/**
* Calculate the psi angle.
*
* @param a an AminoAcid object
* @param b an AminoAcid object
* @return a double
* @throws StructureException if aminoacids not connected or if any of the 4 needed atoms missing
*/
public static double getPsi(AminoAcid a, AminoAcid b)
{
if (!isConnected(a, b))
{
//System.out.println("can not calc Psi - AminoAcids are not connected!");
}
Atom a_N = a.getN();
Atom a_CA = a.getCA();
Atom a_C = a.getC();
Atom b_N = b.getN();
// C and N were checked in isConnected already
if (a_CA == null) { }// System.out.println("Can not calculate Psi, CA atom is missing");
return torsionAngle(a_N, a_CA, a_C, b_N);
}
/**
* Test if two amino acids are connected, i.e.
* if the distance from C to N < 2.5 Angstrom.
*
* If one of the AminoAcids has an atom missing, returns false.
*
* @param a an AminoAcid object
* @param b an AminoAcid object
* @return true if ...
*/
public static Boolean isConnected(AminoAcid a, AminoAcid b)
{
Atom C = null;
Atom N = null;
C = a.getC();
N = b.getN();
if (C == null || N == null)
{
return(false);
}
// one could also check if the CA atoms are < 4 A...
//double distance = getDistance(C,N);
//return distance < 2.5;
return(true);
}
/**
* Calculate the psi angle.
*
* @param a an AminoAcid object
* @param b an AminoAcid object
* @return a double
* @throws StructureException if aminoacids not connected or if any of the 4 needed atoms missing
*/
public static double getPsi(AminoAcid a, AminoAcid b)
{
if (!isConnected(a, b))
{
//System.out.println("can not calc Psi - AminoAcids are not connected!");
}
Atom a_N = a.getN();
Atom a_CA = a.getCA();
Atom a_C = a.getC();
Atom b_N = b.getN();
// C and N were checked in isConnected already
if (a_CA == null)
{
} // System.out.println("Can not calculate Psi, CA atom is missing");
return(torsionAngle(a_N, a_CA, a_C, b_N));
}
/**
* Test if two amino acids are connected, i.e.
* if the distance from C to N < 2.5 Angstrom.
*
* If one of the AminoAcids has an atom missing, returns false.
*
* @param a an AminoAcid object
* @param b an AminoAcid object
* @return true if ...
*/
public static Boolean isConnected(AminoAcid a, AminoAcid b)
{
Atom C = null;
Atom N = null;
C = a.getC();
N = b.getN();
if (C == null || N == null)
return false;
// one could also check if the CA atoms are < 4 A...
//double distance = getDistance(C,N);
//return distance < 2.5;
return true;
}
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;
}