starting to work with 6 cluster receptors

Cluster.cs

@@ -113,6 +113,11 @@ public class Cluster : Nucleus {
                 clonedNucleus.nucleiArray = clonedFirstNucleus.nucleiArray;
             }
         }
+
+        foreach (Nucleus nucleus in this.clusterNuclei) {
+            if (nucleus is Cluster clonedSubCluster)
+                RestoreAllExternalReceivers(clonedSubCluster, this.prefab, this);
+        }
     }
 
     // Sort the nuclei in a correct evaluation order
@@ -204,7 +209,44 @@ public class Cluster : Nucleus {
         return clone;
     }
 
+    private static void RestoreAllExternalReceivers(Cluster clonedCluster, ClusterPrefab prefabParent, Cluster clonedParent) {
+        int clonedClusterIx = GetNucleusIndex(clonedParent.clusterNuclei, clonedCluster);
+        if (prefabParent.nuclei[clonedClusterIx] is not Cluster sourceCluster)
+            return;
+
+        for (int nucleusIx = 0; nucleusIx < sourceCluster.clusterNuclei.Count; nucleusIx++) {
+            Nucleus sourceNucleus = sourceCluster.clusterNuclei[nucleusIx];
+            if (sourceNucleus is not Neuron sourceNeuron)
+                continue;
+
+            Nucleus clonedNucleus = clonedCluster.clusterNuclei[nucleusIx];
+            if (clonedNucleus is not Neuron clonedNeuron)
+                continue;
+
+            // copy the receivers (and thus synapses) from the source to the clone
+            foreach (Nucleus receiver in sourceNeuron.receivers) {
+                int ix = GetNucleusIndex(prefabParent.nuclei, receiver);
+                if (ix < 0 || ix >= clonedParent.clusterNuclei.Count)
+                    continue;
+
+                Nucleus clonedReceiver = clonedParent.clusterNuclei[ix];
+
+                // Find the synapse for the weight
+                float weight = 1;
+                foreach (Synapse synapse in receiver.synapses) {
+                    // Find the weight for this synapse
+                    if (synapse.nucleus == sourceNucleus) {
+                        weight = synapse.weight;
+                        break;
+                    }
+                }
+
+                clonedNeuron.AddReceiver(clonedReceiver, weight);
+            }
+        }
+    }
     protected void RestoreExternalReceivers(Cluster clone, ClusterPrefab prefabParent, Cluster clonedParent) {
+        // Loop over all nuclei of this (the prefab of the clone?)
         for (int nucleusIx = 0; nucleusIx < this.clusterNuclei.Count; nucleusIx++) {
             Nucleus prefabNucleus = this.clusterNuclei[nucleusIx];
             if (prefabNucleus is not Neuron prefabNeuron)
@@ -217,7 +259,7 @@ public class Cluster : Nucleus {
             // Copy the receivers, which will also create the synapses
             foreach (Nucleus receiver in prefabNeuron.receivers) {
                 int ix = GetNucleusIndex(prefabParent.nuclei, receiver);
-                if (ix < 0)
+                if (ix < 0 || ix >= clonedParent.clusterNuclei.Count)
                     continue;
 
                 //if (clone.clusterNuclei[ix] is not Nucleus clonedReceiver)
@@ -249,7 +291,7 @@ public class Cluster : Nucleus {
         return -1;
     }
 
-    public int GetNucleusIndex(List<Nucleus> nuclei, Nucleus nucleus) {
+    public static int GetNucleusIndex(List<Nucleus> nuclei, Nucleus nucleus) {
         int i = 0;
         foreach (Nucleus nucleiElement in nuclei) {
             //for (int i = 0; i < nuclei.Length; i++) {
@@ -346,13 +388,13 @@ public class Cluster : Nucleus {
 
             //if (current is Neuron neuron) {
 
-                foreach (Nucleus receiver in receivers) {
+            foreach (Nucleus receiver in receivers) {
-                    if (visited.Contains(receiver)) {
+                if (visited.Contains(receiver)) {
-                        inDegree[receiver]--;
+                    inDegree[receiver]--;
-                        if (inDegree[receiver] == 0) // If all dependencies resolved
+                    if (inDegree[receiver] == 0) // If all dependencies resolved
-                            queue.Enqueue(receiver);
+                        queue.Enqueue(receiver);
-                    }
                 }
+            }
             //}
         }
 

ClusterReceptor.cs

@@ -31,7 +31,7 @@ public class ClusterReceptor : Cluster, IReceptor {
         //CloneFields(clone);
         // This cloned the prefab with the clusternuclei,
         // but did not clone the receivers outside the cluster
-        RestoreExternalReceivers(clone, this.clusterPrefab, parent);
+        //RestoreExternalReceivers(clone, this.clusterPrefab, parent);
 
         return clone;
     }
@@ -158,7 +158,7 @@ public class ClusterReceptor : Cluster, IReceptor {
             selectedReceiver.name = baseName + ": " + thingName;
         }
 
-        int inputIx = this.GetNucleusIndex(this.clusterNuclei, input);
+        int inputIx = GetNucleusIndex(this.clusterNuclei, input);
         if (inputIx < 0)
             return;
 

Editor/ClusterInspector.cs

@@ -1004,8 +1004,8 @@ public class ClusterInspector : Editor {
                 if (synapse.nucleus.parent is ClusterReceptor receptor) {
                     // the new nucleus is part of a (cluster) receptor,
                     // so we have to change all synapses to this nucleus array elements
-                    int oldNucleusIx = subCluster.GetNucleusIndex(subCluster.clusterNuclei, synapse.nucleus);
+                    int oldNucleusIx = Cluster.GetNucleusIndex(subCluster.clusterNuclei, synapse.nucleus);
-                    int newNucleusIx = subCluster.GetNucleusIndex(subCluster.clusterNuclei, newNucleus);
+                    int newNucleusIx = Cluster.GetNucleusIndex(subCluster.clusterNuclei, newNucleus);
                     foreach (Nucleus element in receptor.nucleiArray) {
                         if (element is not ClusterReceptor clusterReceptor)
                             continue;