deploy: 4c07316

datasources/goldbook_api.html

@@ -574,7 +574,7 @@ <h2>Step 5: Use the term code to retrieve its definition<a class="headerlink" hr
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-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;term&#39;: {&#39;id&#39;: &#39;01093&#39;, &#39;doi&#39;: &#39;10.1351/goldbook.C01093&#39;, &#39;code&#39;: &#39;C01093&#39;, &#39;status&#39;: &#39;current&#39;, &#39;longtitle&#39;: &#39;IUPAC Gold Book - cis-trans isomers&#39;, &#39;title&#39;: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39;, &#39;termversion&#39;: &#39;2.3.3&#39;, &#39;lastupdated&#39;: &#39;2014-02-24&#39;, &#39;definitions&#39;: [{&#39;id&#39;: &#39;1&#39;, &#39;text&#39;: &#39;Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]&#39;, &#39;chemicals&#39;: [{&#39;type&#39;: &#39;chemimage&#39;, &#39;title&#39;: &#39;molecular structures showing cis/trans isomerism&#39;, &#39;file&#39;: &#39;https://goldbook.iupac.org/img/inline/C01093.png&#39;}], &#39;links&#39;: [{&#39;title&#39;: &#39;Stereoisomeric&#39;, &#39;type&#39;: &#39;internal&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/S05983&#39;}, {&#39;title&#39;: &#39;olefins&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/O04281&#39;}, {&#39;title&#39;: &#39;cycloalkanes&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01497&#39;}, {&#39;title&#39;: &#39;isomer&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/I03289&#39;}, {&#39;title&#39;: &#39;trans&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01092&#39;}], &#39;sources&#39;: [&quot;PAC, 1996, 68, 2193. &#39;Basic terminology of stereochemistry (IUPAC Recommendations 1996)&#39; on page 2204 (https://doi.org/10.1351/pac199668122193)&quot;]}], &#39;referencedin&#39;: [{&#39;title&#39;: &#39;Wikipedia - Cis-trans izomerie (cs)&#39;, &#39;url&#39;: &#39;https://cs.wikipedia.org/wiki/Cis-trans_izomerie&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis-trans izoméria (sk)&#39;, &#39;url&#39;: &#39;https://sk.wikipedia.org/wiki/Cis-trans_izoméria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis–trans isomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Cis–trans_isomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria cis-trans (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria geométrica (pt)&#39;, &#39;url&#39;: &#39;https://pt.wikipedia.org/wiki/Isomeria_geométrica&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomería cis-trans (es)&#39;, &#39;url&#39;: &#39;https://es.wikipedia.org/wiki/Isomería_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Isomer (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Isomer&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Stereoisomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Stereoisomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис-транс изомеризъм (bg)&#39;, &#39;url&#39;: &#39;https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис–транс ізомерія (uk)&#39;, &#39;url&#39;: &#39;https://uk.wikipedia.org/wiki/Цис–транс_ізомерія&#39;}, {&#39;title&#39;: &#39;Wikipedia - ایزومری سیس–ترانس (fa)&#39;, &#39;url&#39;: &#39;https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس&#39;}, {&#39;title&#39;: &#39;Wikipedia - 顺反异构 (zh)&#39;, &#39;url&#39;: &#39;https://zh.wikipedia.org/wiki/顺反异构&#39;}], &#39;links&#39;: {&#39;html&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/html&#39;, &#39;json&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/json&#39;, &#39;xml&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/xml&#39;, &#39;plain&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/plain&#39;, &#39;pdf&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/pdf&#39;}, &#39;citation&#39;: &quot;Citation: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39; in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093&quot;, &#39;license&#39;: &#39;The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.&#39;, &#39;collection&#39;: &#39;If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .&#39;, &#39;disclaimer&#39;: &#39;The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.&#39;, &#39;accessed&#39;: &#39;2024-01-29T18:21:57+00:00&#39;}}
