From fe077e332225bd9a6fa732f535e77f41fdf2307c Mon Sep 17 00:00:00 2001 From: John May Date: Fri, 20 Jan 2017 16:57:54 +0000 Subject: [PATCH] Fix bad or malformed HTML warnings. --- .../org/openscience/cdk/config/Elements.java | 6 +- .../cdk/graph/ConnectedComponents.java | 4 +- .../org/openscience/cdk/graph/Cycles.java | 4 +- .../org/openscience/cdk/graph/GraphUtil.java | 4 +- .../openscience/cdk/graph/RelevantCycles.java | 8 +- .../openscience/cdk/graph/ShortestPaths.java | 49 +- .../cdk/ringsearch/RingSearch.java | 22 +- .../java/org/openscience/cdk/ReactionSet.java | 4 +- .../main/java/org/openscience/cdk/Ring.java | 2 +- .../org/openscience/cdk/interfaces/IRing.java | 2 +- .../openscience/cdk/tools/ILoggingTool.java | 2 +- .../openscience/cdk/isomorphism/Mappings.java | 14 +- .../openscience/cdk/silent/ReactionSet.java | 4 +- .../java/org/openscience/cdk/silent/Ring.java | 2 +- .../openscience/cdk/graph/rebond/Bspt.java | 4 +- .../openscience/cdk/math/FortranFormat.java | 2 +- .../openscience/cdk/stereo/Stereocenters.java | 4 +- .../cdk/fingerprint/PubchemFingerprinter.java | 10 +- .../SubstructureFingerprinter.java | 602 +++++++++--------- .../openscience/cdk/tools/GridGenerator.java | 4 +- .../org/openscience/cdk/io/ShelXReader.java | 2 +- .../openscience/cdk/tools/DataFeatures.java | 4 +- .../cdk/smiles/SmilesGenerator.java | 14 +- .../cdk/group/PermutationGroup.java | 6 +- 24 files changed, 390 insertions(+), 389 deletions(-) diff --git a/base/core/src/main/java/org/openscience/cdk/config/Elements.java b/base/core/src/main/java/org/openscience/cdk/config/Elements.java index 3706049a27..28cb54f770 100644 --- a/base/core/src/main/java/org/openscience/cdk/config/Elements.java +++ b/base/core/src/main/java/org/openscience/cdk/config/Elements.java @@ -298,7 +298,7 @@ public int group() { * size of an atom that forms part of one covalent bond. * * @return covalent radius - null if not available - * @see Covalent radius */ public Double covalentRadius() { return rCov; @@ -310,7 +310,7 @@ public Double covalentRadius() { * atom. * * @return van der Waals radius - null if not available - * @see Van de Waals radius */ public Double vdwRadius() { return rW; @@ -324,7 +324,7 @@ public Double vdwRadius() { * available 'null' is returned. * * @return Pauling electronegativity - null if not available - * @see Pauling Electronegativity */ public Double electronegativity() { return electronegativity; diff --git a/base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java b/base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java index 309b0444cd..bc0b25b8b9 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java @@ -5,13 +5,13 @@ /** * Compute the connected components of an adjacency list. * - * 
+ * 
{@code
  *     int[][]             g          = GraphUtil.toAdjList(container(l
  *     ConnectedComponents cc         = new ConnectedComponents(g);
  *     int[]               components = cc.components();
  *     for (int v = 0; v < g.length; v++)
  *         components[v];
- * 

+ * }
* * @author John May * @cdk.module core diff --git a/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java b/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java index feb8ff9848..478afaa0ae 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java @@ -453,10 +453,10 @@ public static void markRingAtomsAndBonds(IAtomContainer mol, int[][] adjList, Ed /** * Use an auxiliary cycle finder if the primary method was intractable. * - * 
+     * 
{@code
      * // all cycles or all cycles size <= 6
      * CycleFinder cf = Cycles.or(Cycles.all(), Cycles.all(6));
-     * 

+     * }
* * It is possible to nest multiple levels. * diff --git a/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java b/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java index 810a158bb9..7f4bee62d9 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java @@ -190,7 +190,7 @@ public static int[][] toAdjList(IAtomContainer container, EdgeToBondMap bondMap) * graph} to {@literal include} in the subgraph. The provided vertices also * provide the mapping between vertices in the subgraph and the original. * - * 
+     * 
{@code
      * int[][] g  = toAdjList(naphthalene);
      * int[]   vs = new int[]{0, 1, 2, 3, 4, 5};
      *
@@ -199,7 +199,7 @@ public static int[][] toAdjList(IAtomContainer container, EdgeToBondMap bondMap)
      * for(int v = 0; v < h.length; v++) {
      *     // vs[v] is 'v' in 'g'
      * }
-     * 

+     * }
* * @param graph adjacency list graph * @param include the vertices of he graph to include in the subgraph diff --git a/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java index a3d5a62423..99cff1fbdc 100644 --- a/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java +++ b/base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java @@ -40,7 +40,7 @@ * in number but can be checked (see {@link #size()}) before construction * {@cdk.cite Vismara97}. * - * 
+ * 
{@code
  * // import static org.openscience.cdk.graph.GraphUtil.*;
  * IAtomContainer m = ...;
  *
@@ -69,7 +69,7 @@
  *         }
  *     }
  * }
- *
+ * }
  * 

  *
  * @author John May
@@ -139,7 +139,7 @@ private List independent(final Collection cycles) {
     /**
      * Reconstruct the paths of all relevant cycles.
      *
-     * 
+     * 
{@code
      * RelevantCycles relevant = ...
      *
      * // ensure the number is manageable
@@ -148,7 +148,7 @@ private List independent(final Collection cycles) {
      *     // process the path
      *   }
      * }
-     * 

+     * }

      *
      * @return array of vertex paths
      */
diff --git a/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java b/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java
index 60842f4d4d..a6cb720981 100644
--- a/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java
+++ b/base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java
@@ -35,7 +35,7 @@
  * the paths. When no path is found (i.e. not-connected) an empty path is always
  * returned. 
  *
- * 
+ * 
{@code
  * IAtomContainer benzene = MoleculeFactory.makeBenzene();
  *
  * IAtom c1 = benzene.getAtom(0);
@@ -57,6 +57,7 @@
  * int[][] paths = sp.pathsTo(c4);
  * int[] org = paths[0];  // paths[0] == path
  * int[] alt = paths[1];
+ * }
  * 

  *
  *  If shortest paths from multiple start atoms are required {@link
@@ -273,7 +274,7 @@ private void compute(final int[][] adjacent, final int[] ordering) {
      * is a member of a different fragment, or the vertex is not present in the
      * container at all.
      *
-     * 
+     * 
{@code
      * ShortestPaths sp = ...;
      *
      * // reconstruct first path
@@ -283,7 +284,7 @@ private void compute(final int[][] adjacent, final int[] ordering) {
      * if(sp.nPathsTo(5) == 1){
      *     int[] path = sp.pathTo(5); // reconstruct the path
      * }
-     * 

+     * }

      *
      * @param end the end vertex to find a path to
      * @return path from the start to the end vertex
@@ -307,7 +308,7 @@ public int[] pathTo(int end) {
      * a member of a different fragment, or the atom is not present in the
      * container at all.
      *
-     * 
+     * 
{@code
      * ShortestPaths sp   = ...;
      * IAtom         end  = ...;
      *
@@ -318,7 +319,7 @@ public int[] pathTo(int end) {
      * if(sp.nPathsTo(end) == 1){
      *     int[] path = sp.pathTo(end); // reconstruct the path
      * }
-     * 

+     * }

      *
      * @param end the end vertex to find a path to
      * @return path from the start to the end vertex
@@ -358,7 +359,7 @@ public boolean isPrecedingPathTo(int end) {
      * at maximum 1024 paths). It is safer to check the number of paths ({@link
      * #nPathsTo(int)}) before attempting to reconstruct all shortest paths.
      *
-     * 
+     * 
{@code
      * int           threshold = 20;
      * ShortestPaths sp        = ...;
      *
@@ -369,7 +370,7 @@ public boolean isPrecedingPathTo(int end) {
      * if(sp.nPathsTo(5) < threshold){
      *     int[][] path = sp.pathsTo(5); // reconstruct shortest paths
      * }
-     * 

