public static atom_info findMole(Vector3 pos)
{
float best_dist = 100;
atom_info c_best = new atom_info("null", 0, 0, 0, null);
foreach (var i in atomlist)
{
float c = Vector3.Distance(pos, i.pos);
if (c < 0.15 && c < best_dist)
{
c_best = i;
best_dist = c;
}
}
return(c_best);
}
public static void create_vessel(atom_info a1, atom_info a2)
{
Vector3 p1 = a1.pos;
Vector3 p2 = a2.pos;
Vector3 pos = Vector3.Lerp(p1, p2, (float)0.5);
GameObject segObj = GameObject.CreatePrimitive(PrimitiveType.Cylinder);
segObj.transform.parent = bp.transform;
segObj.name = a1.name + "-" + a2.name + " " + pos;
Vector3 newScale = segObj.transform.localScale;
newScale.y = Vector3.Distance(p1, p2) * .5f;
newScale.x = .01f;
newScale.z = .01f;
segObj.transform.localScale = newScale;
segObj.transform.position = pos;
segObj.transform.up = p2 - p1;
}
GameObject draw_atom(atom_info i)
{
GameObject sphere = GameObject.CreatePrimitive(PrimitiveType.Sphere);
sphere.transform.parent = Atom_Parent.transform;
sphere.name = i.name + "\t" + i.pos.ToString();
sphere.transform.position = i.pos;
switch (i.name)
{
case "Pb":
sphere.transform.localScale = new Vector3(0.08f, 0.08f, 0.08f);
sphere.GetComponent <Renderer>().material.color = colors[1];
i.set_radius(1.47f);
i.set_weight(207.2f);
break;
case "I":
sphere.transform.localScale = new Vector3(0.07f, 0.07f, 0.07f);
sphere.GetComponent <Renderer>().material.color = colors[2];
i.set_radius(1.33f);
i.set_weight(126.904f);
break;
case "C":
sphere.transform.localScale = new Vector3(0.06f, 0.06f, 0.06f);
sphere.GetComponent <Renderer>().material.color = colors[3];
i.set_radius(0.77f);
i.set_weight(12.011f);
break;
case "H":
sphere.transform.localScale = new Vector3(0.03f, 0.03f, 0.03f);
sphere.GetComponent <Renderer>().material.color = colors[4];
i.set_radius(0.37f);
i.set_weight(1.008f);
break;
case "N":
sphere.transform.localScale = new Vector3(0.06f, 0.06f, 0.06f);
sphere.GetComponent <Renderer>().material.color = colors[5];
i.set_radius(0.75f);
i.set_weight(14.007f);
break;
case "Zn":
sphere.transform.localScale = new Vector3(0.07f, 0.07f, 0.07f);
sphere.GetComponent <Renderer>().material.color = colors[6];
i.set_radius(1.31f);
i.set_weight(65.38f);
break;
case "Cu":
sphere.transform.localScale = new Vector3(0.07f, 0.07f, 0.07f);
sphere.GetComponent <Renderer>().material.color = colors[0];
i.set_radius(1.38f);
i.set_weight(63.546f);
break;
case "S":
sphere.transform.localScale = new Vector3(0.05f, 0.05f, 0.05f);
sphere.GetComponent <Renderer>().material.color = colors[2];
i.set_radius(1.02f);
i.set_weight(32.06f);
break;
default:
sphere.transform.localScale = new Vector3(0.05f, 0.05f, 0.05f);
sphere.GetComponent <Renderer>().material.color = colors[6];
i.set_radius(1f);
i.set_weight(10f);
break;
}
i.set_sphere(sphere);
return(sphere);
}
private void read_atom(String filename)
{
atomlist = new List <atom_info>();
try
{
string line;
StreamReader fileReader = new StreamReader(filename, Encoding.Default);
// The first two lines of the file are metadata
// The first line is the number of atoms
// The second line is the types of atoms
line = fileReader.ReadLine();
// Convert this line to a int
int numAtoms;
numAtoms = int.Parse(line);
line = fileReader.ReadLine();
string[] atomTypesRAW = line.Split(' ');
List <string> atomTypes = new List <string>();
// This line is harder to read because VESTA XYZ files are dumb IMO...
for (int i = 0; i < atomTypesRAW.Length; i++)
{
// Make sure split string is valid
// If so add it to our array
if (atomTypesRAW[i].Length > 0)
{
atomTypes.Add(atomTypesRAW[i]);
}
}
// Now read all the atoms in the file. We can read lines for the numAtoms in the file
for (int i = 0; i < numAtoms; i++)
{
line = fileReader.ReadLine();
// For right now, just make a sphere for every atom we see (sphere size of .5 or something)
string[] atomDataRAW = line.Split(' ');
// There should be 4 pieces of valid data. The first one is the atom name. The rest are float values of position in the molecule
bool readName = false; // Simple check to see if we have read a name or not
string atomName = "C";
float? x = null;
float? y = null;
float? z = null;
for (int j = 0; j < atomDataRAW.Length; j++)
{
if (atomDataRAW[j].Length > 0)
{
if (!readName)
{
atomName = atomDataRAW[j];
readName = true;
}
else
{
if (x == null)
{
x = float.Parse(atomDataRAW[j], System.Globalization.CultureInfo.InvariantCulture.NumberFormat);
}
else if (y == null)
{
y = float.Parse(atomDataRAW[j], System.Globalization.CultureInfo.InvariantCulture.NumberFormat);
}
else
{
z = float.Parse(atomDataRAW[j], System.Globalization.CultureInfo.InvariantCulture.NumberFormat);
}
}
}
}
atom_info atm = new atom_info(atomName, x.GetValueOrDefault() / 22.0f, y.GetValueOrDefault() / 22.0f, z.GetValueOrDefault() / 22.0f, null);
atm.set_sphere(draw_atom(atm));
atomlist.Add(atm);
}
}
catch (Exception e)
{
Debug.LogError("Something Went Wrong: " + e.Message + "\n" + e.StackTrace + " " + e.Source);
Debug.LogError(filename);
return;
}
Atom_Parent.transform.parent = null;
var children = Atom_Parent.transform.Cast <Transform>().ToList();
var pos = Vector3.zero;
foreach (var C in children)
{
pos += C.position;
C.parent = null;
}
pos /= children.Count;
Atom_Parent.transform.position = pos;
overallParent.transform.position = pos;
foreach (var C in children)
{
C.parent = Atom_Parent.transform;
}
Atom_Parent.transform.parent = overallParent.transform;
}
//public LineRenderer lineRenderer;
public atom_bond(atom_info atom1, atom_info atom2)
{
this.atom1 = atom1;
this.atom2 = atom2;
}
