public static Monomer[] getNucleicMonomers(Group[] groups, int firstGroupIndex)
{
NucleicMonomer previous = null;
int count = 0;
for (int i = firstGroupIndex; i < groups.Length; ++i, ++count)
{
Group group = groups[i];
if (!(group is NucleicMonomer))
{
break;
}
NucleicMonomer current = (NucleicMonomer)group;
if (current.polymer != null)
{
break;
}
if (!current.isConnectedAfter(previous))
{
break;
}
previous = current;
}
if (count == 0)
{
return(null);
}
Monomer[] monomers = new Monomer[count];
for (int j = 0; j < count; ++j)
{
monomers[j] = (NucleicMonomer)groups[firstGroupIndex + j];
}
return(monomers);
}
public static new Monomer validateAndAllocate(Chain chain, string group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
{
sbyte[] offsets = scanForOffsets(firstAtomIndex, specialAtomIndexes, interestingNucleicAtomIDs);
if (offsets == null)
{
return(null);
}
NucleicMonomer nucleicMonomer = new NucleicMonomer(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, offsets);
return(nucleicMonomer);
}
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 override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
{
return(true);
}
Atom myPhosphorusAtom = PhosphorusAtom;
if (myPhosphorusAtom == null)
{
return(false);
}
if (!(possiblyPreviousMonomer is NucleicMonomer))
{
return(false);
}
NucleicMonomer other = (NucleicMonomer)possiblyPreviousMonomer;
return(other.O3PrimeAtom.isBonded(myPhosphorusAtom));
}
private void distinguishAndPropogateGroup(int groupIndex, Chain chain, string group3,
int seqcode, int firstAtomIndex, int maxAtomIndex)
{
// System.out.println("distinguish & propogate group:" +
// " group3:" + group3 +
// " seqcode:" + Group.getSeqcodeString(seqcode) +
// " firstAtomIndex:" + firstAtomIndex +
// " maxAtomIndex:" + maxAtomIndex);
int distinguishingBits = 0;
// clear previous specialAtomIndexes
for (int i = JmolConstants.ATOMID_MAX; --i >= 0;)
{
specialAtomIndexes[i] = Int32.MinValue;
}
if (specialAtomIDs != null)
{
for (int i = maxAtomIndex; --i >= firstAtomIndex;)
{
int specialAtomID = specialAtomIDs[i];
if (specialAtomID > 0)
{
if (specialAtomID < JmolConstants.ATOMID_DISTINGUISHING_ATOM_MAX)
{
distinguishingBits |= 1 << specialAtomID;
}
specialAtomIndexes[specialAtomID] = i;
}
}
}
int lastAtomIndex = maxAtomIndex - 1;
if (lastAtomIndex < firstAtomIndex)
{
throw new System.NullReferenceException();
}
Group group = null;
// System.out.println("distinguishingBits=" + distinguishingBits);
if ((distinguishingBits & JmolConstants.ATOMID_PROTEIN_MASK) == JmolConstants.ATOMID_PROTEIN_MASK)
{
// System.out.println("may be an AminoMonomer");
group = AminoMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (distinguishingBits == JmolConstants.ATOMID_ALPHA_ONLY_MASK)
{
// System.out.println("AlphaMonomer.validateAndAllocate");
group = AlphaMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (((distinguishingBits & JmolConstants.ATOMID_NUCLEIC_MASK) == JmolConstants.ATOMID_NUCLEIC_MASK))
{
group = NucleicMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (distinguishingBits == JmolConstants.ATOMID_PHOSPHORUS_ONLY_MASK)
{
// System.out.println("PhosphorusMonomer.validateAndAllocate");
group = PhosphorusMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
if (group == null)
{
group = new Group(chain, group3, seqcode, firstAtomIndex, lastAtomIndex);
}
chain.addGroup(group);
groups[groupIndex] = group;
////////////////////////////////////////////////////////////////
for (int i = maxAtomIndex; --i >= firstAtomIndex;)
{
atoms[i].Group = group;
}
}
public static new Monomer validateAndAllocate(Chain chain, string group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
{
sbyte[] offsets = scanForOffsets(firstAtomIndex, specialAtomIndexes, interestingNucleicAtomIDs);
if (offsets == null)
return null;
NucleicMonomer nucleicMonomer = new NucleicMonomer(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, offsets);
return nucleicMonomer;
}