+     * }

      *
      * @param end the end vertex
      * @return all shortest paths from the start to the end vertex
@@ -387,7 +388,7 @@ public int[][] pathsTo(int end) {
      * size arrays of vertex indices. When there is no path an empty array is
      * returned. It is considered there to be no path if the end vertex belongs
      * to the same container but is a member of a different fragment, or the
-     * vertex is not present in the container at all. 
+     * vertex is not present in the container at all.
      *
      * Important: for every possible branch the number of possible paths
      * doubles and could be in the order of tens of thousands. Although the
@@ -395,7 +396,7 @@ public int[][] pathsTo(int end) {
      * at maximum 1024 paths). It is safer to check the number of paths ({@link
      * #nPathsTo(int)}) before attempting to reconstruct all shortest paths.
      *
-     * 
+     * 
{@code
      * int           threshold = 20;
      * ShortestPaths sp        = ...;
      * IAtom         end       = ...;
@@ -407,7 +408,7 @@ public int[][] pathsTo(int end) {
      * if(sp.nPathsTo(end) < threshold){
      *     int[][] path = sp.pathsTo(end); // reconstruct shortest paths
      * }
-     * 

+     * }

      *
      * @param end the end atom
      * @return all shortest paths from the start to the end vertex
@@ -425,7 +426,7 @@ public int[][] pathsTo(IAtom end) {
      * is a member of a different fragment, or the vertex is not present in the
      * container at all.
      *
-     * 
+     * 
{@code
      * ShortestPaths sp = ...;
      *
      * // reconstruct a shortest path
@@ -435,7 +436,7 @@ public int[][] pathsTo(IAtom end) {
      * if(sp.nPathsTo(5) == 1){
      *     IAtom[] path = sp.atomsTo(5); // reconstruct shortest path
      * }
-     * 

+     * }

      *
      * @param end the end vertex to find a path to
      * @return path from the start to the end atoms as fixed size
@@ -467,7 +468,7 @@ public IAtom[] atomsTo(int end) {
      * container at all.
      *
      *
-     * 
+     * 
{@code
      * ShortestPaths sp   = ...;
      * IAtom         end  = ...;
      *
@@ -478,7 +479,7 @@ public IAtom[] atomsTo(int end) {
      * if(sp.nPathsTo(end) == 1){
      *     IAtom[] path = sp.atomsTo(end); // reconstruct shortest path
      * }
-     * 

+     * }

      *
      * @param end the end atom to find a path to
      * @return path from the start to the end atoms as fixed size
@@ -497,13 +498,13 @@ public IAtom[] atomsTo(IAtom end) {
      * vertex belongs to the same container but is a member of a different
      * fragment, or the vertex is not present in the container at all.
      *
-     * 
+     * 
{@code
      * ShortestPaths sp   = ...;
      *
      * sp.nPathsTo(5); // number of paths
      *
      * sp.nPathsTo(-1); // returns 0 - there are no paths
-     * 

+     * }

      *
      * @param end the end vertex to which the number of paths will be
      *            returned
@@ -519,7 +520,7 @@ public int nPathsTo(int end) {
      * atom belongs to the same container but is a member of a different
      * fragment, or the atom is not present in the container at all.
      *
-     * 
+     * 
{@code
      * ShortestPaths sp   = ...;
      * IAtom         end  = ...l
      *
@@ -527,7 +528,7 @@ public int nPathsTo(int end) {
      *
      * sp.nPathsTo(null);           // returns 0 - there are no paths
      * sp.nPathsTo(new Atom("C"));  // returns 0 - there are no paths
-     * 

+     * }

      *
      * @param end the end vertex to which the number of paths will be
      *            returned
@@ -543,7 +544,7 @@ public int nPathsTo(IAtom end) {
      * Formally, there is a path if the distance is less then the number of
      * vertices.
      *
-     * 
+     * 
{@code
      * IAtomContainer container = ...;
      * ShortestPaths  sp        = ...; // start = 0
      *
@@ -552,7 +553,7 @@ public int nPathsTo(IAtom end) {
      * if(sp.distanceTo(5) < n) {
      *     // these is a path from 0 to 5
      * }
-     * 

+     * }

      *
      * Conveniently the distance is also the index of the last vertex in the
      * path.
@@ -582,7 +583,7 @@ public int distanceTo(int end) {
      * Formally, there is a path if the distance is less then the number of
      * atoms.
      *
-     * 
+     * 
{@code
      * IAtomContainer container = ...;
      * ShortestPaths  sp        = ...; // start atom
      * IAtom          end       = ...;
@@ -592,13 +593,13 @@ public int distanceTo(int end) {
      * if( sp.distanceTo(end) < n ) {
      *     // these is a path from start to end
      * }
-     *
+     * }
      * 

      *
      * Conveniently the distance is also the index of the last vertex in the
      * path.
      *
-     * 
+     * 
{@code
      * IAtomContainer container = ...;
      * ShortestPaths  sp        = ...; // start atom
      * IAtom          end       = ...;
@@ -606,7 +607,7 @@ public int distanceTo(int end) {
      * int atoms = sp.atomsTo(end);
      * // end == atoms[sp.distanceTo(end)];
      *
-     * 

+     * }

      *
      * @param end atom to measure the distance to
      * @return distance to the given atom
diff --git a/base/core/src/main/java/org/openscience/cdk/ringsearch/RingSearch.java b/base/core/src/main/java/org/openscience/cdk/ringsearch/RingSearch.java
index 14ac518a32..a10a6c84eb 100644
--- a/base/core/src/main/java/org/openscience/cdk/ringsearch/RingSearch.java
+++ b/base/core/src/main/java/org/openscience/cdk/ringsearch/RingSearch.java
@@ -64,7 +64,7 @@
  * 
  *
  * 
Example Usage

- * 
+ * 
{@cdoe
  * // construct the search for a given molecule, if an adjacency list
  * // representation (int[][]) is available this can be passed to the
  * // constructor for improved performance
@@ -92,8 +92,8 @@
  * }
  * for(IAtomContainer fragment : ringSearch.isolatedRingFragments()){
  *     ....
- * }                *
- * 

+ * }
+ * }

  *
  * @author John May
  * @cdk.module core
@@ -193,7 +193,7 @@ public boolean cyclic(int u, int v) {
     /**
      * Determine whether the provided atom belongs to a ring (is cyclic).
      *
-     * 
+     * 
{@code
      * IAtomContainer mol        = ...;
      * RingSearch     ringSearch = new RingSearch(mol);
      *
@@ -202,7 +202,7 @@ public boolean cyclic(int u, int v) {
      *         ...
      *     }
      * }
-     * 

+     * }

      *
      * @param atom an atom
      * @return whether the atom is in a ring
@@ -232,7 +232,7 @@ public boolean cyclic(IBond bond) {
     /**
      * Determine whether the vertex at index i is a cyclic vertex.
      *
-     * 
+     * 
{@code
      * IAtomContainer  mol    = ...;
      * RingSearch      tester = new RingSearch(mol);
      *
@@ -242,7 +242,7 @@ public boolean cyclic(IBond bond) {
      *         ...
      *     }
      * }
-     * 

+     * }

      *
      * @param i atom index
      * @return whether the vertex at the given index is in a cycle
@@ -263,7 +263,7 @@ public int[] cyclic() {
     /**
      * Construct the sets of vertices which belong to isolated rings.
      *
-     * 
+     * 
{@code
      * IAtomContainer  biphenyl   = ...;
      * RingSearch      ringSearch = new RingSearch(biphenyl);
      *
@@ -273,7 +273,7 @@ public int[] cyclic() {
      * isolated[0].length; // 6 vertices in one benzene
      * isolated[1].length; // 6 vertices in the other benzene
      *
-     * 

