void Start()
{
List <Atom> atoms;
List <List <int> > connections;
string model_name;
try {
model_name = ParseInputModelFile();
PDBParser.ParseAtomsAndConnections(@"Assets/MModels/" + model_name, out atoms, out connections);
}
catch (System.IO.IOException) {
print("Parsing input error");
return;
}
/* Spawn the objects */
foreach (Atom atom in atoms)
{
/* Units in Nano meters */
Vector3 atom_position = new Vector3(atom.x_, atom.y_, atom.z_);
atoms_bounding_box_.AddPoint(atom_position);
/* Instantiate the atom */
GameObject temp = Instantiate(prefab_atom, atom_position, Quaternion.identity);
temp.transform.parent = transform;
temp.isStatic = this.gameObject.isStatic;
/* Find ISphere component, and set the atom information */
ISphere isphere = temp.GetComponent <ISphere>();
isphere.atom_ = atom;
ispheres_.Add(isphere);
/* Insert to the dictionaries used */
InsertToAtomsDictionary(isphere);
InsertToResiudesDictionary(isphere);
InsertToChainsDictionary(isphere);
}
/* Parse connections, currently the application does not do something with these connections */
foreach (List <int> c in connections)
{
int atom_id = c[0];
for (int i = 1; i < c.Count; i++)
{
ISphere connection_isphere = ispheres_[c[i]];
ispheres_[atom_id].connections_.Add(connection_isphere);
}
}
/* Spawn bonds */
Transform bonds_transform = transform.GetChild(0);
int bonds = 0;
/* For all resisudes */
foreach (KeyValuePair <int, List <ISphere> > value in residue_dictionary)
{
/* Get combinations of two atoms */
List <ISphere> resiude_atoms = value.Value;
for (int ia = 0; ia < resiude_atoms.Count; ia++)
{
ISphere a = resiude_atoms[ia];
Vector3 a_position = a.transform.position;
float a_covalent_radius = AtomicRadii.GetCovalentRadius(a.atom_.element_);
for (int ib = 0; ib < resiude_atoms.Count; ib++)
{
if (!(ia > ib))
{
continue;
}
ISphere b = resiude_atoms[ib];
Vector3 b_position = b.transform.position;
float b_covalent_radius = AtomicRadii.radii_covalent[b.atom_.element_];
/* If their distance is smaller then the sume of radius + plus a bias, then spawn a bond */
float distance = Vector3.Distance(a_position, b_position);
if (distance <= a_covalent_radius + b_covalent_radius + 0.015)
{
bonds++;
GameObject temp = Instantiate(prefab_bond, a_position, Quaternion.identity);
temp.transform.parent = bonds_transform;
temp.isStatic = this.gameObject.isStatic;
/* Rotate it accordingly */
Vector3 direction = b_position - a_position;
Quaternion toRotation = Quaternion.FromToRotation(new Vector3(0, 1, 0), direction);
temp.transform.rotation = toRotation;
/* Set size and radius */
ICylinder icylinder = temp.GetComponent <ICylinder>();
icylinder.radius_ = AtomicRadii.ball_and_stick_bond_radius;
icylinder.height_ = distance;
}
}
}
}
Debug.Log("Spawned: " + bonds + " bonds");
/* Position the model and the camera in the world */
SetCameraAndPanelBoxPosition(atoms_bounding_box_);
bonds_selected_[0] = null;
bonds_selected_[1] = null;
/* Set some default info on the world panel */
SELECTION_MODE_SPHERE_RADIUS = AtomicRadii.ball_and_stick_radius * 5.0f;
transform.GetChild(1).GetComponent <ModePanel>().SetRadius(SELECTION_MODE_SPHERE_RADIUS);
info_ui_ = Camera.main.transform.Find("AtomInfoBox").GetComponent <AtomInfoBox>();
}
// Start is called before the first frame update
void Start()
{
List <Atom> atoms;
List <List <int> > connections;
PDBParser.ParseAtomsAndConnections(@"Assets/MModels/1tes.pdb", out atoms, out connections);
//PDBParser.ParseAtomsAndConnections(@"Assets/MModels/4f0h.pdb", out atoms, out connections);
//PDBParser.ParseAtomsAndConnections(@"Assets/MModels/1s5l.pdb", out atoms, out connections);
//PDBParser.ParseAtomsAndConnections(@"Assets/MModels/1ea4.pdb", out atoms, out connections);
Bounds atoms_bounding_box = new Bounds();
foreach (Atom atom in atoms)
{
/* Units in Nano meters */
Vector3 atom_position = new Vector3(atom.x_, atom.y_, atom.z_);
atoms_bounding_box.Encapsulate(atom_position);
/* Instantiate the object */
GameObject temp = Instantiate(prefab_atom, atom_position, Quaternion.identity);
temp.transform.parent = transform;
temp.isStatic = this.gameObject.isStatic;
InsertToResiudesDictionary(atom, temp);
}
Transform bonds_transform = transform.GetChild(0);
int bonds = 0;
foreach (KeyValuePair <int, List <Tuple <GameObject, Atom> > > value in residue_dictionary)
{
List <Tuple <GameObject, Atom> > resiude_atoms = value.Value;
for (int ia = 0; ia < resiude_atoms.Count; ia++)
{
GameObject a = resiude_atoms[ia].Item1;
Vector3 a_position = a.transform.position;
float a_covalent_radius = AtomicRadii.GetCovalentRadius(resiude_atoms[ia].Item2.element_);
for (int ib = 0; ib < resiude_atoms.Count; ib++)
{
if (!(ia > ib))
{
continue;
}
GameObject b = resiude_atoms[ib].Item1;
Vector3 b_position = b.transform.position;
float b_covalent_radius = AtomicRadii.radii_covalent[resiude_atoms[ib].Item2.element_];
float distance = Vector3.Distance(a_position, b_position);
if (distance <= a_covalent_radius + b_covalent_radius + 0.015)
{
bonds++;
GameObject temp = Instantiate(prefab_bond, a_position, Quaternion.identity);
temp.transform.parent = bonds_transform;
temp.isStatic = this.gameObject.isStatic;
Vector3 direction = b_position - a_position;
Quaternion toRotation = Quaternion.FromToRotation(new Vector3(0, 1, 0), direction);
temp.transform.rotation = toRotation;
ICylinderBench icylinder = temp.GetComponent <ICylinderBench>();
if (icylinder != null)
{
icylinder.radius_ = AtomicRadii.ball_and_stick_bond_radius;
icylinder.height_ = distance;
}
else
{
temp.transform.localScale = new Vector3(0.5f, 0.5f * distance, 0.5f);
}
}
}
}
}
Debug.Log("Spawned: " + bonds + " bonds");
}
