From b8af5f3ccd1055c967f3875e678de2b9397ea97a Mon Sep 17 00:00:00 2001
From: hzhang <zhangh40@msu.edu>
Date: Wed, 26 Jun 2024 14:23:02 +0800
Subject: [PATCH] Bug Fix

---
 Concepts/Bond2D.cs                            | 57 +++++++++++
 GlobalAccess/GlobalScene.cs                   |  3 +-
 Scenes/Bond.cs                                | 34 -------
 Scenes/Bond.tscn                              | 18 ----
 Scenes/Bottle.cs                              |  2 +
 Scenes/CompoundConstructor.cs                 | 94 +++++++++++++++---
 Scenes/Flask.cs                               |  7 +-
 Scenes/Flask.tscn                             | 10 ++
 Scenes/FlaskContent.cs                        |  9 +-
 Scenes/MainControlPanel.cs                    | 44 ++++++++-
 Scenes/MainControlPanel.tscn                  | 13 ++-
 Scenes/MainScene.cs                           |  4 +-
 Scenes/MainScene.tscn                         |  2 +-
 Scenes/MultiBond.cs                           |  9 ++
 Scenes/SelfBond.cs                            | 25 +++++
 Scenes/SingleBond.cs                          | 97 +++++++++++++++++++
 Scenes/StringLoader.cs                        |  4 +-
 Scenes/VirtualChemDemo.tscn                   | 87 -----------------
 ...ualChemDemo.cs => VirtualChemistryDemo.cs} |  2 +-
 Tests/Line2d.cs                               | 71 ++++++++++++++
 Tests/Test2.cs                                | 12 +++
 Tests/TestScene.cs                            | 37 +++++++
 22 files changed, 467 insertions(+), 174 deletions(-)
 create mode 100644 Concepts/Bond2D.cs
 delete mode 100755 Scenes/Bond.cs
 delete mode 100644 Scenes/Bond.tscn
 create mode 100644 Scenes/MultiBond.cs
 create mode 100644 Scenes/SelfBond.cs
 create mode 100755 Scenes/SingleBond.cs
 delete mode 100644 Scenes/VirtualChemDemo.tscn
 rename Scenes/{VirtualChemDemo.cs => VirtualChemistryDemo.cs} (93%)
 create mode 100644 Tests/Line2d.cs
 create mode 100644 Tests/Test2.cs
 create mode 100644 Tests/TestScene.cs

diff --git a/Concepts/Bond2D.cs b/Concepts/Bond2D.cs
new file mode 100644
index 0000000..adb039e
--- /dev/null
+++ b/Concepts/Bond2D.cs
@@ -0,0 +1,57 @@
+using System.Collections.Generic;
+using System.Linq;
+using Godot;
+using VirtualChemDemo.Scenes;
+using VirtualChemistry.Chemistry.Bonds.Implements;
+
+namespace VirtualChemDemo.Concepts;
+
+public abstract partial class Bond2D : Line2D
+{
+    public BaseBond BondFrom { get; set; }
+    public BaseBond BondTo { get; set; }
+    public Atom AtomFrom { get; set; }
+    public Atom AtomTo { get; set; }
+    protected Label BondTypeA { get; set; }
+    protected Label BondTypeB { get; set; }
+    /*public string TypeA { get; set; }
+    public string TypeB { get; set; }*/
+    public int Index { get; set; } = 999;
+    public int Multi { get; set; } = -1;
+
+    public override void _Ready()
+    {
+        BondTypeA = GetNode<Label>("BondTypeA");
+        BondTypeB = GetNode<Label>("BondTypeB");
+    }
+
+    public void Reindex()
+    {
+        HashSet<Bond2D> bonds = new();
+        foreach (Bond2D bond in GlobalScene.CompoundConstructor.BondMap[AtomFrom])
+        {
+            if (
+                (bond.AtomTo == AtomTo && bond.AtomFrom == AtomFrom) ||
+                (bond.AtomFrom == AtomTo && bond.AtomTo == AtomFrom)
+            )
+                bonds.Add(bond);
+        }
+
+        int idx = 1;
+        foreach (Bond2D bond in bonds.OrderBy(x => x.Index))
+        {
+            if (bond.Index != idx)
+                bond.Index = idx;
+            idx++;
+            bond.Multi = bonds.Count;
+        }
+    }
+
+    public abstract void BondUpdate();
+    public static Bond2D Resolve(BaseBond b1, BaseBond b2)
+    {
+        if (b1.Atom == b2.Atom)
+            return ResourceLoader.Load<PackedScene>("res://Scenes/SelfBond.tscn").Instantiate<SelfBond>();
+        return ResourceLoader.Load<PackedScene>("res://Scenes/SingleBond.tscn").Instantiate<SingleBond>();
+    }
+}
\ No newline at end of file
diff --git a/GlobalAccess/GlobalScene.cs b/GlobalAccess/GlobalScene.cs
index 6dfe167..3cbbcdb 100755
--- a/GlobalAccess/GlobalScene.cs
+++ b/GlobalAccess/GlobalScene.cs
@@ -2,10 +2,11 @@ public static class GlobalScene
 {
     public static MainScene MainScene { get; set; }
     public static CompoundConstructor CompoundConstructor { get; set; }
-    public static VirtualChemDemo Demo { get; set; }
+    public static VirtualChemistryDemo Demo { get; set; }
     public static MainControlPanel MainControlPanel { get; set; }
     public static Flask Flask { get; set; }
 
