public TreeViaShape(double _x, double _y, double _thickness, double _height, double depth, double angle = 0, bool polygon = false, bool leaves = false)
{
if (leaves)
{
Line leaf = new Line();
leaf.Stroke = Brushes.Black;
leaf.StrokeStartLineCap = PenLineCap.Round;
leaf.StrokeEndLineCap = PenLineCap.Triangle;
leaf.StrokeThickness = 2;
leaf.X1 = _x; // + _thickness / 2 * Math.Cos(angle);
leaf.Y1 = _y; // + _thickness / 2 * Math.Sin(angle);
leaf.X2 = leaf.X1 + 5 * Math.Sin(angle);
leaf.Y2 = leaf.Y1 - 5 * Math.Cos(angle);
brunch = leaf;
return;
}
if (polygon)
{
Polygon pol = new Polygon();
pol.Stroke = Brushes.Black;
pol.Fill = Brushes.Black;
pol.FillRule = FillRule.Nonzero;
pol.Points.Add(new Point(_x, _y));
pol.Points.Add(new Point(_x + (1 - thick_coef) * _thickness / 2, _y - _height));
pol.Points.Add(new Point(_x + (1 + thick_coef) * _thickness / 2, _y - _height));
pol.Points.Add(new Point(_x + _thickness, _y));
if (angle > 0)
{
pol.RenderTransform = new RotateTransform(angle / rad2deg,
_thickness, 0);
}
else
{
pol.RenderTransform = new RotateTransform(angle / rad2deg,
0, 0);
}
}
else
{
brunch = new Rectangle();
brunch.Height = _height;
brunch.Width = _thickness;
brunch.Stroke = Brushes.Black;
brunch.Fill = Brushes.Black;
Canvas.SetLeft(brunch, _x);
Canvas.SetTop(brunch, _y);
//if (angle > 0)
//brunch.RenderTransform = new RotateTransform(angle / rad2deg,
// _thickness,
// _height);
//else
brunch.RenderTransform = new RotateTransform(angle / rad2deg,
0, _height);
}
_thickness = _thickness * thick_coef;
//_y -= _height;
if (_height > 5 && depth < 350)
{
_x += _height * Math.Sin(angle) + ((brunch.Width - _thickness) / 2) * Math.Cos(angle);
_y += _height * (1 - Math.Cos(angle)) - ((brunch.Width - _thickness) / 2) * Math.Sin(-angle);
if (StaticRandom.NextDouble() < 0.9 || _thickness > 4)
{
center = new TreeViaShape(_x, _y - _height * height_coef,
_thickness,
_height * height_coef,
depth + _height,
angle,
polygon);
}
if (StaticRandom.NextDouble() < 0.7 && (angle > -110 * rad2deg || _height < 15))
{
double new_height = _height * StaticRandom.NextGaussian(0.8, 0.2, 0.3, 0.9);
//double new_height = _height * StaticRandom.NextDouble(0.7, 0.9);
left = new TreeViaShape(_x, _y - new_height,
StaticRandom.NextDouble(_thickness * 0.6, _thickness * 0.9),
new_height,
depth + _height,
angle - StaticRandom.NextDouble(10, 46) * rad2deg,
polygon);
}
if (StaticRandom.NextDouble() < 0.7 && (angle < 110 * rad2deg || _height < 15))
{
double new_height = _height * StaticRandom.NextGaussian(0.8, 0.2, 0.3, 0.9);
//double new_height = _height * StaticRandom.NextDouble(0.7, 0.9);
right = new TreeViaShape(_x, _y - new_height,
StaticRandom.NextDouble(_thickness * 0.6, _thickness * 0.9),
new_height,
depth + _height,
angle + StaticRandom.NextDouble(10, 46) * rad2deg,
polygon);
}
}
else
{
_x += _height * Math.Sin(angle) + (brunch.Width / 2) * Math.Cos(angle);
_y += _height * (1 - Math.Cos(angle)) + (brunch.Width / 2) * Math.Sin(Math.Abs(angle));
center = new TreeViaShape(_x, _y, _thickness, _height, 0, angle, polygon, true);
left = new TreeViaShape(_x - StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Sin(angle),
_y + StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Cos(angle),
_thickness, _height, 0,
angle - StaticRandom.NextDouble(60, 90) * rad2deg, polygon, true);
right = new TreeViaShape(_x - StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Sin(angle),
