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 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 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 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 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 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;
}
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);
}
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;
}