     public static StringLoader StringLoader { get; set; }
+    public static bool ElasticContainer { get; set; } = false;
 }
 
diff --git a/Scenes/Bond.cs b/Scenes/Bond.cs
deleted file mode 100755
index f5dff52..0000000
--- a/Scenes/Bond.cs
+++ /dev/null
@@ -1,34 +0,0 @@
-using Godot;
-
-public partial class Bond : Line2D
-{
-	public Atom AtomFrom { get; set; }
-	public Atom AtomTo { get; set; }
-	private Label BondTypeA { get; set; }
-	private Label BondTypeB { get; set; }
-	public string TypeA { get; set; }
-	public string TypeB { get; set; }
-
-	public override void _Ready()
-	{
-		BondTypeA = GetNode<Label>("BondTypeA");
-		BondTypeB = GetNode<Label>("BondTypeB");
-	}
-
-	public void BondUpdate()
-	{
-		Vector2 v1 = AtomFrom.Position + new Vector2(32, 32);
-		Vector2 v2 = AtomTo.Position + new Vector2(32, 32);
-		Vector2 m = (v1 + v2) / 2;
-		Points = new[] { v1, m, v2 };
-		BondTypeA.Position = m - new Vector2(10, 10);
-		BondTypeB.Position = m + new Vector2(10, 10);
-		BondTypeA.Text = TypeA;
-		BondTypeB.Text = TypeB;
-	}
-
-	// Called every frame. 'delta' is the elapsed time since the previous frame.
-	public override void _Process(double delta)
-	{
-	}
-}
diff --git a/Scenes/Bond.tscn b/Scenes/Bond.tscn
deleted file mode 100644
index c5b9a1a..0000000
--- a/Scenes/Bond.tscn
+++ /dev/null
@@ -1,18 +0,0 @@
-[gd_scene load_steps=2 format=3 uid="uid://ngc8dex7loqv"]
-
-[ext_resource type="Script" path="res://Scenes/Bond.cs" id="1_rpgkt"]
-
-[node name="Bond" type="Line2D"]
-default_color = Color(1, 0.0392157, 1, 0.690196)
-joint_mode = 2
-begin_cap_mode = 2
-end_cap_mode = 2
-script = ExtResource("1_rpgkt")
-
-[node name="BondTypeA" type="Label" parent="."]
-offset_right = 40.0
-offset_bottom = 23.0
-
-[node name="BondTypeB" type="Label" parent="."]
-offset_right = 40.0
-offset_bottom = 23.0
diff --git a/Scenes/Bottle.cs b/Scenes/Bottle.cs
index 5480be5..cc7186a 100755
--- a/Scenes/Bottle.cs
+++ b/Scenes/Bottle.cs
@@ -65,6 +65,8 @@ public partial class Bottle : MenuButton, IChemicalContainer
 				GlobalScene.MainScene.SwitchToConstructor();
 				break;
 			case 3:
+				if (GlobalScene.Flask.Content.Layers.Count == 0)
+					return;
 				Content = GlobalScene.Flask.Content;
 				Content.Container = this;
 				GlobalScene.Flask.Content = HeterogeneousMixture.Null;
diff --git a/Scenes/CompoundConstructor.cs b/Scenes/CompoundConstructor.cs
index 7d3bde6..5661743 100755
--- a/Scenes/CompoundConstructor.cs
+++ b/Scenes/CompoundConstructor.cs
@@ -1,7 +1,10 @@
 using System;
+using System.Collections;
 using System.Collections.Generic;
 using System.Linq;
 using Godot;
+using VirtualChemDemo;
+using VirtualChemDemo.Concepts;
 using VirtualChemistry.Chemistry.Atoms.Implements;
 using VirtualChemistry.Chemistry.Atoms.Resolver;
 using VirtualChemistry.Chemistry.Bonds.Implements;
@@ -15,7 +18,7 @@ public partial class CompoundConstructor : Panel
 	public HashSet<Atom> Atoms { get; set; } = new();
 	public BaseBond ConnectPending { get; set; } = BaseBond.Null;
 	public Atom PendingAtom { get; set; }
-	public Dictionary<Atom, HashSet<Bond>> BondMap { get; set; } = new();
+	public Dictionary<Atom, HashSet<Bond2D>> BondMap { get; set; } = new();
 
 	// Called when the node enters the scene tree for the first time.
 	public override void _Ready()
@@ -25,9 +28,65 @@ public partial class CompoundConstructor : Panel
 		HomogeneousMixture = HeterogeneousMixture.AddLayer();
 	}
 