+     * }

      *
      * @return array of isolated fragments, defined by the vertices in the
      *         fragment
@@ -285,7 +285,7 @@ public int[][] isolated() {
     /**
      * Construct the sets of vertices which belong to fused ring systems.
      *
-     * 
+     * 
{@code
      * IAtomContainer  mol        = ...;
      * RingSearch      ringSearch = new RingSearch(mol);
      *
@@ -296,7 +296,7 @@ public int[][] isolated() {
      * fused[1].length; // e.g. 10 vertices in the second system
      * fused[2].length; // e.g. 4 vertices in the third system
      *
-     * 

+     * }

      *
      * @return array of fused fragments, defined by the vertices in the
      *         fragment
diff --git a/base/data/src/main/java/org/openscience/cdk/ReactionSet.java b/base/data/src/main/java/org/openscience/cdk/ReactionSet.java
index fba939165f..0470a6f291 100644
--- a/base/data/src/main/java/org/openscience/cdk/ReactionSet.java
+++ b/base/data/src/main/java/org/openscience/cdk/ReactionSet.java
@@ -40,11 +40,11 @@
  *
  * and
  *
- * 
+ * 
{@code
  * for (int i=0; i < reactionSet.getReactionCount(); i++) {
  *    IReaction reaction = reactionSet.getReaction(i);
  * }
- * 

+ * }

  *
  * @cdk.module data
  * @cdk.githash
diff --git a/base/data/src/main/java/org/openscience/cdk/Ring.java b/base/data/src/main/java/org/openscience/cdk/Ring.java
index 149f169537..03da7ea071 100644
--- a/base/data/src/main/java/org/openscience/cdk/Ring.java
+++ b/base/data/src/main/java/org/openscience/cdk/Ring.java
@@ -27,7 +27,7 @@
  * Class representing a ring structure in a molecule.
  * A ring is a linear sequence of
  * N atoms interconnected to each other by covalent bonds,
- * such that atom i (1 < i < N) is bonded to
+ * such that atom i (1 < i < N) is bonded to
  * atom i-1 and atom i + 1 and atom 1 is bonded to atom N and atom 2.
  *
  * @cdk.module  data
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java
index b8302168a0..6917f756f7 100644
--- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java
+++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java
@@ -22,7 +22,7 @@
  * Class representing a ring structure in a molecule.
  * A ring is a linear sequence of
  * N atoms interconnected to each other by covalent bonds,
- * such that atom i (1 < i < N) is bonded to
+ * such that atom i (1 < i < N) is bonded to
  * atom i-1 and atom i + 1 and atom 1 is bonded to atom N and atom 2.
  *
  * @cdk.module  interfaces
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java b/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java
index d31b805dc1..9c1c84c90e 100644
--- a/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java
+++ b/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java
@@ -82,7 +82,7 @@
  * 

  *
  * 
In addition to the methods specific in the interfance, implementations
- * must also implement the static method create(Class) which
+ * must also implement the static method {@code create(Class)} which
  * can be used by the {@link LoggingToolFactory} to instantiate the
  * implementation.
  *
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java
index 536e0683fc..a45bf52450 100644
--- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java
+++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java
@@ -57,12 +57,12 @@
  * The primary function is to provide an iterable of matches - each match is
  * a permutation (mapping) of the query graph indices (atom indices).
  *
- * 
+ * 
{@code
  * for (int[] p : mappings) {
  *     for (int i = 0; i < p.length; i++)
  *         // query.getAtom(i) is mapped to target.getAtom(p[i]);
  * }
- * 

+ * }

  *
  * The matches can be filtered to provide only those that have valid
  * stereochemistry.
@@ -181,7 +181,7 @@ public final class Mappings implements Iterable {
      * Filter the mappings and keep only those which match the provided
      * predicate (Guava).
      *
-     * 
+     * 
{@code
      *
      *     final IAtomContainer query;
      *     final IAtomContainer target;
@@ -195,7 +195,7 @@ public final class Mappings implements Iterable {
      *                                        return input[0] == 0;
      *                                    }});
      *
-     * 

+     * }

      *
      * @param predicate a predicate
      * @return fluent-api reference
@@ -208,7 +208,7 @@ public Mappings filter(final Predicate predicate) {
      * Map the mappings to another type. Each mapping is transformed using the
      * provided function.
      *
-     * 
+     * 
{@code
      *
      *     final IAtomContainer query;
      *     final IAtomContainer target;
@@ -217,7 +217,7 @@ public Mappings filter(final Predicate predicate) {
      *                                .matchAll(target);
      *
      *     // a string that indicates the mapping of atom elements and numbers
-     *     Iterable<String> strs = mappings.map(new Function<int[], String>() {
+     *     Iterable<String> strs = mappings.map(new Function() {
      *         public String apply(int[] input) {
      *             StringBuilder sb = new StringBuilder();
      *             for (int i = 0; i < input.length; i++) {
@@ -231,7 +231,7 @@ public Mappings filter(final Predicate predicate) {
      *             return sb.toString();
      *         }});
      *
-     * 

+     * }

      *
      * @param f function to transform a mapping
      * @return iterable of the transformed type
diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java b/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java
index bebf40301a..40a2e52dfd 100644
--- a/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java
+++ b/base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java
@@ -40,11 +40,11 @@
  *
  * and
  *
- * 
+ * 
{@code
  * for (int i=0; i < reactionSet.getReactionCount(); i++) {
  *    IReaction reaction = reactionSet.getReaction(i);
  * }
- * 

+ * }

  *
  * @cdk.module  silent
  * @cdk.githash
diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java b/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java
index 4b1c7f83bd..35916eefe0 100644
--- a/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java
+++ b/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java
@@ -27,7 +27,7 @@
  * Class representing a ring structure in a molecule.
  * A ring is a linear sequence of
  * N atoms interconnected to each other by covalent bonds,
- * such that atom i (1 < i < N) is bonded to
+ * such that atom i (1 < i < N) is bonded to
  * atom i-1 and atom i + 1 and atom 1 is bonded to atom N and atom 2.
  *
  * @cdk.module  silent
diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/rebond/Bspt.java b/base/standard/src/main/java/org/openscience/cdk/graph/rebond/Bspt.java
index 938fe6fee6..a17e2d240d 100644
--- a/base/standard/src/main/java/org/openscience/cdk/graph/rebond/Bspt.java
+++ b/base/standard/src/main/java/org/openscience/cdk/graph/rebond/Bspt.java
@@ -35,8 +35,8 @@
  * 
  *    mySplitDimension = (parentSplitDimension + 1) % 3;
  * 

- *  A split value is stored in the node. Values which are <= splitValue are
- *  stored down the left branch. Values which are >= splitValue are stored
+ *  A split value is stored in the node. Values which are ≤ splitValue are
+ *  stored down the left branch. Values which are ≥ splitValue are stored
  *  down the right branch. When this happens, the search must proceed down
  *  both branches.
  *  Planar and crystalline substructures can generate values which are == along
diff --git a/base/standard/src/main/java/org/openscience/cdk/math/FortranFormat.java b/base/standard/src/main/java/org/openscience/cdk/math/FortranFormat.java
index 27a4079f72..a214946345 100644
--- a/base/standard/src/main/java/org/openscience/cdk/math/FortranFormat.java
+++ b/base/standard/src/main/java/org/openscience/cdk/math/FortranFormat.java
@@ -27,7 +27,7 @@
  * Converts a String representation of a Fortran double to a double.
  *
  * 
A modified version of the atof method provided in the Core Java
- * books by Cay S. Horstmann & Gary Cornell.  The main difference
+ * books by Cay S. Horstmann & Gary Cornell.  The main difference
  * here is that we scan for Fortran double precision characters
  * ('D' and 'd') which often cause the C versions of atof to
  * barf.
diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java b/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
index 25a373674b..d5aa4ddfa5 100644
--- a/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
+++ b/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
@@ -135,7 +135,7 @@ public final class Stereocenters {
      * Determine the stereocenter atoms in the provided container based on
      * connectivity.
      *
-     * 
+     * 
{@code
      * IAtomContainer container = ...;
      * Stereocenters  centers   = Stereocenters.of(container);
      * for (int i = 0; i < container.getAtomCount(); i++) {
@@ -143,7 +143,7 @@ public final class Stereocenters {
      *
      *     }
      * }
-     * 

