/// <summary>
/// Adds a specific amount of molecules to the placement queue.
/// </summary>
/// <param name="species">Species to place</param>
/// <param name="count">Quantity of that species to place</param>
public void AddMolecules(MoleculeSpecies species, int count)
{
for (int i = 0; i < count; i++)
{
molecules.Enqueue(species);
}
}
private string SpeciesToString(MoleculeSpecies species)
{
if (species == null)
{
return("?");
}
return(species.Name);
}
/// <summary>
/// Adds a Species to COPASI
/// </summary>
/// <returns>COPASI Metabolite</returns>
/// <param name="species">Species.</param>
public CMetab AddSpecies(MoleculeSpecies species)
{
CCompartment compartment = this.compartment;
int status = CMetab.REACTIONS;
CMetab metab = model.createMetabolite(species.Name, compartment.getObjectName());
metab.setStatus(status);
copasiMetabBySpecies.Add(species, metab);
return(metab);
}
public MoleculeSpecies Popup(MoleculeSpecies selected, bool small)
{
int i = ArrayUtility.IndexOf <MoleculeSpecies> (moleculeSpecies, selected);
if (small)
{
i = EditorGUILayout.Popup(i, moleculeSpeciesString, GUILayout.MaxWidth(40));
}
else
{
i = EditorGUILayout.Popup(i, moleculeSpeciesString);
}
return(GetSelection(moleculeSpecies, i));
}
/// <summary>
/// Place all the molecules in the placement queue.
/// </summary>
public void Place()
{
while (molecules.Count > 0)
{
// Get next species to add
MoleculeSpecies s = molecules.Dequeue();
// Get random location
// s.Size is subtracted so never half of the molecule reaches outside the defined radius
Vector3 l = Location + Random.insideUnitSphere * (Utility.Utils.ScaleFromNm(Radius) - s.Size);
// create molecule
Molecule m = s.CreateMolecule(l);
// Add DelayedDrag component that resets the drag after a
// specified amount of time
DelayedDrag delayedDrag = m.gameObject.AddComponent <DelayedDrag>();
delayedDrag.delay = DragDelay;
delayedDrag.initialDrag = InitialDrag;
delayedDrag.drag = Molecule.Drag;
}
}
public MoleculeSpeciesPopup(CUE cue, bool nullPossible)
{
MoleculeSpecies[] cueSpecies = cue.Species;
moleculeSpecies = new MoleculeSpecies[cueSpecies.Length + (nullPossible ? 1 : 0)];
moleculeSpeciesString = new string[moleculeSpecies.Length];
int i = 0;
if (nullPossible)
{
moleculeSpecies[i] = null;
moleculeSpeciesString[i] = "none";
i++;
}
foreach (var item in cueSpecies)
{
moleculeSpecies[i] = item;
moleculeSpeciesString[i] = item.Name;
i++;
}
}
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);
}
/// <summary>
/// Remove a species.
/// </summary>
/// <param name="species">Species to remove.</param>
public void RemoveSpecies(MoleculeSpecies species)
{
model.removeMetabolite(GetMetab(species));
copasiMetabBySpecies.Remove(species);
}
/// <summary>
/// Gets the COPASI Metabolite by Species
/// </summary>
/// <returns>The metab.</returns>
/// <param name="species">Species.</param>
public CMetab GetMetab(MoleculeSpecies species)
{
return(copasiMetabBySpecies [species]);
}
