From 8eb1cbea1ac243904e093088bdf8b02d486bbf5e Mon Sep 17 00:00:00 2001
From: Pascal Serrarens <pascal@passer.life>
Date: Fri, 6 Feb 2026 12:17:42 +0100
Subject: [PATCH] Fix brain prefab cloning

---
 Cluster.cs                 |  6 +++---
 Editor/ClusterInspector.cs | 24 ++++++++++--------------
 Nucleus.cs                 |  5 +++--
 3 files changed, 16 insertions(+), 19 deletions(-)

diff --git a/Cluster.cs b/Cluster.cs
index 9d29581..e2a9fae 100644
--- a/Cluster.cs
+++ b/Cluster.cs
@@ -42,13 +42,13 @@ public class Cluster : Nucleus {
 
         // Now clone the connections
         for (int nucleusIx = 0; nucleusIx < prefabNuclei.Length; nucleusIx++) {
-            Nucleus receptor = prefabNuclei[nucleusIx];
+            Nucleus prefabNucleus = prefabNuclei[nucleusIx];
             Nucleus clonedReceptor = clonedNuclei[nucleusIx];
             if (clonedReceptor == null)
                 continue;
 
             // Copy the receivers, which will also create the synapses
-            foreach (Nucleus receiver in receptor.receivers) {
+            foreach (Nucleus receiver in prefabNucleus.receivers) {
                 int ix = GetNucleusIndex(prefabNuclei, receiver);
                 if (ix < 0)
                     continue;
@@ -60,7 +60,7 @@ public class Cluster : Nucleus {
                 float weight = 1;
                 foreach (Synapse synapse in receiver.synapses) {
                     // Find the weight for this synapse
-                    if (synapse.nucleus == receptor) {
+                    if (synapse.nucleus == prefabNucleus) {
                         weight = synapse.weight;
                         break;
                     }
diff --git a/Editor/ClusterInspector.cs b/Editor/ClusterInspector.cs
index 45950e1..541134f 100644
--- a/Editor/ClusterInspector.cs
+++ b/Editor/ClusterInspector.cs
@@ -676,23 +676,19 @@ public class ClusterInspector : Editor {
             if (cluster == null)
                 return;
 
-            IEnumerable<string> synapseNuclei = this.currentNucleus.synapses.Select(synapse => synapse.nucleus != null ? synapse.nucleus.name : "");
-            //IEnumerable<string> perceptei = this.currentNucleus.brain.perceptei.Select(i => i.name).Except(synapseNuclei);
-            IEnumerable<string> nuclei = cluster.nuclei.Select(i => i.name).Except(synapseNuclei);
-            //string[] names = perceptei.Concat(nuclei).ToArray();
-            string[] names = nuclei.ToArray();
+            IEnumerable<Nucleus> synapseNuclei = this.currentNucleus.synapses
+                .Where(synapse => synapse.nucleus != null)
+                .Select(synapse => synapse.nucleus);
+
+            IEnumerable<Nucleus> nuclei = cluster.nuclei
+                .Except(synapseNuclei);
+            IEnumerable<string> nucleiNames = nuclei.Select(n => n.name);
+
+            string[] names = nucleiNames.ToArray();
             int selectedIndex = -1;
             selectedIndex = EditorGUILayout.Popup("Connect to", selectedIndex, names);
             if (selectedIndex >= 0) {
-                // if (selectedIndex < perceptei.Count()) {
-                //     Nucleus n = this.currentNucleus.brain.perceptei[selectedIndex];
-                //     n.AddReceiver(this.currentNucleus);
-                // }
-                // else {
-                //     Nucleus n = this.currentNucleus.brain.nuclei[selectedIndex - perceptei.Count()];
-                //     n.AddReceiver(this.currentNucleus);
-                // }
-                Nucleus receptor = cluster.nuclei[selectedIndex];
+                Nucleus receptor = nuclei.ElementAt(selectedIndex);
                 receptor.AddReceiver(this.currentNucleus);
             }
         }
diff --git a/Nucleus.cs b/Nucleus.cs
index 9847a68..8652637 100644
--- a/Nucleus.cs
+++ b/Nucleus.cs
@@ -91,8 +91,9 @@ public abstract class Nucleus {
         UpdateStateIsolated(new float3(0, 0, 0));
     }
 
-    public virtual void UpdateStateIsolated(float3 bias) {
-    }
+    public abstract void UpdateStateIsolated(float3 bias);
+    // public virtual void UpdateStateIsolated(float3 bias) {
+    // }
 
     public virtual void UpdateNuclei() {
         this.stale++;