+     * }

      *
      * @param container input container
      * @return the stereocenters
diff --git a/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java b/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java
index a11aa72b6a..161caac65c 100644
--- a/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java
+++ b/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java
@@ -66,12 +66,12 @@
  * 
  * Some SMARTS patterns have been modified from the original code, since they
  * were based on explicit H matching. As a result, we replace the explicit H's
- * with a query of the #N&!H0 where N is the atomic number. Thus bit 344 was
- * originally [#6](~[#6])([H]) but is written here as
- * [#6&!H0]~[#6]. In some cases, where the H count can be reduced
+ * with a query of the {@code #&!H0} where {@code } is the atomic number. Thus bit 344 was
+ * originally {@code [#6](~[#6])([H])} but is written here as
+ * {@code [#6&!H0]~[#6]}. In some cases, where the H count can be reduced
  * to single possibility we directly use that H count. An example is bit 35,
- * which was [#6](~[#6])(~[#6])(~[#6])([H]) and is rewritten as
- * [#6H1](~[#6])(~[#6])(~[#6].
+ * which was {@code [#6](~[#6])(~[#6])(~[#6])([H])} and is rewritten as
+ * {@code [#6H1](~[#6])(~[#6])(~[#6])}.
  * 
  *
  * Warning - this class is not thread-safe and uses stores intermediate steps
diff --git a/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java b/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
index 99c4aad277..34de85a16d 100644
--- a/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
+++ b/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
@@ -44,313 +44,313 @@
  * 
  * 
  * 
- * 0Primary carbon[CX4H3][#6]
- * 1Secondary carbon[CX4H2]([#6])[#6]
- * 2Tertiary carbon[CX4H1]([#6])([#6])[#6]
- * 3Quaternary carbon[CX4]([#6])([#6])([#6])[#6]
- * 4Alkene[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]
- * 5Alkyne[CX2]#[CX2]
- * 6Allene[CX3]=[CX2]=[CX3]
- * 7Alkylchloride[ClX1][CX4]
- * 8Alkylfluoride[FX1][CX4]
- * 9Alkylbromide[BrX1][CX4]
- * 10Alkyliodide[IX1][CX4]
- * 11Alcohol[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
- * 12Primary alcohol[OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
- * 13Secondary alcohol[OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
- * 14Tertiary alcohol[OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
- * 15Dialkylether[OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
- * 16Dialkylthioether[SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
- * 17Alkylarylether[OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
- * 18Diarylether[c][OX2][c]
- * 19Alkylarylthioether[SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
- * 20Diarylthioether[c][SX2][c]
- * 21Oxonium[O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
- * 22Amine[NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
- * 23Primary aliph amine[NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
- * 24Secondary aliph amine[NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
- * 25Tertiary aliph amine[NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
- * 26Quaternary aliph ammonium[NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
- * 27Primary arom amine[NX3H2+0,NX4H3+]c
- * 28Secondary arom amine[NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
- * 29Tertiary arom amine[NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
- * 30Quaternary arom ammonium[NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
- * 31Secondary mixed amine[NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
- * 32Tertiary mixed amine[NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
- * 33Quaternary mixed ammonium[NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
- * 34Ammonium[N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]
- * 35Alkylthiol[SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
- * 36Dialkylthioether[SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
- * 37Alkylarylthioether[SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
- * 38Disulfide[SX2D2][SX2D2]
- * 391,2-Aminoalcohol[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
- * 401,2-Diol[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
- * 411,1-Diol[OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
- * 42Hydroperoxide[OX2H][OX2]
- * 43Peroxo[OX2D2][OX2D2]
- * 44Organolithium compounds[LiX1][#6,#14]
- * 45Organomagnesium compounds[MgX2][#6,#14]
- * 46Organometallic compounds[!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
- * 47Aldehyde[$([CX3H][#6]),$([CX3H2])]=[OX1]
- * 48Ketone[#6][CX3](=[OX1])[#6]
- * 49Thioaldehyde[$([CX3H][#6]),$([CX3H2])]=[SX1]
- * 50Thioketone[#6][CX3](=[SX1])[#6]
- * 51Imine[NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
- * 52Immonium[NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
- * 53Oxime[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
- * 54Oximether[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
- * 55Acetal[OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
- * 56Hemiacetal[OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
- * 57Aminal[NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]
- * 58Hemiaminal[NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
- * 59Thioacetal[SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
- * 60Thiohemiacetal[SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
- * 61Halogen acetal like[NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
- * 62Acetal like[NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
- * 63Halogenmethylen ester and similar[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
- * 64NOS methylen ester and similar[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
- * 65Hetero methylen ester and similar[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
- * 66Cyanhydrine[NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
- * 67Chloroalkene[ClX1][CX3]=[CX3]
- * 68Fluoroalkene[FX1][CX3]=[CX3]
- * 69Bromoalkene[BrX1][CX3]=[CX3]
- * 70Iodoalkene[IX1][CX3]=[CX3]
- * 71Enol[OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
- * 72Endiol[OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
- * 73Enolether[OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
- * 74Enolester[OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
- * 75Enamine[NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
- * 76Thioenol[SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
- * 77Thioenolether[SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
- * 78Acylchloride[CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]
- * 79Acylfluoride[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]
- * 80Acylbromide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]
- * 81Acyliodide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
- * 82Acylhalide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
- * 83Carboxylic acid[CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
- * 84Carboxylic ester[CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
- * 85Lactone[#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
- * 86Carboxylic anhydride[CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
- * 87Carboxylic acid derivative[$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
- * 88Carbothioic acid[CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
- * 89Carbothioic S ester[CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
- * 90Carbothioic S lactone[#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
- * 91Carbothioic O ester[CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
- * 92Carbothioic O lactone[#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
- * 93Carbothioic halide[CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
- * 94Carbodithioic acid[CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
- * 95Carbodithioic ester[CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
- * 96Carbodithiolactone[#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
- * 97Amide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 98Primary amide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
- * 99Secondary amide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
- * 100Tertiary amide[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
- * 101Lactam[#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 102Alkyl imide[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
- * 103N hetero imide[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
- * 104Imide acidic[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
- * 105Thioamide[$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 106Thiolactam[#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 107Oximester[#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
- * 108Amidine[NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
- * 109Hydroxamic acid[CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
- * 110Hydroxamic acid ester[CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
- * 111Imidoacid[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
- * 112Imidoacid cyclic[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
- * 113Imidoester[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
- * 114Imidolactone[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
- * 115Imidothioacid[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
- * 116Imidothioacid cyclic[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
- * 117Imidothioester[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
- * 118Imidothiolactone[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
- * 119Amidine[#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
- * 120Imidolactam[#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]
- * 121Imidoylhalide[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
- * 122Imidoylhalide cyclic[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
- * 123Amidrazone[$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
- * 124Alpha aminoacid[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
- * 125Alpha hydroxyacid[OX2H][C][CX3](=[OX1])[OX2H,OX1-]
- * 126Peptide middle[NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
- * 127Peptide C term[NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
- * 128Peptide N term[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
- * 129Carboxylic orthoester[#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]
- * 130Ketene[CX3]=[CX2]=[OX1]
- * 131Ketenacetal[#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]
- * 132Nitrile[NX1]#[CX2]
- * 133Isonitrile[CX1-]#[NX2+]
- * 134Vinylogous carbonyl or carboxyl derivative[#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
- * 135Vinylogous acid[#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
- * 136Vinylogous ester[#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
- * 137Vinylogous amide[#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 138Vinylogous halide[#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
- * 139Carbonic acid dieester[#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
- * 140Carbonic acid esterhalide[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
