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| -rw-r--r-- | docs/index.html | 27 | ||||
| -rw-r--r-- | docs/reference/chent.html | 8 | ||||
| -rw-r--r-- | docs/reference/plot.chent.html | 4 | ||||
| -rw-r--r-- | inst/examples/caffeine.R | 4 | ||||
| -rw-r--r-- | inst/examples/octanol.R | 4 | ||||
| -rw-r--r-- | man/chent.Rd | 8 | ||||
| -rw-r--r-- | man/plot.chent.Rd | 4 |
7 files changed, 37 insertions, 22 deletions
diff --git a/docs/index.html b/docs/index.html index 5e6442f..f463fe0 100644 --- a/docs/index.html +++ b/docs/index.html @@ -72,19 +72,8 @@ <div id="chents" class="section level1"> <div class="page-header"><h1 class="hasAnchor"> <a href="#chents" class="anchor"></a>chents</h1></div> -<p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R, made available under the GNU public license. This means:</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode R"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">This program is free software<span class="op">:</span><span class="st"> </span>you can redistribute it and<span class="op">/</span>or modify it under</a> -<a class="sourceLine" id="cb1-2" data-line-number="2">the terms of the GNU General Public License as published by the Free Software</a> -<a class="sourceLine" id="cb1-3" data-line-number="3">Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later</a> -<a class="sourceLine" id="cb1-4" data-line-number="4">version.</a> -<a class="sourceLine" id="cb1-5" data-line-number="5"></a> -<a class="sourceLine" id="cb1-6" data-line-number="6">This program is distributed <span class="cf">in</span> the hope that it will be useful, but WITHOUT</a> -<a class="sourceLine" id="cb1-7" data-line-number="7">ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a> -<a class="sourceLine" id="cb1-8" data-line-number="8">FOR A PARTICULAR PURPOSE. See the GNU General Public License <span class="cf">for</span> more</a> -<a class="sourceLine" id="cb1-9" data-line-number="9">details.</a> -<a class="sourceLine" id="cb1-10" data-line-number="10"></a> -<a class="sourceLine" id="cb1-11" data-line-number="11">You should have received a copy of the GNU General Public License along with</a> -<a class="sourceLine" id="cb1-12" data-line-number="12">this program. If not, see <span class="op"><</span>http<span class="op">:</span><span class="er">//</span>www.gnu.org<span class="op">/</span>licenses<span class="op">/</span><span class="er">></span></a></code></pre></div> + +<p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R.</p> <div id="features" class="section level2"> <h2 class="hasAnchor"> <a href="#features" class="anchor"></a>Features</h2> @@ -93,6 +82,10 @@ <li>If PythonInR is installed and configured, and RDKit is available via PythonInR, some additional chemical information is computed and a 2D graph can be plotted</li> <li>Additional information can be read from a local .yaml file</li> </ul> +</div> +<div id="examples" class="section level2"> +<h2 class="hasAnchor"> +<a href="#examples" class="anchor"></a>Examples</h2> <p>Some examples are available from the <a href="http://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</p> </div> </div> @@ -119,7 +112,13 @@ </ul> </div> - </div> + <div class="dev-status"> +<h2>Dev status</h2> +<ul class="list-unstyled"> +<li><a href="https://travis-ci.com/jranke/chents"><img src="https://travis-ci.com/jranke/chents.svg?branch=master" alt="Build Status"></a></li> +</ul> +</div> +</div> </div> <footer><div class="copyright"> diff --git a/docs/reference/chent.html b/docs/reference/chent.html index aa367f6..1608eb0 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -159,7 +159,9 @@ configured for use with PythonInR</p></dd> #> PubChem synonyms (up to 10): #> [1] "957" "1-octanol" "Octan-1-ol" "octanol" #> [5] "111-87-5" "N-octanol" "Capryl alcohol" "Octyl alcohol" -#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"grConvert"</span>)) { + <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>oct</span>) +}</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> #> <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N @@ -172,7 +174,9 @@ configured for use with PythonInR</p></dd> #> [3] "58-08-2" "Guaranine" #> [5] "1,3,7-Trimethylxanthine" "Thein" #> [7] "Cafeina" "Methyltheobromine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre> +#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"grConvert"</span>)) { + <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>) +}</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index cde7a87..cc4d376 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -141,7 +141,9 @@ #> [3] "58-08-2" "Guaranine" #> [5] "1,3,7-Trimethylxanthine" "Thein" #> [7] "Cafeina" "Methyltheobromine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></div></pre> +#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"grConvert"</span>)) { + <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>) +}</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/inst/examples/caffeine.R b/inst/examples/caffeine.R index 29a7e0b..f5711f3 100644 --- a/inst/examples/caffeine.R +++ b/inst/examples/caffeine.R @@ -1,3 +1,5 @@ caffeine <- chent$new("caffeine") print(caffeine) -plot(caffeine) +if (requireNamespace("grConvert")) { + plot(caffeine) +} diff --git a/inst/examples/octanol.R b/inst/examples/octanol.R index 3e42c38..b13d9ce 100644 --- a/inst/examples/octanol.R +++ b/inst/examples/octanol.R @@ -1,3 +1,5 @@ oct <- chent$new("1-octanol", smiles = "CCCCCCCCO") print(oct) -plot(oct) +if (requireNamespace("grConvert")) { + plot(oct) +} diff --git a/man/chent.Rd b/man/chent.Rd index 8d85de1..a90a3b3 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -55,9 +55,13 @@ configured for use with PythonInR} \examples{ oct <- chent$new("1-octanol", smiles = "CCCCCCCCO") print(oct) -plot(oct) +if (requireNamespace("grConvert")) { + plot(oct) +} caffeine <- chent$new("caffeine") print(caffeine) -plot(caffeine) +if (requireNamespace("grConvert")) { + plot(caffeine) +} } \keyword{data} diff --git a/man/plot.chent.Rd b/man/plot.chent.Rd index 416675d..a406533 100644 --- a/man/plot.chent.Rd +++ b/man/plot.chent.Rd @@ -17,5 +17,7 @@ Plot method for chent objects \examples{ caffeine <- chent$new("caffeine") print(caffeine) -plot(caffeine) +if (requireNamespace("grConvert")) { + plot(caffeine) +} } |