/// <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 Âle;ngstrom.
/// </summary>
public virtual void rebond(IAtomContainer container)
{
container.removeAllBonds();
maxCovalentRadius = 0.0;
// construct a new binary space partition tree
bspt = new Bspt(3);
IAtom[] atoms = container.Atoms;
for (int i = atoms.Length; --i >= 0; )
{
IAtom atom = atoms[i];
double myCovalentRadius = atom.CovalentRadius;
if (myCovalentRadius == 0.0)
{
//throw new CDKException("Atom(s) does not have covalentRadius defined.");
}
else
{
if (myCovalentRadius > maxCovalentRadius)
maxCovalentRadius = myCovalentRadius;
TupleAtom tupleAtom = new TupleAtom(atom);
bspt.addTuple(tupleAtom);
}
}
// rebond all atoms
for (int i = atoms.Length; --i >= 0; )
{
bondAtom(container, atoms[i]);
}
}
public EnumerateSphere(Bspt bspt, Bspt.Tuple center, double distance, bool tHemisphere)
{
this.bspt = bspt;
this.distance = distance;
this.distance2 = distance * distance;
this.center = center;
this.tHemisphere = tHemisphere;
centerValues = new double[bspt.dimMax];
for (int dim = bspt.dimMax; --dim >= 0;)
{
centerValues[dim] = center.getDimValue(dim);
}
stack = new Node[Bspt.stackDepth];
sp = 0;
Bspt.Element ele = bspt.eleRoot;
while (ele is Node)
{
Node node = (Node)ele;
if (center.getDimValue(node.dim) - distance <= node.splitValue)
{
if (sp == Bspt.stackDepth)
{
System.Console.Out.WriteLine("Bspt.EnumerateSphere tree stack overflow");
}
stack[sp++] = node;
ele = node.eleLE;
}
else
{
ele = node.eleGE;
}
}
leaf = (Leaf)ele;
i = 0;
}
public RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
{
this.maxCovalentRadius = maxCovalentRadius;
this.bondTolerance = bondTolerance;
this.minBondDistance = minBondDistance;
this.bspt = null;
}
public RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
{
this.maxCovalentRadius = maxCovalentRadius;
this.bondTolerance = bondTolerance;
this.minBondDistance = minBondDistance;
this.bspt = null;
}
public EnumerateNear(Bspt bspt, Bspt.Tuple center, double distance)
{
this.distance = distance;
this.center = center;
stack = new Node[Bspt.stackDepth];
sp = 0;
Bspt.Element ele = bspt.eleRoot;
while (ele is Node)
{
Node node = (Node)ele;
if (center.getDimValue(node.dim) - distance <= node.splitValue)
{
if (sp == Bspt.stackDepth)
{
System.Console.Out.WriteLine("Bspt.EnumerateNear tree stack overflow");
}
stack[sp++] = node;
ele = node.eleLE;
}
else
{
ele = node.eleGE;
}
}
leaf = (Leaf)ele;
i = 0;
}
/// <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 Âle;ngstrom.
/// </summary>
public virtual void rebond(IAtomContainer container)
{
container.removeAllBonds();
maxCovalentRadius = 0.0;
// construct a new binary space partition tree
bspt = new Bspt(3);
IAtom[] atoms = container.Atoms;
for (int i = atoms.Length; --i >= 0;)
{
IAtom atom = atoms[i];
double myCovalentRadius = atom.CovalentRadius;
if (myCovalentRadius == 0.0)
{
//throw new CDKException("Atom(s) does not have covalentRadius defined.");
}
else
{
if (myCovalentRadius > maxCovalentRadius)
{
maxCovalentRadius = myCovalentRadius;
}
TupleAtom tupleAtom = new TupleAtom(atom);
bspt.addTuple(tupleAtom);
}
}
// rebond all atoms
for (int i = atoms.Length; --i >= 0;)
{
bondAtom(container, atoms[i]);
}
}
public EnumerateAll(Bspt bspt)
{
stack = new Node[Bspt.stackDepth];
sp = 0;
Bspt.Element ele = bspt.eleRoot;
while (ele is Node)
{
Node node = (Node)ele;
if (sp == Bspt.stackDepth)
{