-	// Called every frame. 'delta' is the elapsed time since the previous frame.
+	private static class AtomPositionFixMemory
+	{
+		public static Atom[] SavedAtoms { get; set; } = null;
+		private static int I { get; set; }
+		private static int J { get; set; }
+		public static int Max => SavedAtoms.Length;
+
+		public static void Reset()
+		{
+			SavedAtoms = null;
+			I = 0;
+			J = 0;
+		}
+
+		public static void OneStep()
+		{
+			if (J >= Max)
+			{
+				J = 0;
+				I++;
+			}
+			if (I >= Max)
+			{
+				Reset();
+				return;
+			}
+
+			if (I == J)
+			{
+				J++;
+				return;
+			}
+
+			Atom a1 = SavedAtoms[I];
+			Atom a2 = SavedAtoms[J];
+
+			if ((a1.Position - a2.Position).Length() < 64)
+			{
+				Vector2 pd = a1.Position - a2.Position;
+				if (pd == Vector2.Zero)
+					pd = new Vector2(J % 3 - 2, I % 3 - 1);
+				a1.Position += pd;
+				a2.Position -= pd;
+				if (GlobalScene.CompoundConstructor.BondMap.TryGetValue(a1, out var bonds1))
+					foreach (Bond2D b1 in bonds1)
+						b1.BondUpdate();					
+				if(GlobalScene.CompoundConstructor.BondMap.TryGetValue(a2, out var bonds2))
+					foreach (Bond2D b2 in bonds2)
+						b2.BondUpdate();
+			}
+			J++;
+		}
+	}
+	
 	public override void _Process(double delta)
 	{
+		if (AtomPositionFixMemory.SavedAtoms == null)
+			AtomPositionFixMemory.SavedAtoms = Atoms.ToArray();
+		AtomPositionFixMemory.OneStep();
 	}
 
 	public override bool _CanDropData(Vector2 atPosition, Variant data)
@@ -40,7 +99,7 @@ public partial class CompoundConstructor : Panel
 		Atom a = data.As<Atom>(); 
 		a.Position = atPosition;
 		if(BondMap.ContainsKey(a))
-			foreach (Bond b in BondMap[a])
+			foreach (Bond2D b in BondMap[a])
 				b.BondUpdate();
 	}
 
@@ -56,6 +115,7 @@ public partial class CompoundConstructor : Panel
 		at.Position = new(500, 500);
 		HomogeneousMixture.AddCompound(c, true, true);
 		Atoms.Add(at);
+		AtomPositionFixMemory.Reset();
 	}
 
 	public void RemoveAtomOf(Atom atom)
@@ -63,11 +123,11 @@ public partial class CompoundConstructor : Panel
 		foreach (BaseBond b in atom.BaseAtom.ConnectedBonds)
 			b.Disconnect();
 
-		Bond[] toRemove = Array.Empty<Bond>();
-		if (BondMap.TryGetValue(atom, out HashSet<Bond> value))
+		Bond2D[] toRemove = Array.Empty<Bond2D>();
+		if (BondMap.TryGetValue(atom, out HashSet<Bond2D> value))
 			toRemove = value.ToArray();
 		
-		foreach (Bond b in toRemove)
+		foreach (Bond2D b in toRemove)
 		{
 			BondMap[b.AtomFrom].Remove(b);
 			BondMap[b.AtomTo].Remove(b);
@@ -79,29 +139,32 @@ public partial class CompoundConstructor : Panel
 		atom.BaseAtom.Compound = Compound.Null;
 		RemoveChild(atom);
 		Atoms.Remove(atom);
+		AtomPositionFixMemory.Reset();
 	}
 
 	public void ConnectAtoms(Atom a, BaseBond b)
 	{
 		b.Connect(ConnectPending);
-		Bond bond = ResourceLoader.Load<PackedScene>("res://Scenes/Bond.tscn").Instantiate<Bond>();
+		Bond2D bond = Bond2D.Resolve(b, ConnectPending);
 		bond.AtomFrom = PendingAtom;
 		bond.AtomTo = a;
-		bond.TypeA = ConnectPending.BondType;
-		bond.TypeB = b.BondType;
+		bond.BondFrom = ConnectPending;
+		bond.BondTo = b;
 		
 		if (!BondMap.ContainsKey(a))
-			BondMap[a] = new HashSet<Bond>();
+			BondMap[a] = new HashSet<Bond2D>();
 		BondMap[a].Add(bond);
 		if (!BondMap.ContainsKey(PendingAtom!))
-			BondMap[PendingAtom] = new HashSet<Bond>();
+			BondMap[PendingAtom] = new HashSet<Bond2D>();
 		BondMap[PendingAtom].Add(bond);
 		ConnectPending = BaseBond.Null;
 		a.AtomActions.BuildMenu();
 		PendingAtom.AtomActions.BuildMenu();
 		PendingAtom = null;
 		AddChild(bond);
-		bond.BondUpdate();
+		foreach (Bond2D bd in BondMap[a])
+			bd.BondUpdate();
+		
 	}
 
 	private void Back()
@@ -111,11 +174,14 @@ public partial class CompoundConstructor : Panel
 
 	private void Build()
 	{
+		if(HomogeneousMixture.Compounds.Count==0)
+			return;
 		HeterogeneousMixture.Container = GlobalScene.Demo.SelectedBottle;
 		GlobalScene.Demo.SelectedBottle.Content = HeterogeneousMixture;
 		GlobalScene.Demo.SelectedBottle.BuildMenu();
 		
