Allow aromaticity status of bonds to be preserved through kekulisatio…

…n/localisation.
johnmay · Jul 20, 2024 · 166f6b8 · 166f6b8
1 parent 61c10fc
commit 166f6b8
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Showing 8 changed files with 204 additions and 91 deletions.
diff --git a/core/src/main/java/uk/ac/ebi/beam/Bond.java b/core/src/main/java/uk/ac/ebi/beam/Bond.java
@@ -106,6 +106,34 @@ public enum Bond {
             return UP;
         }
 
+        @Override boolean directional() {
+            return true;
+        }
+    },
+    /**
+     * This is an internal quirk to allow the aromaticity of input to be preserved when
+     * we kekulize. The up/down bonds may be between aromatic atoms:
+     * {@code O=c1cccc\c1=C/C} Since the double bond is exo, the / \ must be aromatic.
+     */
+    UP_AROMATIC("/", 1) {
+        @Override public Bond inverse() {
+            return DOWN_AROMATIC;
+        }
+
+        @Override boolean directional() {
+            return true;
+        }
+    },
+    /**
+     * This is an internal quirk to allow the aromaticity of input to be preserved when
+     * we kekulize. The up/down bonds may be between aromatic atoms:
+     * {@code O=c1cccc\c1=C/C} Since the double bond is exo, the / \ must be aromatic.
+     */
+    DOWN_AROMATIC("\\", 1) {
+        @Override public Bond inverse() {
+            return UP_AROMATIC;
+        }
+
         @Override boolean directional() {
             return true;
         }

diff --git a/core/src/main/java/uk/ac/ebi/beam/Localise.java b/core/src/main/java/uk/ac/ebi/beam/Localise.java
@@ -95,6 +95,20 @@ private static Graph assign(Graph g, BitSet subset, BitSet aromatic, Matching m)
                 int v = e.other(u);
                 if (v < u) {
                     switch (e.bond()) {
+                        case UP:
+                        case UP_AROMATIC:
+                            if (aromatic.get(u) && aromatic.get(v))
+                                e.bond(Bond.UP_AROMATIC);
+                            else
+                                e.bond(Bond.UP);
+                            break;
+                        case DOWN:
+                        case DOWN_AROMATIC:
+                            if (aromatic.get(u) && aromatic.get(v))
+                                e.bond(Bond.DOWN_AROMATIC);
+                            else
+                                e.bond(Bond.DOWN);
+                            break;
                         case SINGLE:
                             if (aromatic.get(u) && aromatic.get(v)) {
                                 e.bond(Bond.SINGLE);