// αR: −100° ≤ φ ≤ −30°, −80° ≤ ψ ≤ −5°;
// near-αR: −175° ≤ φ ≤ −100°, −55° ≤ ψ ≤ −5°;
// αL: 5° ≤ φ ≤ 75°, 25° ≤ ψ ≤ 120°;
// β: −180° ≤ φ ≤ −50°, 80° ≤ ψ ≤ −170°;
// PIR: −180° ≤ φ ≤ −115°, 50° ≤ ψ ≤ 100°;
// PIIL: −110° ≤ φ ≤ −50°, 120° ≤ ψ ≤ 180°
public static SS[] GetPhiPsiSS(IChain peptide, int minStructureLength = 1)
{
int start = 1;
SS[] bins = new SS[peptide.Count];
for (int i = 1; i < peptide.Count - 1; i++)
{
// Make the bin assignment
if (i != peptide.Count - 1)
{
double phi = peptide.GetPhiDegrees(i);
double psi = peptide.GetPsiDegrees(i);
if (-100 <= phi && phi <= -30 && -80 <= psi && psi <= -5)
{
bins[i] = SS.Helix;
}
if (-180 <= phi && phi <= -50 && (psi <= -170 || 80 <= psi))
{
bins[i] = SS.Extended;
}
}
// Clear preceding assignments in range [start, i-1] if there
// is a transition before the minimum structure length
if (bins[i] != bins[start])
{
if (i - start < minStructureLength)
{
for (int j = start; j < i; j++)
{
bins[j] = SS.Loop;
}
}
start = i;
}
}
for (int i = 0; i < peptide.Count; i++)
{
if (bins[i] == SS.Undefined)
{
bins[i] = SS.Loop;
}
}
return(bins);
}
public double GetPhiDegrees(int index)
{
return(_template.GetPhiDegrees(index));
}