 		Clear();
+		Back();
 	}
 
 	private void Clear(bool save = true)
@@ -127,13 +193,13 @@ public partial class CompoundConstructor : Panel
 			return;
 		}
 
-		HashSet<Bond> removedBonds = new();
+		HashSet<Bond2D> removedBonds = new();
 		foreach (Atom atom in Atoms)
 		{
 			RemoveChild(atom);
 			if (!BondMap.ContainsKey(atom))
 				continue;
-			foreach (Bond bond in BondMap[atom])
+			foreach (Bond2D bond in BondMap[atom])
 			{
 				if (!removedBonds.Contains(bond))
 					RemoveChild(bond);
diff --git a/Scenes/Flask.cs b/Scenes/Flask.cs
index 9e97a21..5cbb2f9 100755
--- a/Scenes/Flask.cs
+++ b/Scenes/Flask.cs
@@ -7,7 +7,7 @@ public partial class Flask : TextureRect, IChemicalContainer
 {
 	public double ContainerVolume { get; set; } = 0.5;
 	private TextureRect InnerLayer { get; set; }
-	public double Volume() => ContainerVolume;
+	public double Volume() => GlobalScene.ElasticContainer ? Content.Volume : ContainerVolume;
 
 	public HeterogeneousMixture Content { get; set; }
 	public double EnvironmentPressure { get; set; }
@@ -55,6 +55,11 @@ public partial class Flask : TextureRect, IChemicalContainer
 		InnerLayer = GetNode<TextureRect>("InnerLayer");
 	}
 
+	private void ShowAll()
+	{
+		GlobalScene.MainControlPanel.BuildAllTree();
+	}
+
 	// Called every frame. 'delta' is the elapsed time since the previous frame.
 	public override void _Process(double delta)
 	{
diff --git a/Scenes/Flask.tscn b/Scenes/Flask.tscn
index 9f5590a..4f5798d 100644
--- a/Scenes/Flask.tscn
+++ b/Scenes/Flask.tscn
@@ -21,3 +21,13 @@ offset_right = 40.0
 offset_bottom = 40.0
 mouse_filter = 2
 texture = ExtResource("1_b34pm")
+
+[node name="ShowAll" type="Button" parent="."]
+layout_mode = 0
+offset_left = 185.0
+offset_top = 107.0
+offset_right = 229.0
+offset_bottom = 138.0
+text = "Show All"
+
+[connection signal="pressed" from="ShowAll" to="." method="ShowAll"]
diff --git a/Scenes/FlaskContent.cs b/Scenes/FlaskContent.cs
index 5b64b52..14c6c1f 100755
--- a/Scenes/FlaskContent.cs
+++ b/Scenes/FlaskContent.cs
@@ -8,7 +8,7 @@ public partial class FlaskContent : ColorRect
 
 	public HomogeneousMixture Mixture { get; set; } = HomogeneousMixture.Null;
 	private const double ContainerHeight = 512d;
-	public double ContainerVolume => Mixture.HeterogeneousMixture.Container.Volume();
+	private double ContainerVolume => Mixture.HeterogeneousMixture.Container.Volume();
 	public double Volume => Mixture.Volume;
 	private TextureButton Mask { get; set; }
 
@@ -31,22 +31,21 @@ public partial class FlaskContent : ColorRect
 		double height = (Volume / ContainerVolume) * ContainerHeight;
 		Position = new Vector2(Position.X, 512-(float)(StartFrom + height));
 		Size = new Vector2(Size.X, (float)height);
-		//Mask.Size = Size;
 		Color = Color.Color8(
 			Mixture.ColorRed,
 			Mixture.ColorGreen,
 			Mixture.ColorGreen,
 			Mixture.ColorTransparent
 		);
-		/*
-		Animation a = AP.GetAnimation("HeightChange");
+		
+		/*Animation a = AP.GetAnimation("HeightChange");
 		a.TrackSetKeyValue(0, 0, Size);
 		a.TrackSetKeyValue(0, 1, new Vector2(Size.X, (float)height));
 		AP.Play("HeightChange");
 		AP.Play("PositionChange");
 		a = AP.GetAnimation("PositionChange");
 		a.TrackSetKeyValue(0,0,Position);
-		a.TrackSetKeyValue(0,1, new Vector2(Position.X, -(float)StartFrom));
+		a.TrackSetKeyValue(0,1, new Vector2(Position.X, 512-(float)(StartFrom + height)));
 		Color = Color.Color8(Mixture.ColorRed, Mixture.ColorGreen, Mixture.ColorGreen, Mixture.ColorTransparent);
 		AP.Play();*/
 	}
diff --git a/Scenes/MainControlPanel.cs b/Scenes/MainControlPanel.cs
index b7d2b4a..499d043 100644
--- a/Scenes/MainControlPanel.cs
+++ b/Scenes/MainControlPanel.cs
@@ -16,7 +16,7 @@ public partial class MainControlPanel : HBoxContainer
 	private Label FreeVolume { get; set; }
 	private Label Stiffness { get; set; }
 	private Tree Compounds { get; set; }
-	// Called when the node enters the scene tree for the first time.
+
 	public override void _Ready()
 	{
 		EnvTemperature = GetNode<HSlider>("V1/EnvTemperature");
@@ -53,13 +53,43 @@ public partial class MainControlPanel : HBoxContainer
 		BuildTree();
 	}
 