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;term&#39;: {&#39;id&#39;: &#39;01093&#39;, &#39;doi&#39;: &#39;10.1351/goldbook.C01093&#39;, &#39;code&#39;: &#39;C01093&#39;, &#39;status&#39;: &#39;current&#39;, &#39;longtitle&#39;: &#39;IUPAC Gold Book - cis-trans isomers&#39;, &#39;title&#39;: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39;, &#39;termversion&#39;: &#39;2.3.3&#39;, &#39;lastupdated&#39;: &#39;2014-02-24&#39;, &#39;definitions&#39;: [{&#39;id&#39;: &#39;1&#39;, &#39;text&#39;: &#39;Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]&#39;, &#39;chemicals&#39;: [{&#39;type&#39;: &#39;chemimage&#39;, &#39;title&#39;: &#39;molecular structures showing cis/trans isomerism&#39;, &#39;file&#39;: &#39;https://goldbook.iupac.org/img/inline/C01093.png&#39;}], &#39;links&#39;: [{&#39;title&#39;: &#39;Stereoisomeric&#39;, &#39;type&#39;: &#39;internal&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/S05983&#39;}, {&#39;title&#39;: &#39;olefins&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/O04281&#39;}, {&#39;title&#39;: &#39;cycloalkanes&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01497&#39;}, {&#39;title&#39;: &#39;isomer&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/I03289&#39;}, {&#39;title&#39;: &#39;trans&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01092&#39;}], &#39;sources&#39;: [&quot;PAC, 1996, 68, 2193. &#39;Basic terminology of stereochemistry (IUPAC Recommendations 1996)&#39; on page 2204 (https://doi.org/10.1351/pac199668122193)&quot;]}], &#39;referencedin&#39;: [{&#39;title&#39;: &#39;Wikipedia - Cis-trans izomerie (cs)&#39;, &#39;url&#39;: &#39;https://cs.wikipedia.org/wiki/Cis-trans_izomerie&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis-trans izoméria (sk)&#39;, &#39;url&#39;: &#39;https://sk.wikipedia.org/wiki/Cis-trans_izoméria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis–trans isomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Cis–trans_isomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria cis-trans (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria geométrica (pt)&#39;, &#39;url&#39;: &#39;https://pt.wikipedia.org/wiki/Isomeria_geométrica&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomería cis-trans (es)&#39;, &#39;url&#39;: &#39;https://es.wikipedia.org/wiki/Isomería_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Isomer (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Isomer&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Stereoisomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Stereoisomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис-транс изомеризъм (bg)&#39;, &#39;url&#39;: &#39;https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис–транс ізомерія (uk)&#39;, &#39;url&#39;: &#39;https://uk.wikipedia.org/wiki/Цис–транс_ізомерія&#39;}, {&#39;title&#39;: &#39;Wikipedia - ایزومری سیس–ترانس (fa)&#39;, &#39;url&#39;: &#39;https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس&#39;}, {&#39;title&#39;: &#39;Wikipedia - 顺反异构 (zh)&#39;, &#39;url&#39;: &#39;https://zh.wikipedia.org/wiki/顺反异构&#39;}], &#39;links&#39;: {&#39;html&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/html&#39;, &#39;json&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/json&#39;, &#39;xml&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/xml&#39;, &#39;plain&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/plain&#39;, &#39;pdf&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/pdf&#39;}, &#39;citation&#39;: &quot;Citation: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39; in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093&quot;, &#39;license&#39;: &#39;The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.&#39;, &#39;collection&#39;: &#39;If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .&#39;, &#39;disclaimer&#39;: &#39;The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.&#39;, &#39;accessed&#39;: &#39;2024-01-29T19:03:26+00:00&#39;}}
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datasources/pubchem_pugrest1.html