- * 141Carbonic acid monoester[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
- * 142Carbonic acid derivatives[!#6][#6X3](=[!#6])[!#6]
- * 143Thiocarbonic acid dieester[#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
- * 144Thiocarbonic acid esterhalide[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
- * 145Thiocarbonic acid monoester[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
- * 146Urea[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
- * 147Thiourea[#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
- * 148Isourea[#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
- * 149Isothiourea[#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
- * 150Guanidine[N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
- * 151Carbaminic acid[NX3]C(=[OX1])[O;X2H,X1-]
- * 152Urethan[#7X3][#6](=[OX1])[#8X2][#6]
- * 153Biuret[#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
- * 154Semicarbazide[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
- * 155Carbazide[#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
- * 156Semicarbazone[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
- * 157Carbazone[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
- * 158Thiosemicarbazide[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
- * 159Thiocarbazide[#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
- * 160Thiosemicarbazone[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
- * 161Thiocarbazone[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
- * 162Isocyanate[NX2]=[CX2]=[OX1]
- * 163Cyanate[OX2][CX2]#[NX1]
- * 164Isothiocyanate[NX2]=[CX2]=[SX1]
- * 165Thiocyanate[SX2][CX2]#[NX1]
- * 166Carbodiimide[NX2]=[CX2]=[NX2]
- * 167Orthocarbonic derivatives[CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
- * 168Phenol[OX2H][c]
- * 1691,2-Diphenol[OX2H][c][c][OX2H]
- * 170Arylchloride[Cl][c]
- * 171Arylfluoride[F][c]
- * 172Arylbromide[Br][c]
- * 173Aryliodide[I][c]
- * 174Arylthiol[SX2H][c]
- * 175Iminoarene[c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
- * 176Oxoarene[c]=[OX1]
- * 177Thioarene[c]=[SX1]
- * 178Hetero N basic H[nX3H1+0]
- * 179Hetero N basic no H[nX3H0+0]
- * 180Hetero N nonbasic[nX2,nX3+]
- * 181Hetero O[o]
- * 182Hetero S[sX2]
- * 183Heteroaromatic[a;!c]
- * 184Nitrite[NX2](=[OX1])[O;$([X2]),$([X1-])]
- * 185Thionitrite[SX2][NX2]=[OX1]
- * 186Nitrate[$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]
- * 187Nitro[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
- * 188Nitroso[NX2](=[OX1])[!#7;!#8]
- * 189Azide[NX1]~[NX2]~[NX2,NX1]
- * 190Acylazide[CX3](=[OX1])[NX2]~[NX2]~[NX1]
- * 191Diazo[$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]
- * 192Diazonium[#6][NX2+]#[NX1]
- * 193Nitrosamine[#7;!$(N*=O)][NX2]=[OX1]
- * 194Nitrosamide[NX2](=[OX1])N-*=O
- * 195N-Oxide[$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]
- * 196Hydrazine[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
- * 197Hydrazone[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
- * 198Hydroxylamine[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
- * 199Sulfon[$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
- * 200Sulfoxide[$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
- * 201Sulfonium[S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
- * 202Sulfuric acid[SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
- * 203Sulfuric monoester[SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
- * 204Sulfuric diester[SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
- * 205Sulfuric monoamide[SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
- * 206Sulfuric diamide[SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 207Sulfuric esteramide[SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
- * 208Sulfuric derivative[SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
- * 209Sulfonic acid[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
- * 210Sulfonamide[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 211Sulfonic ester[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
- * 212Sulfonic halide[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
- * 213Sulfonic derivative[SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
- * 214Sulfinic acid[SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
- * 215Sulfinic amide[SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 216Sulfinic ester[SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
- * 217Sulfinic halide[SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
- * 218Sulfinic derivative[SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
- * 219Sulfenic acid[SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
- * 220Sulfenic amide[SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 221Sulfenic ester[SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
- * 222Sulfenic halide[SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
- * 223Sulfenic derivative[SX2;$([H1]),$([H0][#6])][!#6]
- * 224Phosphine[PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
- * 225Phosphine oxide[PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
- * 226Phosphonium[P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
- * 227Phosphorylen[PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
- * 228Phosphonic acid[PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
- * 229Phosphonic monoester[PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
- * 230Phosphonic diester[PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
- * 231Phosphonic monoamide[PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 232Phosphonic diamide[PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 233Phosphonic esteramide[PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 234Phosphonic acid derivative[PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
- * 235Phosphoric acid[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
- * 236Phosphoric monoester[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
- * 237Phosphoric diester[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
- * 238Phosphoric triester[PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
- * 239Phosphoric monoamide[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 240Phosphoric diamide[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 241Phosphoric triamide[PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 242Phosphoric monoestermonoamide[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 243Phosphoric diestermonoamide[PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 244Phosphoric monoesterdiamide[PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 245Phosphoric acid derivative[PX4D4](=[!#6])([!#6])([!#6])[!#6]
- * 246Phosphinic acid[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
- * 247Phosphinic ester[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
- * 248Phosphinic amide[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 249Phosphinic acid derivative[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
- * 250Phosphonous acid[PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
- * 251Phosphonous monoester[PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
- * 252Phosphonous diester[PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
- * 253Phosphonous monoamide[PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 254Phosphonous diamide[PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 255Phosphonous esteramide[PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 256Phosphonous derivatives[PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
- * 257Phosphinous acid[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
- * 258Phosphinous ester[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
- * 259Phosphinous amide[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
- * 260Phosphinous derivatives[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
- * 261Quart silane[SiX4]([#6])([#6])([#6])[#6]
- * 262Non-quart silane[SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
- * 263Silylmonohalide[SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
- * 264Het trialkylsilane[SiX4]([!#6])([#6])([#6])[#6]
- * 265Dihet dialkylsilane[SiX4]([!#6])([!#6])([#6])[#6]
- * 266Trihet alkylsilane[SiX4]([!#6])([!#6])([!#6])[#6]
- * 267Silicic acid derivative[SiX4]([!#6])([!#6])([!#6])[!#6]
- * 268Trialkylborane[BX3]([#6])([#6])[#6]
- * 269Boric acid derivatives[BX3]([!#6])([!#6])[!#6]
- * 270Boronic acid derivative[BX3]([!#6])([!#6])[!#6]
- * 271Borohydride[BH1,BH2,BH3,BH4]
- * 272Quaternary boron[BX4]
+ * 0Primary carbon{@code [CX4H3][#6]}
+ * 1Secondary carbon{@code [CX4H2]([#6])[#6]}
+ * 2Tertiary carbon{@code [CX4H1]([#6])([#6])[#6]}
+ * 3Quaternary carbon{@code [CX4]([#6])([#6])([#6])[#6]}
+ * 4Alkene{@code [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]}
+ * 5Alkyne{@code [CX2]#[CX2]}
+ * 6Allene{@code [CX3]=[CX2]=[CX3]}
+ * 7Alkylchloride{@code [ClX1][CX4]}
+ * 8Alkylfluoride{@code [FX1][CX4]}
+ * 9Alkylbromide{@code [BrX1][CX4]}
+ * 10Alkyliodide{@code [IX1][CX4]}
+ * 11Alcohol{@code [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]}
+ * 12Primary alcohol{@code [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]}
+ * 13Secondary alcohol{@code [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]}
+ * 14Tertiary alcohol{@code [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]}
+ * 15Dialkylether{@code [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]}
+ * 16Dialkylthioether{@code [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]}
+ * 17Alkylarylether{@code [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]}
+ * 18Diarylether{@code [c][OX2][c]}
+ * 19Alkylarylthioether{@code [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]}
+ * 20Diarylthioether{@code [c][SX2][c]}
+ * 21Oxonium{@code [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]}
+ * 22Amine{@code [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]}
+ * 23Primary aliph amine{@code [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]}
+ * 24Secondary aliph amine{@code [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]}
+ * 25Tertiary aliph amine{@code [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]}
+ * 26Quaternary aliph ammonium{@code [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]}
+ * 27Primary arom amine{@code [NX3H2+0,NX4H3+]c}
+ * 28Secondary arom amine{@code [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]}
+ * 29Tertiary arom amine{@code [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]}
+ * 30Quaternary arom ammonium{@code [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]}
+ * 31Secondary mixed amine{@code [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]}
+ * 32Tertiary mixed amine{@code [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]}
+ * 33Quaternary mixed ammonium{@code [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]}
+ * 34Ammonium{@code [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]}
+ * 35Alkylthiol{@code [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]}
+ * 36Dialkylthioether{@code [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]}
