void OnGUI()
{
CUE cue = CUE.GetInstance();
ReactionType[] reactionTypes = cue.ReactionTypes;
// Make a background box
GUI.Box(new Rect(10, 10, 300, 30 + reactionTypes.Length * 25), "Reaction For Molecule");
if (GUI.Button(new Rect(20, 40, 280, 20), "Attach"))
{
ThreadStart myThreadDelegate = new ThreadStart(ThreadWork.DoWork);
Thread myThread = new Thread(myThreadDelegate);
myThread.Start();
Thread.Sleep(100);
Debug.Log("Main - aborting my thread.");
myThread.Abort();
myThread.Join();
Debug.Log("Main ending.");
}
int i = 1;
foreach (var item in reactionTypes)
{
if (GUI.Button(new Rect(20, 40 + 25 * i, 280, 20), item.ToString()))
{
}
i++;
}
}
protected override void OnItemGui(MoleculeSpecies item)
{
if (item == null)
{
base.OnItemGui(item);
return;
}
CUE cue = CUE.GetInstance();
item.Name = EditorGUILayout.TextField("Name", item.Name);
item.InitialQuantity = EditorGUILayout.IntField("Initial Quantity [1]", item.InitialQuantity);
item.Mass = EditorGUILayout.FloatField("Mass [u]", item.Mass);
EditorGUILayout.LabelField("~Size [nm]", Utils.ScaleToNm(item.Size).ToString());
//EditorGUILayout.LabelField("ID", item.GetInstanceID().ToString());
EditorUtility.SetDirty(item);
if (GUILayout.Button("remove"))
{
cue.RemoveSpecies(item);
EditorUtility.SetDirty(cue);
}
}
/// <summary>
/// Set a molecule ready for reactiong.
/// Called when molecules collide with each other.
/// When all molecules are ready, cue.ReactionManager.PerformReaction is called.
/// </summary>
/// <param name="molecule">Molecule.</param>
public void Ready(Molecule molecule)
{
bool allReady = true;
for (int i = 0; i < molecules.Count; i++)
{
if (molecule == molecules[i])
{
ready[i] = true;
if (!allReady)
{
break;
}
}
allReady = allReady & ready[i];
}
if (allReady && !performed)
{
performed = true;
CUE cue = CUE.GetInstance();
cue.ReactionManager.PerformReaction(this);
}
}
private void Deselect()
{
CameraControl.Follow = null;
CUE cue = CUE.GetInstance();
cue.ReactionManager.SelectedMolecule = null;
RemoveScript();
}
void OnDrawGizmos()
{
Gizmos.color = new Color(0, 0, 1, 0.5f);
CUE cue = CUE.GetInstance();
float r = Utils.GetSphereRadius(cue.Volume);
Gizmos.DrawSphere(Vector3.zero, Utils.ScaleFromNm(r));
}
/// <summary>
/// Simulates one step.
/// </summary>
private void SimulateStep()
{
Debug.Log("Step");
CUE cue = CUE.GetInstance();
SimulationStep step = simulator.Step(cue.SimulationStep);
EnqueueStep(step);
nextStep = nextStep.AddSeconds(cue.VisualizationStep);
}
public override void OnInspectorGUI()
{
Molecule t = (Molecule)target;
CUE cue = CUE.GetInstance();
MoleculeSpeciesPopup speciesPopup = new MoleculeSpeciesPopup(cue, false);
t.Species = speciesPopup.Popup(t.Species, false);
EditorUtility.SetDirty(t);
if (GUILayout.Button("show CellUnity Editor"))
{
CellUnityWindow.Init();
}
}
public void Reload()
{
CUE cue = CUE.GetInstance();
SimulationState oldState = state;
if (state != SimulationState.Stopped)
{
Stop();
}
if (simulator == null)
{
this.simulator = new Copasi.CopasiSimulator();
simulator.Init(cue);
}
else
{
simulator.Reload();
}
cue.ScriptManager.GetOrAddScript <CellUnity.Simulation.SimulatorScript>();
simulationThread = new Thread(new ThreadStart(RunSimulation));
simulationThread.IsBackground = true;
// restore old state
if (oldState == SimulationState.Running)
{
Start();
}
else if (oldState == SimulationState.Paused)
{
Pause();
}
else if (oldState == SimulationState.Stopped)
{
state = SimulationState.Stopped;
}
}
protected override void OnItemGui(ReactionType item)
{
CUE cue = CUE.GetInstance();
if (item == null)
{
base.OnItemGui(item);
return;
}
item.Name = EditorGUILayout.TextField("Name", item.Name);
EditorGUILayout.BeginHorizontal();
item.Reagents = GuiSpeciesList(cue, item.Reagents);
EditorGUILayout.LabelField(" \u2192 ", GUILayout.MaxWidth(30));
item.Products = GuiSpeciesList(cue, item.Products);
EditorGUILayout.EndHorizontal();
item.Rate = EditorGUILayout.FloatField("Rate [nl/(nmol*s)]", item.Rate);
EditorUtility.SetDirty(item);
if (Application.isPlaying)
{
if (GUILayout.Button("start reaction"))
{
cue.ReactionManager.InitiateReaction(item, true);
}
}
if (GUILayout.Button("remove"))
{
cue.RemoveReaction(item);
EditorUtility.SetDirty(cue);
}
}
/// <summary>
/// Should be called every frame.