+	public void BuildAllTree()
+	{
+		Compounds.Clear();
+		TreeItem root = Compounds.CreateItem();
+		root.SetText(0, "Mixtures: ");
+		int i = 1;
+		foreach (HomogeneousMixture h in GlobalScene.Flask.Content.LayerOrder)
+		{
+			TreeItem sRoot = Compounds.CreateItem(root);
+			sRoot.SetText(0,$"Mixture{i} Amt{h.Amount}");
+			foreach (var group in h.Compounds.GroupBy(x => x.Expression))
+			{
+				TreeItem t = Compounds.CreateItem(root);
+				t.SetText(0, group.Key);
+				t.SetSelectable(0, false);
+				int j = 1;
+				foreach (Compound c in group)
+				{
+					TreeItem x = Compounds.CreateItem(t);
+					x.SetText(0, $"{j}th isomer");
+					x.SetMeta("isoExp", c.IsoRepresentation);
+					j++;
+				}
+				i++;
+			}
+		}
+	}
+
 	private void BuildTree()
 	{
 		Compounds.Clear();
 		var groups = SelectedMixture.Compounds.GroupBy(x => x.Expression);
+		TreeItem root = Compounds.CreateItem(null);
+		root.SetText(0, "Compounds: ");
 		foreach (var group in groups)
 		{
-			TreeItem t = Compounds.CreateItem();
+			TreeItem t = Compounds.CreateItem(root);
 			t.SetText(0, group.Key);
 			t.SetSelectable(0, false);
 			int i = 1;
@@ -108,4 +138,14 @@ public partial class MainControlPanel : HBoxContainer
 		GlobalScene.Flask.ContainerVolume = vol;
 		GlobalScene.Flask.Update();
 	}
+
+	private void SetElasticContainer(bool on)
+	{
+		GlobalScene.ElasticContainer = on;
+		if (on)
+			ContainerVolume.Editable = false;
+		else
+			ContainerVolume.Editable = true;
+		
+	}
 }
diff --git a/Scenes/MainControlPanel.tscn b/Scenes/MainControlPanel.tscn
index ba0f4fc..3cdbe58 100644
--- a/Scenes/MainControlPanel.tscn
+++ b/Scenes/MainControlPanel.tscn
@@ -44,6 +44,12 @@ min_value = 0.2
 max_value = 20.0
 step = 0.2
 value = 1.0
+ticks_on_borders = true
+
+[node name="ElasticContainer" type="CheckBox" parent="V1"]
+layout_mode = 2
+tooltip_text = "Volume of container always equal to the volume of content"
+text = "Elastic Container"
 
 [node name="VSeparator" type="VSeparator" parent="."]
 layout_mode = 2
@@ -138,12 +144,8 @@ layout_mode = 2
 [node name="V3" type="VBoxContainer" parent="."]
 layout_mode = 2
 
-[node name="Label" type="Label" parent="V3"]
-layout_mode = 2
-text = "Compounents"
-
 [node name="Compounds" type="Tree" parent="V3"]
-custom_minimum_size = Vector2(150, 200)
+custom_minimum_size = Vector2(250, 200)
 layout_mode = 2
 
 [node name="VSeparator4" type="VSeparator" parent="."]
@@ -154,4 +156,5 @@ layout_mode = 2
 [connection signal="pressed" from="V1/RemoveBottom" to="." method="RemoveBottom"]
 [connection signal="value_changed" from="V1/EnvTemperature" to="." method="SetTemperature"]
 [connection signal="value_changed" from="V1/ContainerVolume" to="." method="SetVolume"]
+[connection signal="toggled" from="V1/ElasticContainer" to="." method="SetElasticContainer"]
 [connection signal="item_selected" from="V3/Compounds" to="." method="IsomerSelectedHandler"]
diff --git a/Scenes/MainScene.cs b/Scenes/MainScene.cs
index d3ddbfb..efb81a0 100644
--- a/Scenes/MainScene.cs
+++ b/Scenes/MainScene.cs
@@ -4,12 +4,12 @@ using System;
 public partial class MainScene : Node2D
 {
 	public Node CurrentScene { get; set; }
-	public VirtualChemDemo Demo { get; set; }
+	public VirtualChemistryDemo Demo { get; set; }
 
 	public override void _Ready()
 	{
 		GlobalScene.MainScene = this;
-		Demo = GetNode<VirtualChemDemo>("Demo");
+		Demo = GetNode<VirtualChemistryDemo>("Demo");
 		CurrentScene = Demo;
 	}
 
diff --git a/Scenes/MainScene.tscn b/Scenes/MainScene.tscn
index 4f1377c..73db2f2 100644
--- a/Scenes/MainScene.tscn
+++ b/Scenes/MainScene.tscn
@@ -1,7 +1,7 @@
 [gd_scene load_steps=3 format=3 uid="uid://cgdqxc2mx6w8l"]
 