+ * 37Alkylarylthioether{@code [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]}
+ * 38Disulfide{@code [SX2D2][SX2D2]}
+ * 391,2-Aminoalcohol{@code [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]}
+ * 401,2-Diol{@code [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]}
+ * 411,1-Diol{@code [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]}
+ * 42Hydroperoxide{@code [OX2H][OX2]}
+ * 43Peroxo{@code [OX2D2][OX2D2]}
+ * 44Organolithium compounds{@code [LiX1][#6,#14]}
+ * 45Organomagnesium compounds{@code [MgX2][#6,#14]}
+ * 46Organometallic compounds{@code [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]}
+ * 47Aldehyde{@code [$([CX3H][#6]),$([CX3H2])]=[OX1]}
+ * 48Ketone{@code [#6][CX3](=[OX1])[#6]}
+ * 49Thioaldehyde{@code [$([CX3H][#6]),$([CX3H2])]=[SX1]}
+ * 50Thioketone{@code [#6][CX3](=[SX1])[#6]}
+ * 51Imine{@code [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]}
+ * 52Immonium{@code [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]}
+ * 53Oxime{@code [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]}
+ * 54Oximether{@code [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]}
+ * 55Acetal{@code [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]}
+ * 56Hemiacetal{@code [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]}
+ * 57Aminal{@code [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]}
+ * 58Hemiaminal{@code [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]}
+ * 59Thioacetal{@code [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]}
+ * 60Thiohemiacetal{@code [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]}
+ * 61Halogen acetal like{@code [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]}
+ * 62Acetal like{@code [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]}
+ * 63Halogenmethylen ester and similar{@code [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]}
+ * 64NOS methylen ester and similar{@code [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]}
+ * 65Hetero methylen ester and similar{@code [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]}
+ * 66Cyanhydrine{@code [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]}
+ * 67Chloroalkene{@code [ClX1][CX3]=[CX3]}
+ * 68Fluoroalkene{@code [FX1][CX3]=[CX3]}
+ * 69Bromoalkene{@code [BrX1][CX3]=[CX3]}
+ * 70Iodoalkene{@code [IX1][CX3]=[CX3]}
+ * 71Enol{@code [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]}
+ * 72Endiol{@code [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]}
+ * 73Enolether{@code [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]}
+ * 74Enolester{@code [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]}
+ * 75Enamine{@code [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]}
+ * 76Thioenol{@code [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]}
+ * 77Thioenolether{@code [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]}
+ * 78Acylchloride{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]}
+ * 79Acylfluoride{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]}
+ * 80Acylbromide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]}
+ * 81Acyliodide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]}
+ * 82Acylhalide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]}
+ * 83Carboxylic acid{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]}
+ * 84Carboxylic ester{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]}
+ * 85Lactone{@code [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]}
+ * 86Carboxylic anhydride{@code [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])}
+ * 87Carboxylic acid derivative{@code [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]}
+ * 88Carbothioic acid{@code [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]}
+ * 89Carbothioic S ester{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]}
+ * 90Carbothioic S lactone{@code [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]}
+ * 91Carbothioic O ester{@code [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]}
+ * 92Carbothioic O lactone{@code [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]}
+ * 93Carbothioic halide{@code [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]}
+ * 94Carbodithioic acid{@code [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]}
+ * 95Carbodithioic ester{@code [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]}
+ * 96Carbodithiolactone{@code [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]}
+ * 97Amide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 98Primary amide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]}
+ * 99Secondary amide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]}
+ * 100Tertiary amide{@code [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]}
+ * 101Lactam{@code [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 102Alkyl imide{@code [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])}
+ * 103N hetero imide{@code [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])}
+ * 104Imide acidic{@code [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])}
+ * 105Thioamide{@code [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 106Thiolactam{@code [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 107Oximester{@code [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]}
+ * 108Amidine{@code [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]}
+ * 109Hydroxamic acid{@code [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]}
+ * 110Hydroxamic acid ester{@code [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]}
+ * 111Imidoacid{@code [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]}
+ * 112Imidoacid cyclic{@code [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]}
+ * 113Imidoester{@code [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]}
+ * 114Imidolactone{@code [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]}
+ * 115Imidothioacid{@code [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]}
+ * 116Imidothioacid cyclic{@code [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]}
+ * 117Imidothioester{@code [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]}
+ * 118Imidothiolactone{@code [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]}
+ * 119Amidine{@code [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]}
+ * 120Imidolactam{@code [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]}
+ * 121Imidoylhalide{@code [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]}
+ * 122Imidoylhalide cyclic{@code [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]}
+ * 123Amidrazone{@code [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]}
+ * 124Alpha aminoacid{@code [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]}
+ * 125Alpha hydroxyacid{@code [OX2H][C][CX3](=[OX1])[OX2H,OX1-]}
+ * 126Peptide middle{@code [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]}
+ * 127Peptide C term{@code [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]}
+ * 128Peptide N term{@code [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]}
+ * 129Carboxylic orthoester{@code [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]}
+ * 130Ketene{@code [CX3]=[CX2]=[OX1]}
+ * 131Ketenacetal{@code [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]}
+ * 132Nitrile{@code [NX1]#[CX2]}
+ * 133Isonitrile{@code [CX1-]#[NX2+]}
+ * 134Vinylogous carbonyl or carboxyl derivative{@code [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]}
+ * 135Vinylogous acid{@code [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]}
+ * 136Vinylogous ester{@code [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]}
+ * 137Vinylogous amide{@code [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 138Vinylogous halide{@code [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]}
+ * 139Carbonic acid dieester{@code [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]}
+ * 140Carbonic acid esterhalide{@code [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]}
+ * 141Carbonic acid monoester{@code [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]}
+ * 142Carbonic acid derivatives{@code [!#6][#6X3](=[!#6])[!#6]}
+ * 143Thiocarbonic acid dieester{@code [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]}
+ * 144Thiocarbonic acid esterhalide{@code [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]}
+ * 145Thiocarbonic acid monoester{@code [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]}
+ * 146Urea{@code [#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]}
+ * 147Thiourea{@code [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]}
+ * 148Isourea{@code [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]}
+ * 149Isothiourea{@code [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]}
+ * 150Guanidine{@code [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]}
+ * 151Carbaminic acid{@code [NX3]C(=[OX1])[O;X2H,X1-]}
+ * 152Urethan{@code [#7X3][#6](=[OX1])[#8X2][#6]}
+ * 153Biuret{@code [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]}
+ * 154Semicarbazide{@code [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]}
+ * 155Carbazide{@code [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]}
+ * 156Semicarbazone{@code [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]}
+ * 157Carbazone{@code [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]}
+ * 158Thiosemicarbazide{@code [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]}
+ * 159Thiocarbazide{@code [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]}
+ * 160Thiosemicarbazone{@code [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]}
+ * 161Thiocarbazone{@code [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]}
+ * 162Isocyanate{@code [NX2]=[CX2]=[OX1]}
+ * 163Cyanate{@code [OX2][CX2]#[NX1]}
+ * 164Isothiocyanate{@code [NX2]=[CX2]=[SX1]}
+ * 165Thiocyanate{@code [SX2][CX2]#[NX1]}
+ * 166Carbodiimide{@code [NX2]=[CX2]=[NX2]}
+ * 167Orthocarbonic derivatives{@code [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]}
+ * 168Phenol{@code [OX2H][c]}
+ * 1691,2-Diphenol{@code [OX2H][c][c][OX2H]}
+ * 170Arylchloride{@code [Cl][c]}
+ * 171Arylfluoride{@code [F][c]}
+ * 172Arylbromide{@code [Br][c]}
+ * 173Aryliodide{@code [I][c]}
+ * 174Arylthiol{@code [SX2H][c]}
+ * 175Iminoarene{@code [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]}
+ * 176Oxoarene{@code [c]=[OX1]}
+ * 177Thioarene{@code [c]=[SX1]}
+ * 178Hetero N basic H{@code [nX3H1+0]}
+ * 179Hetero N basic no H{@code [nX3H0+0]}
+ * 180Hetero N nonbasic{@code [nX2,nX3+]}
+ * 181Hetero O{@code [o]}
+ * 182Hetero S{@code [sX2]}
+ * 183Heteroaromatic{@code [a;!c]}
+ * 184Nitrite{@code [NX2](=[OX1])[O;$([X2]),$([X1-])]}
+ * 185Thionitrite{@code [SX2][NX2]=[OX1]}
+ * 186Nitrate{@code [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]}
+ * 187Nitro{@code [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]}
+ * 188Nitroso{@code [NX2](=[OX1])[!#7;!#8]}
+ * 189Azide{@code [NX1]~[NX2]~[NX2,NX1]}
+ * 190Acylazide{@code [CX3](=[OX1])[NX2]~[NX2]~[NX1]}
+ * 191Diazo{@code [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]}
+ * 192Diazonium{@code [#6][NX2+]#[NX1]}
+ * 193Nitrosamine{@code [#7;!$(N*=O)][NX2]=[OX1]}