/// Processes Simulation results and initiates reactions.
/// </summary>
public void Update()
{
if (runInMainThread)
{
MainThreadRunSimulation();
}
// Process Simulation Results
while (true)
{
SimulationStep step;
lock (stepsQueueLock)
{
if (stepsQueue.Count == 0)
{
break;
}
step = stepsQueue.Dequeue();
}
CUE cue = CUE.GetInstance();
System.Text.StringBuilder info = new System.Text.StringBuilder(); // TODO: remove
foreach (ReactionCount item in step.Reactions)
{
info.Append(item.ReactionType.ToString() + ": " + item.Count + "; ");
for (ulong i = 0; i < item.Count; i++)
{
cue.ReactionManager.InitiateReaction(item.ReactionType, true);
}
}
Debug.Log(info.ToString());
}
}
void OnGUI()
{
CUE cue = CUE.GetInstance();
// Get selected molecule
Molecule m = cue.ReactionManager.SelectedMolecule;
// Set following
if (following)
{
CameraControl.Follow = m.gameObject;
}
else
{
CameraControl.Follow = null;
}
// Draw menu or remove script if no moleule is selected
if (m == null)
{
RemoveScript();
}
else
{
GuiBoxReset();
GuiBeginBox("Molecule", 94);
string reaction;
string reactionStatus;
if (m.ReactionPrep != null)
{
reaction = m.ReactionPrep.ReactionType.ToString();
reactionStatus = "performing";
}
else
{
ReactionType selectedReaction = cue.ReactionManager.SelectedReaction;
if (selectedReaction != null)
{
reaction = selectedReaction.ToString();
reactionStatus = "waiting";
}
else
{
reaction = "none";
reactionStatus = "";
}
}
GuiCaptionValue("Species:", m.Species.Name);
GuiCaptionValue("Reaction:", reaction + "\n\r" + reactionStatus);
GUILayout.BeginHorizontal();
if (GUILayout.Button(following ? "Stay" : "Follow"))
{
following = !following;
}
if (GUILayout.Button("Deselect"))
{
Deselect();
}
if (GUILayout.Button("Hide"))
{
Hide();
}
GUILayout.EndHorizontal();
GuiEndBox();
//
// Reactions
//
List <ReactionType> reactions = new List <ReactionType>();
foreach (var r in cue.ReactionTypes)
{
if (Utils.ArrayContains <MoleculeSpecies>(r.Reagents, m.Species))
{
reactions.Add(r);
}
}
GuiBeginBox("Reaction", (reactions.Count + 1) * (guiReactionHeight) + guiReactionSpace);
if (GUILayout.Button("none"))
{
cue.ReactionManager.SelectedReaction = null;
}
GUILayout.Space(guiReactionSpace);
foreach (var r in reactions)
{
if (GUILayout.Button(r.ToString()))
{
cue.ReactionManager.SelectedReaction = r;
}
}
GuiEndBox();
if (Input.GetKey("escape"))
{
Deselect();
}
if (Input.GetKey("return"))
{
Hide();
}
}
}
void OnGUI()
{
CueEditor.CueGui(CUE.GetInstance());
}
public MoleculeSpecies Create()
{
// find a name if not specified
findName();
// create main object of the species
GameObject mol = new GameObject(name);
mol.transform.position = Vector3.zero;
float colliderRadius = 0;
//
// Find center of all gameObjects
//
Vector3 center = Vector3.zero;
foreach (var obj in gameObjects)
{
// set main object as parent
obj.transform.parent = mol.transform;
center += obj.transform.position;
// remove collider for performance boost
if (obj.collider != null)
{
obj.collider.enabled = false;
CellUnity.Utility.ScriptManager.RemoveComponent(obj.collider);
}
}
center = center / gameObjects.Length;
//
// locate object to (0,0,0) by setting center to (0,0,0)
// and calculate the colliderRadius by making sure every atom is inside this radius
//
foreach (var obj in gameObjects)
{
obj.transform.position -= center;
colliderRadius = Math.Max(colliderRadius, Math.Abs(obj.renderer.bounds.min.x));
colliderRadius = Math.Max(colliderRadius, Math.Abs(obj.renderer.bounds.min.y));