@@ -589,9 +589,7 @@ <h3>3. Getting Computed Molecular Properties<a class="headerlink" href="#getting
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>HBondDonorCount  : 1
-</pre></div>
-</div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>HBondAcceptorCoun: 4
+HBondAcceptorCoun: 4
 </pre></div>
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 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>HeavyAtomCount   : 13

datasources/pubchem_pugrest2.html

@@ -492,15 +492,11 @@ <h2>1. Accessing PubChem data using a chemical name<a class="headerlink" href="#
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 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CID             : 2244
-</pre></div>
-</div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>MolecularFormula: C9H8O4
+MolecularFormula: C9H8O4
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>MolecularWeight : 180.16
-</pre></div>
-</div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>IsomericSMILES  : CC(=O)OC1=CC=CC=C1C(=O)O
+IsomericSMILES  : CC(=O)OC1=CC=CC=C1C(=O)O
 </pre></div>
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@@ -599,20 +595,17 @@ <h2>2. Getting chemical names for a given chemical structure<a class="headerlink
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 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>#-- CID 56841568
-</pre></div>
-</div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Aleve-D Sinus &amp; Cold
+Aleve-D Sinus &amp; Cold
 Aleve-D Sinus and Cold
 Naproxen / pseudoephedrine
 Aleve-D Sinus and headache
 141623-29-2
 DTXSID80931146
 2-(6-Methoxynaphthalen-2-yl)propanoic acid--2-(methylamino)-1-phenylpropan-1-ol--hydrogen chloride (1/1/1)
-
-#-- CID 9581
 </pre></div>
 </div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>PSEUDOEPHEDRINE HYDROCHLORIDE
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>#-- CID 9581
+PSEUDOEPHEDRINE HYDROCHLORIDE
 Pseudoephedrine Hcl
 345-78-8
 Rhinalair
@@ -817,8 +810,9 @@ <h2>2. Getting chemical names for a given chemical structure<a class="headerlink
 Pseudoephedrine hydrochloride, European Pharmacopoeia (EP) Reference Standard
 Pseudoephedrine hydrochloride, United States Pharmacopeia (USP) Reference Standard
 Pseudoephedrine hydrochloride, Pharmaceutical Secondary Standard; Certified Reference Material
-
-#-- CID 77098502
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>#-- CID 77098502
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Aleve PM

manipulations/computing_inchis.html

@@ -526,7 +526,7 @@ <h3>1.2 Create a Molecular Object from SMILES<a class="headerlink" href="#create
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-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;rdkit.Chem.rdchem.Mol object at 0x7f416a790f20&gt;
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c4eb0&gt;
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@@ -607,7 +607,7 @@ <h3>1.4 Calculate InChIs for a List of Molecules<a class="headerlink" href="#cal
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-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;rdkit.Chem.rdchem.Mol object at 0x7f416a7913f0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f416a7914d0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f416a7918c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f416a791930&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f416a7919a0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f416a791a10&gt;]
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c5380&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c5460&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c5850&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c58c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c5930&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f7b825c59a0&gt;]
 </pre></div>
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@@ -766,7 +766,7 @@ <h3>2.4 Calculate InChIs for a List of Molecules<a class="headerlink" href="#id3
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-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;openbabel.pybel.Molecule object at 0x7f41980adc10&gt;, &lt;openbabel.pybel.Molecule object at 0x7f41693fbc10&gt;, &lt;openbabel.pybel.Molecule object at 0x7f41693fbad0&gt;, &lt;openbabel.pybel.Molecule object at 0x7f41693fbed0&gt;, &lt;openbabel.pybel.Molecule object at 0x7f41693fbf50&gt;, &lt;openbabel.pybel.Molecule object at 0x7f41693f8bd0&gt;]
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;openbabel.pybel.Molecule object at 0x7f7b819f6d50&gt;, &lt;openbabel.pybel.Molecule object at 0x7f7b811a7c50&gt;, &lt;openbabel.pybel.Molecule object at 0x7f7b811a7f10&gt;, &lt;openbabel.pybel.Molecule object at 0x7f7b811a7550&gt;, &lt;openbabel.pybel.Molecule object at 0x7f7b811a7850&gt;, &lt;openbabel.pybel.Molecule object at 0x7f7b811a79d0&gt;]
 </pre></div>
 </div>
 </div>

manipulations/dataset_search.html

@@ -1015,7 +1015,7 @@ <h3>2.1 - Authentication to the FAIRSharing API<a class="headerlink" href="#auth
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 </pre></div>
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