+ * 194Nitrosamide{@code [NX2](=[OX1])N-*=O}
+ * 195N-Oxide{@code [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]}
+ * 196Hydrazine{@code [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]}
+ * 197Hydrazone{@code [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]}
+ * 198Hydroxylamine{@code [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]}
+ * 199Sulfon{@code [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]}
+ * 200Sulfoxide{@code [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]}
+ * 201Sulfonium{@code [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]}
+ * 202Sulfuric acid{@code [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]}
+ * 203Sulfuric monoester{@code [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]}
+ * 204Sulfuric diester{@code [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]}
+ * 205Sulfuric monoamide{@code [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]}
+ * 206Sulfuric diamide{@code [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 207Sulfuric esteramide{@code [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]}
+ * 208Sulfuric derivative{@code [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]}
+ * 209Sulfonic acid{@code [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]}
+ * 210Sulfonamide{@code [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 211Sulfonic ester{@code [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]}
+ * 212Sulfonic halide{@code [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]}
+ * 213Sulfonic derivative{@code [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]}
+ * 214Sulfinic acid{@code [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]}
+ * 215Sulfinic amide{@code [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 216Sulfinic ester{@code [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]}
+ * 217Sulfinic halide{@code [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]}
+ * 218Sulfinic derivative{@code [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]}
+ * 219Sulfenic acid{@code [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]}
+ * 220Sulfenic amide{@code [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 221Sulfenic ester{@code [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]}
+ * 222Sulfenic halide{@code [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]}
+ * 223Sulfenic derivative{@code [SX2;$([H1]),$([H0][#6])][!#6]}
+ * 224Phosphine{@code [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]}
+ * 225Phosphine oxide{@code [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]}
+ * 226Phosphonium{@code [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]}
+ * 227Phosphorylen{@code [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]}
+ * 228Phosphonic acid{@code [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]}
+ * 229Phosphonic monoester{@code [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]}
+ * 230Phosphonic diester{@code [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]}
+ * 231Phosphonic monoamide{@code [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 232Phosphonic diamide{@code [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 233Phosphonic esteramide{@code [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 234Phosphonic acid derivative{@code [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]}
+ * 235Phosphoric acid{@code [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]}
+ * 236Phosphoric monoester{@code [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]}
+ * 237Phosphoric diester{@code [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]}
+ * 238Phosphoric triester{@code [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]}
+ * 239Phosphoric monoamide{@code [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 240Phosphoric diamide{@code [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 241Phosphoric triamide{@code [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 242Phosphoric monoestermonoamide{@code [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 243Phosphoric diestermonoamide{@code [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 244Phosphoric monoesterdiamide{@code [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 245Phosphoric acid derivative{@code [PX4D4](=[!#6])([!#6])([!#6])[!#6]}
+ * 246Phosphinic acid{@code [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]}
+ * 247Phosphinic ester{@code [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]}
+ * 248Phosphinic amide{@code [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 249Phosphinic acid derivative{@code [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]}
+ * 250Phosphonous acid{@code [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]}
+ * 251Phosphonous monoester{@code [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]}
+ * 252Phosphonous diester{@code [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]}
+ * 253Phosphonous monoamide{@code [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 254Phosphonous diamide{@code [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 255Phosphonous esteramide{@code [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 256Phosphonous derivatives{@code [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]}
+ * 257Phosphinous acid{@code [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]}
+ * 258Phosphinous ester{@code [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]}
+ * 259Phosphinous amide{@code [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]}
+ * 260Phosphinous derivatives{@code [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]}
+ * 261Quart silane{@code [SiX4]([#6])([#6])([#6])[#6]}
+ * 262Non-quart silane{@code [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]}
+ * 263Silylmonohalide{@code [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]}
+ * 264Het trialkylsilane{@code [SiX4]([!#6])([#6])([#6])[#6]}
+ * 265Dihet dialkylsilane{@code [SiX4]([!#6])([!#6])([#6])[#6]}
+ * 266Trihet alkylsilane{@code [SiX4]([!#6])([!#6])([!#6])[#6]}
+ * 267Silicic acid derivative{@code [SiX4]([!#6])([!#6])([!#6])[!#6]}
+ * 268Trialkylborane{@code [BX3]([#6])([#6])[#6]}
+ * 269Boric acid derivatives{@code [BX3]([!#6])([!#6])[!#6]}
+ * 270Boronic acid derivative{@code [BX3]([!#6])([!#6])[!#6]}
+ * 271Borohydride{@code [BH1,BH2,BH3,BH4]}
+ * 272Quaternary boron{@code [BX4]}
  * 273Aromatica
- * 274Heterocyclic[!#6;!R0]
- * 275Epoxide[OX2r3]1[#6r3][#6r3]1
- * 276NH aziridine[NX3H1r3]1[#6r3][#6r3]1
- * 277Spiro[D4R;$(*(@*)(@*)(@*)@*)]
- * 278Annelated rings[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]
- * 279Bridged rings[R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]
- * 280Sugar pattern 1[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
- * 281Sugar pattern 2[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
- * 282Sugar pattern combi[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
- * 283Sugar pattern 2 reducing[OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
- * 284Sugar pattern 2 alpha[OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
- * 285Sugar pattern 2 beta[OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+ * 274Heterocyclic{@code [!#6;!R0]}
+ * 275Epoxide{@code [OX2r3]1[#6r3][#6r3]1}
+ * 276NH aziridine{@code [NX3H1r3]1[#6r3][#6r3]1}
+ * 277Spiro{@code [D4R;$(*(@*)(@*)(@*)@*)]}
+ * 278Annelated rings{@code [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]}
+ * 279Bridged rings{@code [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]}
+ * 280Sugar pattern 1{@code [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]}
+ * 281Sugar pattern 2{@code [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]}
+ * 282Sugar pattern combi{@code [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]}
+ * 283Sugar pattern 2 reducing{@code [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]}
+ * 284Sugar pattern 2 alpha{@code [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]}
+ * 285Sugar pattern 2 beta{@code [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]}
  * 286Conjugated double bond*=*[*]=,#,:[*]
  * 287Conjugated tripple bond*#*[*]=,#,:[*]
  * 288Cis double bond*/[D2]=[D2]/*
  * 289Trans double bond*/[D2]=[D2]/*
- * 290Mixed anhydrides[$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
- * 291Halogen on hetero[FX1,ClX1,BrX1,IX1][!#6]
- * 292Halogen multi subst[F,Cl,Br,I;!$([X1]);!$([X0-])]
- * 293Trifluoromethyl[FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
- * 294C ONS bond[#6]~[#7,#8,#16]
- * 295Charged[!+0]
- * 296Anion[-1,-2,-3,-4,-5,-6,-7]
- * 297Kation[+1,+2,+3,+4,+5,+6,+7]
+ * 290Mixed anhydrides{@code [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]}
+ * 291Halogen on hetero{@code [FX1,ClX1,BrX1,IX1][!#6]}
+ * 292Halogen multi subst{@code [F,Cl,Br,I;!$([X1]);!$([X0-])]}
+ * 293Trifluoromethyl{@code [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])}
+ * 294C ONS bond{@code [#6]~[#7,#8,#16]}
+ * 295Charged{@code [!+0]}
+ * 296Anion{@code [-1,-2,-3,-4,-5,-6,-7]}
+ * 297Kation{@code [+1,+2,+3,+4,+5,+6,+7]}
  * 298Salt([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
- * 2991,3-Tautomerizable[$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]
- * 3001,5-Tautomerizable[$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]
- * 301Rotatable bond[!$(*#*)&!D1]-!@[!$(*#*)&!D1]
- * 302Michael acceptor[CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
- * 303Dicarbodiazene[CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
- * 304CH-acidic[$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
- * 305CH-acidic strong[CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]
- * 306Chiral center specified[$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
+ * 2991,3-Tautomerizable{@code [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]}
+ * 3001,5-Tautomerizable{@code [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]}
+ * 301Rotatable bond{@code [!$(*#*)&!D1]-!@[!$(*#*)&!D1]}
+ * 302Michael acceptor{@code [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]}
+ * 303Dicarbodiazene{@code [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])}
+ * 304CH-acidic{@code [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]}
+ * 305CH-acidic strong{@code [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]}
+ * 306Chiral center specified{@code [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]}
  * 
  *
  *
diff --git a/misc/extra/src/main/java/org/openscience/cdk/tools/GridGenerator.java b/misc/extra/src/main/java/org/openscience/cdk/tools/GridGenerator.java
index 5a06beebca..b83a556e64 100644
--- a/misc/extra/src/main/java/org/openscience/cdk/tools/GridGenerator.java
+++ b/misc/extra/src/main/java/org/openscience/cdk/tools/GridGenerator.java
@@ -262,10 +262,10 @@ public void writeGridInPmeshFormat(String outPutFileName) throws IOException {
     /**
      * Method transforms the grid into pmesh format. Only grid points
      * with specific value defined with cutoff are considered.
-     * 
+     * 
{@code
      * cutoff <0, the values considered must be <=cutoff
      * cutoff >0, the values considered must be >=cutoff
-     * 