colliderRadius = Math.Max(colliderRadius, Math.Abs(obj.renderer.bounds.min.z));
colliderRadius = Math.Max(colliderRadius, Math.Abs(obj.renderer.bounds.max.x));
colliderRadius = Math.Max(colliderRadius, Math.Abs(obj.renderer.bounds.max.y));
colliderRadius = Math.Max(colliderRadius, Math.Abs(obj.renderer.bounds.max.z));
}
// Create a new species and add it to the CUE
CUE cue = CUE.GetInstance();
MoleculeSpecies species = cue.CreateMoleculeSpecies();
species.Name = name;
cue.AddSpecies(species);
// Add the molecule script to the main object
CellUnity.Molecule script = mol.AddComponent <CellUnity.Molecule>();
script.Species = species;
species.Mass = mass;
species.Size = colliderRadius * 2;
// Add a sphere collider to the main object
SphereCollider sphereCollider = mol.AddComponent <SphereCollider> ();
Rigidbody rigidbody = mol.AddComponent <Rigidbody> ();
rigidbody.useGravity = false;
rigidbody.mass = mass;
sphereCollider.radius = colliderRadius;
// Add a diffusion script to the main object
View.Diffusion diffusion = mol.AddComponent <View.Diffusion> ();
diffusion.Intensity = Diffusion;
// create the prefab used as template for the species
string assetPath = "Assets/Molecules/" + name + ".prefab";
UnityEngine.Object prefab = PrefabUtility.CreateEmptyPrefab(assetPath);
PrefabUtility.ReplacePrefab(mol, prefab);
AssetDatabase.Refresh();
species.PrefabPath = assetPath;
EditorUtility.SetDirty(cue);
// Delete game objects
foreach (var obj in gameObjects)
{
GameObject.DestroyImmediate(obj);
}
GameObject.DestroyImmediate(mol);
return(species);
}
// Use this for initialization
void Start()
{
cue = CUE.GetInstance();
Debug.Log("Auto Reaction started");
}
// Use this for initialization
void Start()
{
this.cue = CUE.GetInstance();
}
/// <summary>
/// Initiates a reaction.
/// </summary>
/// <returns><c>true</c>, if the reaction was initiated, <c>false</c> otherwise.</returns>
/// <param name="reaction">Reaction.</param>
/// <param name="queueIfNotPossible">If set to <c>true</c>, the reaction is queued and performed later if the reaction is not possible at the moment.</param>
public bool InitiateReaction(ReactionType reaction, bool queueIfNotPossible)
{
CUE cue = CUE.GetInstance();
ReactionPrep reactionPrep = new ReactionPrep(reaction);
bool moleculesFound;
// Select molecules
// Prefer selected molecule if suitable
if (
selectedMolecule != null && selectedReaction != null && // molecule and reaction must be selected
selectedReaction == reaction && // selected reaction must match current reaction
selectedMolecule.ReactionPrep == null // selected molecule must not be already involved in a reaction
)
{
moleculesFound = cue.Molecules.FindMolecuelsForReaction(reactionPrep, selectedMolecule);
}
else
{
// select random molecules
moleculesFound = cue.Molecules.FindMolecuelsForReaction(reactionPrep);
}
if (moleculesFound)
{
// Ready reactions for 0 to 1 reagents because Collision is never called for these molecules
if (reactionPrep.MoleculeCount == 0)
{
reactionPrep.Ready(null);
}
if (reactionPrep.MoleculeCount == 1)
{
reactionPrep.Ready(reactionPrep.Molecules[0]); // necessary if only one reagent in reaction
}
return(true);
}
else
{
// not sufficient molecules for reaction
reactionPrep.Release(); // remove ReactonPrep from Molecules
if (queueIfNotPossible)
{
// --> queue Reaction for later
ShortKeyDict <ReactionType, int> .Entry entry;
if (!openReactions.Find(reaction, out entry))
{
entry = openReactions.Set(reaction, 0);
}
entry.Value++;
}
return(false);
}
}