/// <summary>
/// Rebonding using a Binary Space Partition Tree. Note, that any bonds
/// defined will be deleted first. It assumes the unit of 3D space to
/// be 1 Å.
/// </summary>
public void Rebond(IAtomContainer container)
{
container.Bonds.Clear();
maxCovalentRadius = 0.0;
// construct a new binary space partition tree
bspt = new Bspt <ITupleAtom>(3);
foreach (var atom in container.Atoms)
{
double myCovalentRadius = atom.CovalentRadius.Value;
if (myCovalentRadius == 0.0)
{
throw new CDKException("Atom(s) does not have covalentRadius defined.");
}
if (myCovalentRadius > maxCovalentRadius)
{
maxCovalentRadius = myCovalentRadius;
}
TupleAtom tupleAtom = new TupleAtom(atom);
bspt.AddTuple(tupleAtom);
}
// rebond all atoms
foreach (var atom in container.Atoms)
{
BondAtom(container, atom);
}
}
public RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
{
this.maxCovalentRadius = maxCovalentRadius;
this.bondTolerance = bondTolerance;
this.minBondDistance = minBondDistance;
this.bspt = null;
}
public Leaf(Bspt bspt, Leaf leaf, int countToKeep)
: this(bspt)
{
for (int i = countToKeep; i < Bspt.leafCountMax; ++i)
{
tuples[count++] = leaf.tuples[i];
leaf.tuples[i] = null;
}
leaf.count = countToKeep;
}
public Leaf(Bspt bspt, Leaf leaf, int countToKeep)
: this(bspt)
{
for (int i = countToKeep; i < Bspt.leafCountMax; ++i)
{
tuples[count++] = leaf.tuples[i];
leaf.tuples[i] = null;
}
leaf.count = countToKeep;
}
public Leaf(Bspt bspt)
{
this.bspt = bspt;
count = 0;
tuples = new Tuple[Bspt.leafCountMax];
}
public SphereIterator(Bspt bspt)
{
this.bspt = bspt;
centerValues = new float[bspt.dimMax];
stack = new Element[bspt.treeDepth];
}
public Leaf(Bspt bspt)
{
this.bspt = bspt;
count = 0;
tuples = new Tuple[Bspt.leafCountMax];
}
public SphereIterator(Bspt bspt)
{
this.bspt = bspt;
centerValues = new float[bspt.dimMax];
stack = new Element[bspt.treeDepth];
}