 [ext_resource type="Script" path="res://Scenes/MainScene.cs" id="1_uwony"]
-[ext_resource type="PackedScene" uid="uid://br78rurjakp3a" path="res://Scenes/VirtualChemDemo.tscn" id="2_vpu75"]
+[ext_resource type="PackedScene" uid="uid://br78rurjakp3a" path="res://Scenes/VirtualChemistryDemo.tscn" id="2_vpu75"]
 
 [node name="MainScene" type="Node2D"]
 script = ExtResource("1_uwony")
diff --git a/Scenes/MultiBond.cs b/Scenes/MultiBond.cs
new file mode 100644
index 0000000..c19241b
--- /dev/null
+++ b/Scenes/MultiBond.cs
@@ -0,0 +1,9 @@
+using VirtualChemDemo.Concepts;
+
+public partial class MultiBond : Bond2D
+{
+    public override void BondUpdate()
+    {
+        throw new System.NotImplementedException();
+    }
+}
\ No newline at end of file
diff --git a/Scenes/SelfBond.cs b/Scenes/SelfBond.cs
new file mode 100644
index 0000000..3a56e65
--- /dev/null
+++ b/Scenes/SelfBond.cs
@@ -0,0 +1,25 @@
+using System.Collections.Generic;
+using Godot;
+using VirtualChemDemo.Concepts;
+
+namespace VirtualChemDemo.Scenes;
+
+public partial class SelfBond : Bond2D
+{
+    public override void BondUpdate()
+    {
+        Reindex();
+        List<Vector2> points = new();
+        Vector2 pcenter = new(30, 0);
+        pcenter = pcenter.Rotated((float)Index * Mathf.Pi * 2f / (float)Multi);
+        Vector2 center = AtomFrom.Position + new Vector2(32, 32) + pcenter; 
+        Vector2 d = AtomFrom.Position + new Vector2(32, 32) - center;
+        for (int i = 0; i <= 24; i++)
+            points.Add(center + d.Rotated(i*Mathf.Pi*2/24));
+        BondTypeA.Position = points[12] + new Vector2(-20, 0);
+        BondTypeB.Position = points[12] + new Vector2(20, 0);
+        Points = points.ToArray();
+        BondTypeA.Text = BondFrom.BondType;
+        BondTypeB.Text = BondTo.BondType;
+    }
+}
\ No newline at end of file
diff --git a/Scenes/SingleBond.cs b/Scenes/SingleBond.cs
new file mode 100755
index 0000000..39605ba
--- /dev/null
+++ b/Scenes/SingleBond.cs
@@ -0,0 +1,97 @@
+using System;
+using Godot;
+using VirtualChemDemo.Concepts;
+
+public partial class SingleBond : Bond2D
+{
+	private static int BIndex(int index, int multi)
+	{
+		if (multi == 1)
+			return 0;
+		if (multi % 2 == 1)
+		{
+			int center = multi / 2 + 1;
+			return center - index;
+		}
+
+		if (multi % 2 == 0)
+		{
+			double center = multi / 2 + 0.5;
+			return (int)(center > index ? Math.Ceiling(center - index) : Math.Floor(center - index));
+		}
+
+		return 0;
+	}
+	private void MakeCurve(float curveRate=20f, int cDir = 1)
+	{
+		Vector2 Start = AtomFrom.Position + new Vector2(32, 32);;
+		Vector2 End = AtomTo.Position + new Vector2(32, 32);;
+		Vector2[] xs = new Vector2[17];
+		int[] x2 = new[] { 4, 12 };
+		int[] x3 = new[] { 2, 6, 10, 14};
+		int[] x4 = new[] { 1, 3, 5, 7, 9, 11, 13, 15 };
+		Vector2 vd = End - Start;
+		Vector2 nor = vd.Rotated(Mathf.Pi / 2 * cDir);
+		Vector2 center = vd / 2 + 4f * nor / curveRate;
+		xs[0] = Start;
+		xs[16] = End;
+		xs[8] = center + xs[0];
+		foreach (int i in x2)
+		{
+			Vector2 v = xs[i + 4] - xs[i - 4];
+			Vector2 n = v.Rotated(Mathf.Pi / 2 * cDir);
+			Vector2 w = v / 2 + 2f * n / curveRate;
+			xs[i] = w + xs[i - 4];
+		}
+
+		foreach (int i in x3)
+		{
+			Vector2 v = xs[i + 2] - xs[i - 2];
+			Vector2 n = v.Rotated(Mathf.Pi / 2 * cDir);
+			Vector2 w = v / 2 + n / curveRate;
+			xs[i] = w + xs[i - 2];
+		}
+
+		foreach (int i in x4)
+		{
+			Vector2 v = xs[i + 1] - xs[i - 1];
+			Vector2 n = v.Rotated(Mathf.Pi / 2 * cDir);
+			Vector2 w = v / 2 + n / curveRate;
+			xs[i] = w + xs[i - 1];
+		}
+		BondTypeA.Position = xs[10];
+		BondTypeB.Position = xs[6];
+		Points = xs;
+	}
+
+	public override void BondUpdate()
+	{
+		Reindex();
+		int bindex = BIndex(Index, Multi);
+		if (bindex == 0)
+		{
+			Vector2 v1 = AtomFrom.Position + new Vector2(32, 32);
+			Vector2 v2 = AtomTo.Position + new Vector2(32, 32);
+			Vector2 m = (v1 + v2) / 2;
+			Points = new[] { v1, m, v2 };
+			BondTypeA.Position = m - new Vector2(10, 10);
+			BondTypeB.Position = m + new Vector2(10, 10);
+		}
+		else
+		{
+			float curveRate = 25 - Math.Abs(bindex)*5;
+			int cDir = bindex > 0 ? 1 : -1;
+			MakeCurve(curveRate, cDir);
+		}
+
+		
+
+		BondTypeA.Text = BondFrom.BondType;
+		BondTypeB.Text = BondTo.BondType;
+	}
+
+	// Called every frame. 'delta' is the elapsed time since the previous frame.
+	public override void _Process(double delta)
+	{
+	}
+}
diff --git a/Scenes/StringLoader.cs b/Scenes/StringLoader.cs
index 9b2ac2e..b7033c7 100644
--- a/Scenes/StringLoader.cs
+++ b/Scenes/StringLoader.cs
@@ -4,10 +4,7 @@ using VirtualChemistry.Chemistry.Mixtures.Resolver;
 
