/// <summary>*************************************************************
/// see:
/// Defining the Axis of a Helix
/// Peter C Kahn
/// Computers Chem. Vol 13, No 3, pp 185-189, 1989
///
/// Simple Methods for Computing the Least Squares Line
/// in Three Dimensions
/// Peter C Kahn
/// Computers Chem. Vol 13, No 3, pp 191-195, 1989
/// **************************************************************
/// </summary>
public virtual void calcCenter()
{
if (center == null)
{
int i = monomerIndex + monomerCount - 1;
center = new Point3f(apolymer.getLeadPoint(i));
while (--i >= monomerIndex)
center.add(apolymer.getLeadPoint(i));
center.scale(1f / monomerCount);
// System.out.println("structure center is at :" + center);
}
}
public void calcLeadMidpointsAndWingVectors()
{
// System.out.println("Polymer.calcLeadMidpointsAndWingVectors");
int count = monomerCount;
leadMidpoints = new Point3f[count + 1];
wingVectors = new Vector3f[count + 1];
bool _hasWingPoints = hasWingPoints();
Vector3f vectorA = new Vector3f();
Vector3f vectorB = new Vector3f();
Vector3f vectorC = new Vector3f();
Vector3f vectorD = new Vector3f();
Point3f leadPointPrev, leadPoint;
leadMidpoints[0] = InitiatorPoint;
leadPoint = getLeadPoint(0);
Vector3f previousVectorD = null;
for (int i = 1; i < count; ++i)
{
leadPointPrev = leadPoint;
leadPoint = getLeadPoint(i);
Point3f midpoint = new Point3f(leadPoint);
midpoint.add(leadPointPrev);
midpoint.scale(0.5f);
leadMidpoints[i] = midpoint;
if (_hasWingPoints)
{
vectorA.sub(leadPoint, leadPointPrev);
vectorB.sub(leadPointPrev, getWingPoint(i - 1));
vectorC.cross(vectorA, vectorB);
vectorD.cross(vectorA, vectorC);
vectorD.normalize();
if (previousVectorD != null && previousVectorD.angle(vectorD) > System.Math.PI / 2)
vectorD.scale(- 1);
previousVectorD = wingVectors[i] = new Vector3f(vectorD);
}
}
leadMidpoints[count] = TerminatorPoint;
if (!_hasWingPoints)
{
if (count < 3)
{
wingVectors[1] = unitVectorX;
}
else
{
// auto-calculate wing vectors based upon lead atom positions only
// seems to work like a charm! :-)
Point3f next, current, prev;
prev = leadMidpoints[0];
current = leadMidpoints[1];
Vector3f previousVectorC = null;
for (int i = 1; i < count; ++i)
{
next = leadMidpoints[i + 1];
vectorA.sub(prev, current);
vectorB.sub(next, current);
vectorC.cross(vectorA, vectorB);
vectorC.normalize();
if (previousVectorC != null && previousVectorC.angle(vectorC) > System.Math.PI / 2)
vectorC.scale(- 1);
previousVectorC = wingVectors[i] = new Vector3f(vectorC);
prev = current;
current = next;
}
}
}
wingVectors[0] = wingVectors[1];
wingVectors[count] = wingVectors[count - 1];
/*
for (int i = 0; i < wingVectors.length; ++i) {
if (wingVectors[i] == null) {
System.out.println("que? wingVectors[" + i + "] == null?");
System.out.println("hasWingPoints=" + hasWingPoints +
" wingVectors.length=" + wingVectors.length +
" count=" + count);
}
else if (Float.isNaN(wingVectors[i].x)) {
System.out.println("wingVectors[" + i + "]=" + wingVectors[i]);
}
}
*/
}
public Point3f findFractionalAdjustment()
{
Point3f pointMin = new Point3f();
Point3f pointMax = new Point3f();
calcAtomsMinMax(pointMin, pointMax);
pointMin.add(pointMax);
pointMin.scale(0.5f);
Point3f fractionalCenter = pointMin;
System.Console.Out.WriteLine("fractionalCenter=" + fractionalCenter);
Point3f adjustment = pointMax;
adjustment.set_Renamed((float) Math.Floor(fractionalCenter.x), (float) Math.Floor(fractionalCenter.y), (float) Math.Floor(fractionalCenter.z));
return adjustment;
}
public virtual void getLeadMidPoint(int groupIndex, Point3f midPoint)
{
if (groupIndex == monomerCount)
{
--groupIndex;
}
else if (groupIndex > 0)
{
midPoint.set_Renamed(getLeadPoint(groupIndex));
midPoint.add(getLeadPoint(groupIndex - 1));
midPoint.scale(0.5f);
return ;
}
midPoint.set_Renamed(getLeadPoint(groupIndex));
}
