public virtual void lookForHbonds(NucleicPolymer other, BitArray bsA, BitArray bsB)
{
//System.out.println("NucleicPolymer.lookForHbonds()");
for (int i = monomerCount; --i >= 0;)
{
NucleicMonomer myNucleotide = (NucleicMonomer)monomers[i];
if (!myNucleotide.Purine)
{
continue;
}
Atom myN1 = myNucleotide.N1;
Atom bestN3 = null;
float minDist2 = 5 * 5;
NucleicMonomer bestNucleotide = null;
for (int j = other.monomerCount; --j >= 0;)
{
NucleicMonomer otherNucleotide = (NucleicMonomer)other.monomers[j];
if (!otherNucleotide.Pyrimidine)
{
continue;
}
Atom otherN3 = otherNucleotide.N3;
float dist2 = myN1.point3f.distanceSquared(otherN3.point3f);
if (dist2 < minDist2)
{
bestNucleotide = otherNucleotide;
bestN3 = otherN3;
minDist2 = dist2;
}
}
if (bestN3 != null)
{
createHydrogenBond(myN1, bestN3, bsA, bsB);
if (myNucleotide.Guanine)
{
createHydrogenBond(myNucleotide.N2, bestNucleotide.O2, bsA, bsB);
createHydrogenBond(myNucleotide.O6, bestNucleotide.N4, bsA, bsB);
}
else
{
createHydrogenBond(myNucleotide.N6, bestNucleotide.O4, bsA, bsB);
}
}
}
}
public virtual void lookForHbonds(NucleicPolymer other, BitArray bsA, BitArray bsB)
{
//System.out.println("NucleicPolymer.lookForHbonds()");
for (int i = monomerCount; --i >= 0; )
{
NucleicMonomer myNucleotide = (NucleicMonomer) monomers[i];
if (!myNucleotide.Purine)
continue;
Atom myN1 = myNucleotide.N1;
Atom bestN3 = null;
float minDist2 = 5 * 5;
NucleicMonomer bestNucleotide = null;
for (int j = other.monomerCount; --j >= 0; )
{
NucleicMonomer otherNucleotide = (NucleicMonomer) other.monomers[j];
if (!otherNucleotide.Pyrimidine)
continue;
Atom otherN3 = otherNucleotide.N3;
float dist2 = myN1.point3f.distanceSquared(otherN3.point3f);
if (dist2 < minDist2)
{
bestNucleotide = otherNucleotide;
bestN3 = otherN3;
minDist2 = dist2;
}
}
if (bestN3 != null)
{
createHydrogenBond(myN1, bestN3, bsA, bsB);
if (myNucleotide.Guanine)
{
createHydrogenBond(myNucleotide.N2, bestNucleotide.O2, bsA, bsB);
createHydrogenBond(myNucleotide.O6, bestNucleotide.N4, bsA, bsB);
}
else
{
createHydrogenBond(myNucleotide.N6, bestNucleotide.O4, bsA, bsB);
}
}
}
}