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Complex HTML table now valid.
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johnmay committed Jan 20, 2017
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* The ESSSR should not be confused with the extended set of smallest rings
* (ESSR) {@cdk.cite Downs89}.
*
* <h4>Algorithm</h4> To our knowledge no algorithm has been published for
* <b>Algorithm</b> To our knowledge no algorithm has been published for
* the ESSSR. The <a href="ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf">PubChem
* Specifications</a> states - <i>"An ESSSR ring is any ring which does not
* share three consecutive atoms with any other ring in the chemical structure.
Expand All @@ -61,7 +61,7 @@
* different phenyl rings it is easy to see the shortest cycle through
* <i>-u-v-w-</i> is the 10 member envelope ring.
*
* <h4>Canonical and Non-Canonical Generation</h4>
* <b>Canonical and Non-Canonical Generation</b>
*
* The algorithm can generate a canonical or non-canonical (preferred) set of
* cycles. As one can see from the above description depending on the order we
Expand All @@ -79,7 +79,7 @@
* of cycles for a graph this is not true for subgraphs. For two graphs
* <i>G</i>, <i>H</i> and a canonical ordering (<i>π</i>). If <i>H</i> is a
* subgraph of <i>G</i> then for two vertices <i>u</i>, <i>v</i>. It follows
* that <i>π(u)</i> < <i>π(v)</i> ∈ <i>H</i> ⇏ <i>π(u)</i> < <i>π(v)</i> ∈
* that <i>π(u)</i> &lt; <i>π(v)</i> ∈ <i>H</i> ⇏ <i>π(u)</i> &lt; <i>π(v)</i> ∈
* <i>G</i>. In other words, we can canonically label a graph and inspect the
* ordering of vertices <i>u</i> and <i>v</i>. We now take a subgraph which
* contains both <i>u</i> and <i>v</i> - the ordering does not need to be the
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* may be absent which would be present if the subgraph was used.
*
* <table style="font-family: courier; font-size: 9pt; color: #666666;">
* <caption></caption>
* <tr><th>PubChem CID</th><th>Diagram</th><th rowspan="2">Size of Rings in
* ESSSR <br/>(fingerprints only store cycles |C| &lt;=
* ESSSR <br>(fingerprints only store cycles |C| &lt;=
* 10)</th><th>Source</th></tr>
* <tr/>
* <tr></tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=135973">135973</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=135973"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=135973" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{3, 3, 4}</td></tr>
* <tr><td>{3, 3, 4}</td></tr>
* <tr><td>{3, 3, 4}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical</td></tr>
* <tr><td>Non-canonical</td></tr>
* <tr><td>PubChem Fingerprint</td></tr>
* </table></td>
* </tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9249">9249</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=9249"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=9249" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{3, 3, <b style="color: #FF4444;"><u>4</u></b>, 6, 6}</td> </tr>
* <tr><td>{3, 3, 4, 6, 6}</td></tr>
* <tr><td>{3, 3, 6, 6}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical - <i>4 member cycle only added if found before larger 6
* member cycles</i></td></tr>
* <tr><td>Non-canonical</td></tr>
Expand All @@ -142,28 +143,28 @@
* </tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=931">931</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=931"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=931" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{6, 6, 10}</td></tr>
* <tr><td>{6, 6, 10}</td></tr>
* <tr><td>{6, 6, 10}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical</td></tr>
* <tr><td>Non-canonical</td></tr>
* <tr><td>PubChem Fingerprint</td></tr>
* </table></td>
* </tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5702">5702</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=5702"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=5702" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{6, 6, 6, 6, <b style="color: #FF4444;"><u>10</u></b>, <b
* style="color: #FF4444;"><u>10</u></b>, 20, 22, 22, 24, 24}</td></tr>
* <tr><td>{6, 6, 6, 6, 10, 10, 20, 22, 22, 24, 24}</td></tr>
* <tr><td>{6, 6, 6, 6}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical - <i>10 member cycles only added if found before larger
* cycles</i></td></tr>
* <tr><td>Non-canonical</td></tr>
Expand All @@ -172,14 +173,14 @@
* </tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=1211">1211</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=1211"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=1211" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{6, 6, 6, 6, 6, 6, <b style="color: #FF4444;"><u>10</u></b>, <b
* style="color: #FF4444;"><u>10</u></b>, 18, 18, 20, 20, 22, 22, 22}</td></tr>
* <tr><td>{6, 6, 6, 6, 6, 6, 10, 10, 18, 18, 20, 20, 22, 22, 22}</td></tr>
* <tr><td>{6, 6, 6, 6, 6, 6, 10, 10}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical - <i>10 member cycles only added if found before larger
* cycles</i></td></tr>
* <tr><td>Non-canonical</td></tr>
Expand All @@ -188,29 +189,29 @@
* </tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=17858819">17858819</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=17858819"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=17858819" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{5, 6, 9}</td></tr>
* <tr><td>{5, 6, 9}</td></tr>
* <tr><td>{5, 6, 9}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical</td></tr>
* <tr><td>Non-canonical</td></tr>
* <tr><td>PubChem Fingerprint</td></tr>
* </table></td>
* </tr>
* <tr>
* <td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=1909">1909</a></td>
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=1909"/></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><img src="http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=1909" alt="Compound Image"></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>{5, 5, 5, 6, <b style="color: #FF4444;"><u>9</u></b>, 16, 17, 17,
* 17,
* 18}</td></tr>
* <tr><td>{5, 5, 5, 6, 9, 16, 17, 17, 17, 18}</td></tr>
* <tr><td>{5, 5, 5, 6}</td></tr>
* </table></td>
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;">
* <td><table style="font-family: courier; font-size: 9pt; color: #666666;"><caption></caption>
* <tr><td>Canonical - <i>9 member cycle only added if found before larger
* cycles</i></td></tr>
* <tr><td>Non-canonical</td></tr>
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