System.Console.Out.WriteLine("Bspt.EnumerateAll tree stack overflow");
}
stack[sp++] = node;
ele = node.eleLE;
}
leaf = (Leaf)ele;
i = 0;
}
public bool addTuple(Bspt.Tuple tuple)
{
if (tuple.getDimValue(dim) < splitValue)
{
if (eleLE.addTuple(tuple))
return true;
eleLE = new Node((dim + 1) % dimMax, dimMax, (Leaf)eleLE);
return eleLE.addTuple(tuple);
}
if (tuple.getDimValue(dim) > splitValue)
{
if (eleGE.addTuple(tuple))
return true;
eleGE = new Node((dim + 1) % dimMax, dimMax, (Leaf)eleGE);
return eleGE.addTuple(tuple);
}
if (eleLE.LeafWithSpace)
eleLE.addTuple(tuple);
else if (eleGE.LeafWithSpace)
eleGE.addTuple(tuple);
else if (eleLE is Node)
eleLE.addTuple(tuple);
else if (eleGE is Node)
eleGE.addTuple(tuple);
else
{
eleLE = new Node((dim + 1) % dimMax, dimMax, (Leaf)eleLE);
return eleLE.addTuple(tuple);
}
return true;
}
public bool addTuple(Bspt.Tuple tuple)
{
if (count == Bspt.leafCount)
return false;
tuples[count++] = tuple;
return true;
}
public EnumerateSphere(Bspt bspt, Bspt.Tuple center, double distance, bool tHemisphere)
{
this.bspt = bspt;
this.distance = distance;
this.distance2 = distance * distance;
this.center = center;
this.tHemisphere = tHemisphere;
centerValues = new double[bspt.dimMax];
for (int dim = bspt.dimMax; --dim >= 0; )
centerValues[dim] = center.getDimValue(dim);
stack = new Node[Bspt.stackDepth];
sp = 0;
Bspt.Element ele = bspt.eleRoot;
while (ele is Node)
{
Node node = (Node)ele;
if (center.getDimValue(node.dim) - distance <= node.splitValue)
{
if (sp == Bspt.stackDepth)
System.Console.Out.WriteLine("Bspt.EnumerateSphere tree stack overflow");
stack[sp++] = node;
ele = node.eleLE;
}
else
{
ele = node.eleGE;
}
}
leaf = (Leaf)ele;
i = 0;
}
private bool isWithin(Bspt.Tuple t)
{
double dist2;
double distT;
distT = t.getDimValue(0) - centerValues[0];
if (tHemisphere && distT < 0)
{
return false;
}
dist2 = distT * distT;
if (dist2 > distance2)
{
return false;
}
for (int dim = bspt.dimMax; --dim > 0; )
{
distT = t.getDimValue(dim) - centerValues[dim];
dist2 += distT * distT;
if (dist2 > distance2)
{
return false;
}
}
this.foundDistance2_Renamed_Field = dist2;
return true;
}
public EnumerateSphere enumHemiSphere(Bspt.Tuple center, double distance)
{
return new EnumerateSphere(this, center, distance, true);
}
public EnumerateNear(Bspt bspt, Bspt.Tuple center, double distance)
{
this.distance = distance;
this.center = center;
stack = new Node[Bspt.stackDepth];
sp = 0;
Bspt.Element ele = bspt.eleRoot;
while (ele is Node)
{
Node node = (Node)ele;
if (center.getDimValue(node.dim) - distance <= node.splitValue)
{
if (sp == Bspt.stackDepth)
System.Console.Out.WriteLine("Bspt.EnumerateNear tree stack overflow");
stack[sp++] = node;
ele = node.eleLE;
}
else
{
ele = node.eleGE;
}
}
leaf = (Leaf)ele;
i = 0;
}
public IEnumerator enumNear(Bspt.Tuple center, double distance)
{
return new EnumerateNear(this, center, distance);
}
public EnumerateAll(Bspt bspt)
{
stack = new Node[Bspt.stackDepth];
sp = 0;
Bspt.Element ele = bspt.eleRoot;
while (ele is Node)
{
Node node = (Node)ele;
if (sp == Bspt.stackDepth)
System.Console.Out.WriteLine("Bspt.EnumerateAll tree stack overflow");
stack[sp++] = node;
ele = node.eleLE;
}
leaf = (Leaf)ele;
i = 0;
}
public void addTuple(Bspt.Tuple tuple)
{
if (!eleRoot.addTuple(tuple))
{
eleRoot = new Node(0, dimMax, (Leaf)eleRoot);
if (!eleRoot.addTuple(tuple))
System.Console.Out.WriteLine("Bspt.addTuple() failed");
}
}