public static double angle(Atom a, Atom b)
{
Vector3D va = new Vector3D(a.getX(), a.getY(), a.getZ());
Vector3D vb = new Vector3D(b.getX(), b.getY(), b.getZ());
return Vector3D.AngleBetween(va, vb);
}
public static double getDistanceFast(Atom a, Atom b)
{
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
return x * x + y * y + z * z;
}
public static Atom add(Atom a, Atom b)
{
Atom c = new Atom();
c.setX(a.getX() + b.getX());
c.setY(a.getY() + b.getY());
c.setZ(a.getZ() + b.getZ());
return c;
}
public static double getDistance(Atom a, Atom b)
{
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
return Math.Sqrt(s);
}
public static double amount(Atom a)
{
return Math.Sqrt(scalarProduct(a, a));
}
public static Atom vectorProduct(Atom a, Atom b)
{
Atom c = new Atom();
c.setX(a.getY() * b.getZ() - a.getZ() * b.getY());
c.setY(a.getZ() * b.getX() - a.getX() * b.getZ());
c.setZ(a.getX() * b.getY() - a.getY() * b.getX());
return c;
}
public static Atom unitVector(Atom a)
{
double amnt = amount(a);
double[] coords = new double[3];
coords[0] = a.getX() / amnt;
coords[1] = a.getY() / amnt;
coords[2] = a.getZ() / amnt;
a.setCoords(coords);
return a;
}
public static double torsionAngle(Atom a, Atom b, Atom c, Atom d)
{
Atom ab = subtract(a, b);
Atom cb = subtract(c, b);
Atom bc = subtract(b, c);
Atom dc = subtract(d, c);
Atom abc = vectorProduct(ab, cb);
Atom bcd = vectorProduct(bc, dc);
double angl = angle(abc, bcd);
/* calc the sign: */
Atom vecprod = vectorProduct(abc, bcd);
double val = scalarProduct(cb, vecprod);
if (val < 0.0) angl = -angl;
return angl;
}
public static Atom subtract(Atom a, Atom b)
{
Atom c = new Atom();
c.setX(a.getX() - b.getX());
c.setY(a.getY() - b.getY());
c.setZ(a.getZ() - b.getZ());
return c;
}
public void setC(Atom c)
{
C = c;
}
public static Atom invert(Atom a)
{
double[] coords = new double[] { 0.0, 0.0, 0.0 };
Atom zero = new Atom();
zero.setCoords(coords);
return subtract(zero, a);
}
public void setO(Atom o)
{
O = o;
}
public void setN(Atom n)
{
N = n;
}
public void setCB(Atom cB)
{
CB = cB;
}
public void setCA(Atom cA)
{
CA = cA;
}
public static double scalarProduct(Atom a, Atom b)
{
return a.getX() * b.getX() + a.getY() * b.getY() + a.getZ() * b.getZ();
}
private Structure loadStructure(string fileName)
{
Structure structure = new Structure();
int l = fileName.Length;
structure.PDBCode = fileName.Substring(l-8,4);
bool flag = false;
string line = "";
StreamReader file = new StreamReader(fileName);
Group g = new Group();
AminoAcid aa = new AminoAcid();
while ((line = file.ReadLine()) != null)
{
if (line.StartsWith("ATOM"))
{
try{
if (flag)
{
g.groupID = (line.ElementAt(21) - 65);
aa.aaID = Convert.ToInt16(line.Substring(22, 4).Trim()); flag = false;
}
if (aa.aaID != (Convert.ToInt16(line.Substring(22, 4).Trim())))
{
g.AA.Add(aa);
aa = new AminoAcid();
aa.aaID = Convert.ToInt16(line.Substring(22, 4).Trim());
}
if (g.groupID != (line.ElementAt(21) - 65))
{
structure.Groups.Add(g);
g = new Group();
g.groupID = (line.ElementAt(21) - 65);
}
Atom ob = new Atom();
ob.setX(Convert.ToDouble(line.Substring(30, 8).Trim()));
ob.setY(Convert.ToDouble(line.Substring(38, 8).Trim()));
ob.setZ(Convert.ToDouble(line.Substring(46, 8).Trim()));
ob.Name = line.Substring(12, 3).Trim();
if (ob.Name.Equals("N")) aa.setN(ob);
else if (ob.Name.Equals("CA")) aa.setCA(ob);
else if (ob.Name.Equals("CB")) aa.setCB(ob);
else if (ob.Name.Equals("O")) aa.setO(ob);
else if (ob.Name.Equals("C")) aa.setC(ob);
}
catch (Exception) { }
}
}
g.AA.Add(aa); structure.Groups.Add(g);
file.Close();
count++;
return structure;
}