 public partial class StringLoader : Window
 {
-
 	public TextEdit Input { get; set; }
-
-	// Called when the node enters the scene tree for the first time.
 	public override void _Ready()
 	{
 		Input = GetNode<TextEdit>("V1/Input");
@@ -21,6 +18,7 @@ public partial class StringLoader : Window
 		HeterogeneousMixture mixture = HeterogeneousMixtureResolver.Resolve(expression);
 		GlobalScene.Demo.SelectedBottle.Content = mixture;
 		mixture.Container = GlobalScene.Demo.SelectedBottle;
+		GlobalScene.Demo.SelectedBottle.BuildMenu();
 		Visible = false;
 	}
 
diff --git a/Scenes/VirtualChemDemo.tscn b/Scenes/VirtualChemDemo.tscn
deleted file mode 100644
index dd0a122..0000000
--- a/Scenes/VirtualChemDemo.tscn
+++ /dev/null
@@ -1,87 +0,0 @@
-[gd_scene load_steps=6 format=3 uid="uid://br78rurjakp3a"]
-
-[ext_resource type="Script" path="res://Scenes/VirtualChemDemo.cs" id="1_aartk"]
-[ext_resource type="PackedScene" uid="uid://re3bwidsx0do" path="res://Scenes/MainControlPanel.tscn" id="2_cfpbe"]
-[ext_resource type="PackedScene" uid="uid://u7apjw1vvak3" path="res://Scenes/Bottle.tscn" id="2_ei0nr"]
-[ext_resource type="PackedScene" uid="uid://bde5n0vfm6jvs" path="res://Scenes/Flask.tscn" id="3_p6s6c"]
-[ext_resource type="PackedScene" uid="uid://cubdalatqln4x" path="res://Scenes/StringLoader.tscn" id="5_5y6ld"]
-
-[node name="VicrtualChemDemo" type="Node2D"]
-script = ExtResource("1_aartk")
-
-[node name="VBoxContainer" type="VBoxContainer" parent="."]
-offset_right = 40.0
-offset_bottom = 40.0
-
-[node name="HSeparator" type="HSeparator" parent="VBoxContainer"]
-layout_mode = 2
-
-[node name="MainControlPanel" parent="VBoxContainer" instance=ExtResource("2_cfpbe")]
-layout_mode = 2
-
-[node name="HSeparator2" type="HSeparator" parent="VBoxContainer"]
-layout_mode = 2
-
-[node name="Potions" type="HBoxContainer" parent="."]
-offset_left = 70.0
-offset_top = 553.0
-offset_right = 670.0
-offset_bottom = 621.0
-
-[node name="Prev" type="Button" parent="Potions"]
-layout_mode = 2
-text = "<-"
-
-[node name="Items" type="HBoxContainer" parent="Potions"]
-layout_mode = 2
-
-[node name="MenusButton" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle2" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle3" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle4" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle5" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle6" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Bottle7" parent="Potions/Items" instance=ExtResource("2_ei0nr")]
-layout_mode = 2
-
-[node name="Next" type="Button" parent="Potions"]
-layout_mode = 2
-text = "->"
-
-[node name="Flask" parent="." instance=ExtResource("3_p6s6c")]
-offset_left = 747.0
-offset_top = 57.0
-offset_right = 875.0
-offset_bottom = 569.0
-
-[node name="HRepr" type="HBoxContainer" parent="."]
-offset_left = 32.0
-offset_top = 272.0
-offset_right = 702.0
-offset_bottom = 352.0
-
-[node name="Label" type="Label" parent="HRepr"]
-layout_mode = 2
-text = "Full Expression"
-
-[node name="FullRepr" type="RichTextLabel" parent="HRepr"]
-custom_minimum_size = Vector2(550, 80)
-layout_mode = 2
-
-[node name="ExpressionLoader" parent="." instance=ExtResource("5_5y6ld")]
-position = Vector2i(250, 200)
diff --git a/Scenes/VirtualChemDemo.cs b/Scenes/VirtualChemistryDemo.cs
similarity index 93%
rename from Scenes/VirtualChemDemo.cs
rename to Scenes/VirtualChemistryDemo.cs
index 0113d10..01284b3 100755
--- a/Scenes/VirtualChemDemo.cs
+++ b/Scenes/VirtualChemistryDemo.cs
@@ -1,6 +1,6 @@
 using Godot;
 