+     * }

      */
     public void writeGridInPmeshFormat(String outPutFileName, double cutOff) throws IOException {
         BufferedWriter writer = new BufferedWriter(new FileWriter(outPutFileName + ".pmesh"));
diff --git a/storage/io/src/main/java/org/openscience/cdk/io/ShelXReader.java b/storage/io/src/main/java/org/openscience/cdk/io/ShelXReader.java
index f8b8b856d8..9caa88dfd6 100644
--- a/storage/io/src/main/java/org/openscience/cdk/io/ShelXReader.java
+++ b/storage/io/src/main/java/org/openscience/cdk/io/ShelXReader.java
@@ -56,7 +56,7 @@
  * 
A reader for ShelX files. It currently supports ShelXL.
  *
  * 
The ShelXL format is described on the net:
- * 
  * http://www.msg.ucsf.edu/local/programs/shelxl/ch_07.html.
  *
  * @cdk.module io
diff --git a/storage/ioformats/src/main/java/org/openscience/cdk/tools/DataFeatures.java b/storage/ioformats/src/main/java/org/openscience/cdk/tools/DataFeatures.java
index d01417093b..17a2cae6bc 100644
--- a/storage/ioformats/src/main/java/org/openscience/cdk/tools/DataFeatures.java
+++ b/storage/ioformats/src/main/java/org/openscience/cdk/tools/DataFeatures.java
@@ -30,10 +30,10 @@
  *
  * 
To test whether a IChemFormat supports a certain feature, the
  * following code can be used:
- * 
+ * 
{@code
  * int features = new XYZFormat().getSupportedDataFeatures();
  * boolean has3DCoords = (features & HAS_3D_COORDINATES) == HAS_3D_COORDINATES;
- * 

+ * }

  *
  * 
This list of constants matches the latest Blue Obelisk Data Features Ontology.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
index ee15bfc388..2dd930e674 100644
--- a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
+++ b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
@@ -150,7 +150,7 @@
  * The output order is obtained by parsing in an auxiliary array during creation. The
  * following snippet demonstrates how we can write coordinates in order.
  *
- * 
+ * 
{@code
  * IAtomContainer  mol = ...;
  * SmilesGenerator sg  = new SmilesGenerator(SmiFlavor.Generic);
  *
@@ -169,7 +169,7 @@
  * // SMILES string suffixed by the coordinates
  * String smi2d = smi + " " + Arrays.toString(coords);
  *
- * 

+ * }

  *
  * Using the output order of SMILES forms the basis of
  * 
@@ -178,7 +178,7 @@
  * grouping (for salts in reactions), polymer repeats, multi center bonds, and coordinates.
  * The CXSMILES layer is appended after the SMILES so that parser which don't interpret it
  * can ignore it.
- * 
+ *
  * The two aggregate flavours are {@link SmiFlavor#CxSmiles} and {@link SmiFlavor#CxSmilesWithCoords}.
  * As with other flavours, fine grain control is possible {@see SmiFlavor}.
  * 

@@ -369,7 +369,7 @@ public String create(IAtomContainer molecule) throws CDKException {
      * where 2D coordinates are stored with a SMILES string. This method
      * forms the basis of CXSMILES.
      *
-     * 
+     * 
{@code
      * IAtomContainer  mol = ...;
      * SmilesGenerator sg  = new SmilesGenerator();
      *
@@ -388,7 +388,7 @@ public String create(IAtomContainer molecule) throws CDKException {
      * // SMILES string suffixed by the coordinates
      * String smi2d = smi + " " + Arrays.toString(coords);
      *
-     * 

+     * }

      *
      * @param molecule the molecule to write
      * @param order    array to store the output order of atoms
@@ -408,7 +408,7 @@ public String create(IAtomContainer molecule, int[] order) throws CDKException {
      * where 2D coordinates are stored with a SMILES string. This method
      * forms the basis of CXSMILES.
      *
-     * 
+     * 
{@code
      * IAtomContainer  mol = ...;
      * SmilesGenerator sg  = new SmilesGenerator();
      *
@@ -427,7 +427,7 @@ public String create(IAtomContainer molecule, int[] order) throws CDKException {
      * // SMILES string suffixed by the coordinates
      * String smi2d = smi + " " + Arrays.toString(coords);
      *
-     * 

+     * }

      *
      * @param molecule the molecule to write
      * @param order    array to store the output order of atoms
diff --git a/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java b/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java
index 811dc9f832..889c918b9a 100644
--- a/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java
+++ b/tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java
@@ -51,9 +51,9 @@
  *
  * 

  * Now let orb(0) = {g(0) : g ∈ G} be the orbit of 0 under G. Then |orb(0)|
- * (the size of the orbit) is n0 for some integer 0 < n0
- * <= n and write orb(0) = {x0,1, x0,2, ...,
- * x0,n0} and for each i, 1 <= i <= n0 choose
+ * (the size of the orbit) is n0 for some integer 0 < n0
+ * ≤ n and write orb(0) = {x0,1, x0,2, ...,
+ * x0,n0} and for each i, 1 ≤ i ≤ n0 choose
  * some h0,1 in G such that h0,i(0) = x0,1. Set
  * U0 = {h0,1, ..., h0,n0}.
  *