_y + StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Cos(angle),
_thickness, _height, 0,
angle + StaticRandom.NextDouble(60, 90) * rad2deg, polygon, true);
}
}
public void GenerateProteins()
{
var angleInverseDistributions = LoadInverseAngleDistributions();
var pdbId = "1a2b";
var aminoAcidSequence = ReadAminoAcidSequenceFromPositionFile($@"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\AminoAcidPositions\pdb{pdbId}_model000.csv");
var distanceMapsDirectory = @"G:\Projects\HumanGenome\generatedProteins\DistanceMaps";
var positionFilesDirectory = @"G:\Projects\HumanGenome\generatedProteins\PositionFiles";
var distanceMean = 380;
var distanceSigma = 4;
var iterations = 1000;
for (int iteration = 0; iteration < iterations; iteration++)
{
var aminoAcidPositions = new List <Point3D> {
new Point3D(0, 0, 0)
};
var lastAminoAcidLetter = aminoAcidSequence[0];
for (var aminoAcidIdx = 1; aminoAcidIdx < aminoAcidSequence.Count; aminoAcidIdx++)
{
var aminoAcidLetter = aminoAcidSequence[aminoAcidIdx];
var distance = StaticRandom.NextGaussian(distanceMean, distanceSigma);
if (aminoAcidPositions.Count < 2)
{
aminoAcidPositions.Add(new Point3D(distance, 0, 0));
lastAminoAcidLetter = aminoAcidLetter;
continue;
}
var angleInverseDistribution = angleInverseDistributions[lastAminoAcidLetter];
var angleInRadians = angleInverseDistribution.ValueAtX(StaticRandom.Rng.NextDouble());
var lastPosition = aminoAcidPositions.Last().To(SIPrefix.Pico, Unit.Meter);
var vector1 = aminoAcidPositions[aminoAcidIdx - 2].VectorTo(aminoAcidPositions[aminoAcidIdx - 1]);
var vector2 = aminoAcidIdx >= 3
? aminoAcidPositions[aminoAcidIdx - 3].VectorTo(aminoAcidPositions[aminoAcidIdx - 2])
: new Vector3D(0, 1, 0);
var bestPositionedPoint = ApproximateAminoAcidPositioner.CalculateAtomPosition(
lastPosition,
vector1,
vector2,
distance.To(SIPrefix.Pico, Unit.Meter),
angleInRadians.To(Unit.Radians),
(2 * Math.PI * (StaticRandom.Rng.NextDouble() - 0.5)).To(Unit.Radians));
var isColliding = CollidesWithExistingPositions(bestPositionedPoint, aminoAcidPositions, out var distanceToClosest);
var bestDistanceToClosest = distanceToClosest;
const int MaxPositionIterations = 3;
var positionIteration = 0;
while (isColliding && positionIteration < MaxPositionIterations)
{
positionIteration++;
var pointCandidate = ApproximateAminoAcidPositioner.CalculateAtomPosition(
lastPosition,
vector1,
vector2,
distance.To(SIPrefix.Pico, Unit.Meter),
angleInRadians.To(Unit.Radians),
(2 * Math.PI * (StaticRandom.Rng.NextDouble() - 0.5)).To(Unit.Radians));
isColliding = CollidesWithExistingPositions(bestPositionedPoint, aminoAcidPositions, out distanceToClosest);
if (!isColliding)
{
bestPositionedPoint = pointCandidate;
break;
}
if (distanceToClosest > bestDistanceToClosest)
{
bestPositionedPoint = pointCandidate;
bestDistanceToClosest = distanceToClosest;
}
}
aminoAcidPositions.Add(bestPositionedPoint.In(SIPrefix.Pico, Unit.Meter));
lastAminoAcidLetter = aminoAcidLetter;
}
var filenameBase = $"pdb{pdbId}_gen{iteration}";
var distanceMap = DistanceMapGenerator.Generate(aminoAcidPositions);
distanceMap.Save(Path.Combine(distanceMapsDirectory, filenameBase + ".png"));
File.WriteAllLines(
Path.Combine(positionFilesDirectory, filenameBase + ".csv"),
Enumerable.Range(0, aminoAcidSequence.Count)
.Select(idx => $"{aminoAcidSequence[idx]};{aminoAcidPositions[idx].ToString()}"));
}
}
