From 3217243cea13b7989ab7126260a2076ba4f41ffa Mon Sep 17 00:00:00 2001 From: John May Date: Fri, 20 Jan 2017 16:30:03 +0000 Subject: [PATCH] Complex HTML table now valid. --- .../cdk/graph/TripletShortCycles.java | 53 ++++++++++--------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java index a3085a7548..f81763c06f 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java @@ -40,7 +40,7 @@ * The ESSSR should not be confused with the extended set of smallest rings * (ESSR) {@cdk.cite Downs89}. * - *

Algorithm

To our knowledge no algorithm has been published for + * Algorithm To our knowledge no algorithm has been published for * the ESSSR. The PubChem * Specifications states - "An ESSSR ring is any ring which does not * share three consecutive atoms with any other ring in the chemical structure. @@ -61,7 +61,7 @@ * different phenyl rings it is easy to see the shortest cycle through * -u-v-w- is the 10 member envelope ring. * - *

Canonical and Non-Canonical Generation

+ * Canonical and Non-Canonical Generation * * 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 @@ -79,7 +79,7 @@ * of cycles for a graph this is not true for subgraphs. For two graphs * G, H and a canonical ordering (π). If H is a * subgraph of G then for two vertices u, v. It follows - * that π(u) < π(v) ∈ H ⇏ π(u) < π(v) ∈ + * that π(u) < π(v) ∈ H ⇏ π(u) < π(v) ∈ * G. In other words, we can canonically label a graph and inspect the * ordering of vertices u and v. We now take a subgraph which * contains both u and v - the ordering does not need to be the @@ -107,19 +107,20 @@ * may be absent which would be present if the subgraph was used. * * + * * - * + * * * - * - *
PubChem CIDDiagramSize of Rings in - * ESSSR
(fingerprints only store cycles |C| <= + * ESSSR
(fingerprints only store cycles |C| <= * 10)		Source
CID 135973 + * + * - *
Compound Image * * * *
{3, 3, 4}
{3, 3, 4}
{3, 3, 4}
 + *
* * * @@ -127,13 +128,13 @@ * * * - * - *
Canonical
Non-canonical
PubChem Fingerprint
CID 9249 + * + * - *
Compound Image * * * *
{3, 3, 4, 6, 6}
{3, 3, 4, 6, 6}
{3, 3, 6, 6}
 + *
* * @@ -142,13 +143,13 @@ * * * - * - *
Canonical - 4 member cycle only added if found before larger 6 * member cycles
Non-canonical
CID 931 + * + * - *
Compound Image * * * *
{6, 6, 10}
{6, 6, 10}
{6, 6, 10}
 + *
* * * @@ -156,14 +157,14 @@ * * * - * - *
Canonical
Non-canonical
PubChem Fingerprint
CID 5702 + * + * - *
Compound Image * * * *
{6, 6, 6, 6, 10, 10, 20, 22, 22, 24, 24}
{6, 6, 6, 6, 10, 10, 20, 22, 22, 24, 24}
{6, 6, 6, 6}
 + *
* * @@ -172,14 +173,14 @@ * * * - * - *
Canonical - 10 member cycles only added if found before larger * cycles
Non-canonical
CID 1211 + * + * - *
Compound Image * * * *
{6, 6, 6, 6, 6, 6, 10, 10, 18, 18, 20, 20, 22, 22, 22}
{6, 6, 6, 6, 6, 6, 10, 10, 18, 18, 20, 20, 22, 22, 22}
{6, 6, 6, 6, 6, 6, 10, 10}
 + *
* * @@ -188,13 +189,13 @@ * * * - * - *
Canonical - 10 member cycles only added if found before larger * cycles
Non-canonical
CID 17858819 + * + * - *
Compound Image * * * *
{5, 6, 9}
{5, 6, 9}
{5, 6, 9}
 + *
* * * @@ -202,15 +203,15 @@ * * * - * - *
Canonical
Non-canonical
PubChem Fingerprint
CID 1909 + * + * - *
Compound Image * * * *
{5, 5, 5, 6, 9, 16, 17, 17, * 17, * 18}
{5, 5, 5, 6, 9, 16, 17, 17, 17, 18}
{5, 5, 5, 6}
 + *
* *
Canonical - 9 member cycle only added if found before larger * cycles
Non-canonical