public virtual void bondAminoHydrogen(int indexDonor, Point3f hydrogenPoint, BitArray bsA, BitArray bsB)
{
AminoMonomer source = (AminoMonomer)monomers[indexDonor];
Point3f sourceAlphaPoint = source.LeadAtomPoint;
Point3f sourceNitrogenPoint = source.NitrogenAtomPoint;
int energyMin1 = 0;
int energyMin2 = 0;
int indexMin1 = -1;
int indexMin2 = -1;
for (int i = monomerCount; --i >= 0;)
{
if ((i == indexDonor || (i + 1) == indexDonor) || (i - 1) == indexDonor)
{
continue;
}
AminoMonomer target = (AminoMonomer)monomers[i];
Point3f targetAlphaPoint = target.LeadAtomPoint;
float dist2 = sourceAlphaPoint.distanceSquared(targetAlphaPoint);
if (dist2 > maxHbondAlphaDistance2)
{
continue;
}
int energy = calcHbondEnergy(sourceNitrogenPoint, hydrogenPoint, target);
if (debugHbonds)
{
System.Console.Out.WriteLine("HbondEnergy=" + energy + " dist2=" + dist2 + " max^2=" + maxHbondAlphaDistance2);
}
if (energy < energyMin1)
{
energyMin2 = energyMin1;
indexMin2 = indexMin1;
energyMin1 = energy;
indexMin1 = i;
}
else if (energy < energyMin2)
{
energyMin2 = energy;
indexMin2 = i;
}
}
if (indexMin1 >= 0)
{
mainchainHbondOffsets[indexDonor] = (short)(indexDonor - indexMin1);
min1Indexes[indexDonor] = (short)indexMin1;
min1Energies[indexDonor] = (short)energyMin1;
createResidueHydrogenBond(indexDonor, indexMin1, bsA, bsB);
if (indexMin2 >= 0)
{
createResidueHydrogenBond(indexDonor, indexMin2, bsA, bsB);
min2Indexes[indexDonor] = (short)indexMin2;
min2Energies[indexDonor] = (short)energyMin2;
}
}
}
// find the longest bond to discard
// but return null if atomChallenger is longer than any
// established bonds
// note that this algorithm works when maximum valence == 0
public Bond getLongestBondToDiscard(Atom atomChallenger)
{
float dist2Longest = point3f.distanceSquared(atomChallenger.point3f);
Bond bondLongest = null;
for (int i = bonds.Length; --i >= 0;)
{
Bond bond = bonds[i];
Atom atomOther = bond.atom1 != this?bond.atom1:bond.atom2;
float dist2 = point3f.distanceSquared(atomOther.point3f);
if (dist2 > dist2Longest)
{
bondLongest = bond;
dist2Longest = dist2;
}
}
// out.println("atom at " + point3f + " suggests discard of " +
// bondLongest + " dist2=" + dist2Longest);
return(bondLongest);
}
public virtual int calcHbondEnergy(Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target)
{
Point3f targetOxygenPoint = target.CarbonylOxygenAtomPoint;
float distON2 = targetOxygenPoint.distanceSquared(nitrogenPoint);
if (distON2 < minimumHbondDistance2)
{
return(-9900);
}
//why would this not have been in here? RMH 03/8/06
// if (distON2 > hbondMax2)
// return 0;
//nevermind! :)
if (debugHbonds)
{
System.Console.Out.WriteLine("calchbondenergy: " + hydrogenPoint.x + "," + hydrogenPoint.y + "," + hydrogenPoint.z);
}
float distOH2 = targetOxygenPoint.distanceSquared(hydrogenPoint);
if (distOH2 < minimumHbondDistance2)
{
return(-9900);
}
Point3f targetCarbonPoint = target.CarbonylCarbonAtomPoint;
float distCH2 = targetCarbonPoint.distanceSquared(hydrogenPoint);
if (distCH2 < minimumHbondDistance2)
{
return(-9900);
}
float distCN2 = targetCarbonPoint.distanceSquared(nitrogenPoint);
if (distCN2 < minimumHbondDistance2)
{
return(-9900);
}
double distOH = System.Math.Sqrt(distOH2);
double distCH = System.Math.Sqrt(distCH2);
double distCN = System.Math.Sqrt(distCN2);
double distON = System.Math.Sqrt(distON2);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int energy = (int)((QConst / distOH - QConst / distCH + QConst / distCN - QConst / distON));
if (debugHbonds)
{
System.Console.Out.WriteLine(" distOH=" + distOH + " distCH=" + distCH + " distCN=" + distCN + " distON=" + distON + " energy=" + energy);
}
if (energy < -9900)
{
return(-9900);
}
if (energy > -500)
{
return(0);
}
return(energy);
}