRAVIS\") == \"\") { atr <- pai$new(\"atrazine\") print(atr) if (!is.null(atr$Picture)) { plot(atr) } } #> BCPC: #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C #> <pai> with ISO common name $iso atrazine #> <chent> #> Identifier $identifier atrazine #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CCNC1=NC(=NC(=N1)Cl)NC(C)C\" #> Molecular weight $mw: 215.7 #> PubChem synonyms (up to 10): #> [1] \"atrazine\" \"1912-24-9\" \"Gesaprim\" \"Atranex\" \"Oleogesaprim\" #> [6] \"Atazinax\" \"Atrasine\" \"Chromozin\" \"Gesoprim\" \"Hungazin\""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for class 'chent' plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) }"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L Creates new instance R6 class.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$clone()","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new( name, ..., concentrations, concentration_units = \"g/L\", density = 1000, density_units = \"g/L\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for class 'chent' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for class 'pai' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for ppp objects (plant protection products) — print.ppp","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"Printing method ppp objects (plant protection products)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"","code":"# S3 method for class 'ppp' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-037","dir":"Changelog","previous_headings":"","what":"version 0.3.7","title":"version 0.3.7","text":"R/chent.R: attempt load chyaml file per default, format file resulting chyaml list object documented need inferred use pfm package.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-036","dir":"Changelog","previous_headings":"","what":"version 0.3.6","title":"version 0.3.6","text":"R/chent.R: Set fields smiles, inchikey mw NA fields still NULL end initialization, source attribute set “user”, assuming initialisation carefully done pubchem rdkit skipped structure well-defined. Please refer ChangeLog commit messages November 2021, changed GNUmakefile include commit messages file .","code":""}] diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 22a04e9..b18fb97 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -12,5 +12,6 @@ <url><loc>https://pkgdown.jrwb.de/chents/reference/ppp.html</loc></url> <url><loc>https://pkgdown.jrwb.de/chents/reference/print.chent.html</loc></url> <url><loc>https://pkgdown.jrwb.de/chents/reference/print.pai.html</loc></url> +<url><loc>https://pkgdown.jrwb.de/chents/reference/print.ppp.html</loc></url> </urlset> |
