public static double getPhi(AminoAcid a, AminoAcid b)
{
if (!isConnected(a, b))
{
//System.out.println("can not calc Phi - AminoAcids are not connected!");
}
Atom a_C = a.getC();
Atom b_N = b.getN();
Atom b_CA = b.getCA();
Atom b_C = b.getC();
// C and N were checked in isConnected already
if (b_CA == null) { }// System.out.println("Can not calculate Phi, CA atom is missing");
return torsionAngle(a_C, b_N, b_CA, b_C);
}
/**
* 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;
}