public void MakeATree(double _x, double _y, double _thickness, double _height, double depth, double angle = 0, bool polygon = false, bool leaves = false)
{
if (leaves)
{
EllipseGeometry leaf = new EllipseGeometry(new Point(_x, _y), leafHOR, leafVER);
leaf.Transform = new RotateTransform(angle / rad2deg, _x, _y);
tree.Children.Add(leaf);
double new_x = _x - StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Sin(angle);
double new_y = _y + StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Cos(angle);
leaf = new EllipseGeometry(new Point(new_x, new_y), leafHOR, leafVER);
leaf.Transform = new RotateTransform(angle / rad2deg + 90, new_x, new_y);
tree.Children.Add(leaf);
new_x = _x - StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Sin(angle);
new_y = _y + StaticRandom.NextDouble(_height / 5, _height / 2) * Math.Cos(angle);
leaf = new EllipseGeometry(new Point(new_x, new_y), leafHOR, leafVER);
leaf.Transform = new RotateTransform(angle / rad2deg - 90, new_x, new_y);
tree.Children.Add(leaf);
return;
}
if (polygon)
{
StreamGeometry a = new StreamGeometry();
using (var b = a.Open())
{
b.BeginFigure(new Point(_x, _y + _height), true, true);
b.LineTo(new Point(_x + (1 - thick_coef) * _thickness / 2, _y), true, true);
b.LineTo(new Point(_x + (1 + thick_coef) * _thickness / 2, _y), true, true);
b.LineTo(new Point(_x + _thickness, _y + _height), true, true);
b.Close();
}
a.Transform = new RotateTransform(angle / rad2deg, _x, _y + _height);
tree.Children.Add(a);
}
else
{
Rect rectangle = new Rect(new Point(_x, _y), new Size(_thickness, _height));
RectangleGeometry brunch = new RectangleGeometry(rectangle);
if (angle > 0)
{
brunch.Transform = new RotateTransform(angle / rad2deg,
_x + _thickness,
_y + _height);
}
else
{
brunch.Transform = new RotateTransform(angle / rad2deg,
_x,
_y + _height);
}
tree.Children.Add(brunch);
}
//_y -= _height;
if (_height > 5 && depth < 350)
{
_x += _height * Math.Sin(angle) + (1 - thick_coef) * _thickness / 2 * Math.Cos(angle);
_y += _height * (1 - Math.Cos(angle)) - (1 - thick_coef) * _thickness / 2 * Math.Sin(-angle);
_thickness = _thickness * thick_coef;
if (StaticRandom.NextDouble() < 0.9 || _thickness > 4)
{
double new_height = _height * StaticRandom.NextGaussian(0.85, 0.1, 0.7, 1);
MakeATree(_x, _y - new_height,
_thickness,
new_height,
depth + _height,
angle, polygon);
}
if (StaticRandom.NextDouble() < 0.7 && (angle > -110 * rad2deg || _height < 15))
{
double new_height = _height * StaticRandom.NextGaussian(0.8, 0.2, 0.3, 0.9);
//double new_height = _height * StaticRandom.NextDouble(0.7, 0.9);
MakeATree(_x, _y - new_height,
StaticRandom.NextDouble(_thickness * 0.6, _thickness * 0.9),
new_height,
depth + _height,
angle - StaticRandom.NextDouble(10, 46) * rad2deg, polygon);
}
if (StaticRandom.NextDouble() < 0.7 && (angle < 110 * rad2deg || _height < 15))
{
double new_height = _height * StaticRandom.NextGaussian(0.8, 0.2, 0.3, 0.9);
//double new_height = _height * StaticRandom.NextDouble(0.7, 0.9);
MakeATree(_x, _y - new_height,
StaticRandom.NextDouble(_thickness * 0.6, _thickness * 0.9),
new_height,
depth + _height,
angle + StaticRandom.NextDouble(10, 46) * rad2deg, polygon);
}
}
else
{
_x += _height * Math.Sin(angle) + thick_coef * _thickness / 2 * Math.Cos(angle);
_y += _height * (1 - Math.Cos(angle)) + thick_coef * _thickness / 2 * Math.Sin(Math.Abs(angle));
MakeATree(_x, _y, _thickness, _height, 0, angle, polygon, true);
}
return;
}