-public partial class VirtualChemDemo : Node2D
+public partial class VirtualChemistryDemo : Node2D
 {
 	public Flask Flask { get; set; }
 	public RichTextLabel FullRepr { get; set; }
diff --git a/Tests/Line2d.cs b/Tests/Line2d.cs
new file mode 100644
index 0000000..3ee8773
--- /dev/null
+++ b/Tests/Line2d.cs
@@ -0,0 +1,71 @@
+using Godot;
+using System;
+
+public partial class Line2d : Line2D
+{
+	private TestScene Test { get; set; }
+	public Vector2 Start => Test.A.Position;
+	public Vector2 End => Test.B.Position;
+	public float CurveRate { get; set; } = 20;
+	public int CDir { get; set; } = 1;
+
+	private void MakeCurve(float curveRate=20f, int cDir = 1)
+	{
+		Vector2[] xs = new Vector2[17];
+		int[] x2 = new[] { 4, 12 };
+		int[] x3 = new[] { 2, 6, 10, 14};
+		int[] x4 = new[] { 1, 3, 5, 7, 9, 11, 13, 15 };
+		Vector2 vd = End - Start;
+		Vector2 nor = vd.Rotated(Mathf.Pi / 2 * cDir);
+		Vector2 center = vd / 2 + 4f * nor / curveRate;
+		xs[0] = Start;
+		xs[16] = End;
+		xs[8] = center + xs[0];
+		foreach (int i in x2)
+		{
+			Vector2 v = xs[i + 4] - xs[i - 4];
+			Vector2 n = v.Rotated(Mathf.Pi / 2 * cDir);
+			Vector2 w = v / 2 + 2f * n / curveRate;
+			xs[i] = w + xs[i - 4];
+		}
+
+		foreach (int i in x3)
+		{
+			Vector2 v = xs[i + 2] - xs[i - 2];
+			Vector2 n = v.Rotated(Mathf.Pi / 2 * cDir);
+			Vector2 w = v / 2 + n / curveRate;
+			xs[i] = w + xs[i - 2];
+		}
+
+		foreach (int i in x4)
+		{
+			Vector2 v = xs[i + 1] - xs[i - 1];
+			Vector2 n = v.Rotated(Mathf.Pi / 2 * cDir);
+			Vector2 w = v / 2 + n / curveRate;
+			xs[i] = w + xs[i - 1];
+		}
+
+		Points = xs;
+	}
+
+	private void T()
+	{
+		Points = new[] { new Vector2(1, 1), new Vector2(2, 3) };
+		GD.Print(Points.Length);
+	}
+
+	// Called when the node enters the scene tree for the first time.
+	public override void _Ready()
+	{
+		Test = GetParent<TestScene>();
+		
+		GD.Print("Ready");
+	}
+
+	// Called every frame. 'delta' is the elapsed time since the previous frame.
+	public override void _Process(double delta)
+	{
+		//T();
+		MakeCurve(CurveRate, CDir);
+	}
+}
diff --git a/Tests/Test2.cs b/Tests/Test2.cs
new file mode 100644
index 0000000..e821fae
--- /dev/null
+++ b/Tests/Test2.cs
@@ -0,0 +1,12 @@
+using Godot;
+
+public partial class Test2 : Node2D
+{
+	public override void _Ready()
+	{
+		GD.Print("READY  ddd");
+	}
+	public override void _Process(double delta)
+	{
+	}
+}
diff --git a/Tests/TestScene.cs b/Tests/TestScene.cs
new file mode 100644
index 0000000..404f0c4
--- /dev/null
+++ b/Tests/TestScene.cs
@@ -0,0 +1,37 @@
+using Godot;
+using System;
+
+public partial class TestScene : Node2D
+{
+	public Marker2D A { get; set; }
+	public Marker2D B { get; set; }
+
+	public Line2d L1 { get; set; }
+
+	public Line2d L2 { get; set; }
+	public Line2d L3 { get; set; }
+	public Line2d L4 { get; set; }
+	// Called when the node enters the scene tree for the first time.
+	public override void _Ready()
+	{
+		A = GetNode<Marker2D>("A");
+		B = GetNode<Marker2D>("B");
+		L1 = GetNode<Line2d>("L1");
+		L2 = GetNode<Line2d>("L2");
+		L3 = GetNode<Line2d>("L3");
+		L4 = GetNode<Line2d>("L4");
+		L1.CurveRate = 20;
+		L1.CDir = 1;
+		L2.CurveRate = 10;
+		L1.CDir = 1;
+		L3.CurveRate = 10;
+		L3.CDir = -1;
+		L4.CurveRate = 20;
+		L4.CDir = -1;
+	}
+
+	// Called every frame. 'delta' is the elapsed time since the previous frame.
+	public override void _Process(double delta)
+	{
+	}
+}