public override void CreateGeometryForObjects(Device device, ICollection <IAtom> objs, GeomDataBufferStream geomStream,
int stream, ref BufferedGeometryData buffer,
CompleteOutputDescription coDesc)
{
// fillable fields
int positionPos = -1;
int normalPos = -1;
int diffusePos = -1;
int texPos = -1;
// match field locations
//int[] fieldsPos = new int[fields.Length];
for (int i = 0; i < fields.Length; i++)
{
for (int gf = 0; gf < geomStream.Fields.Length; gf++)
{
if (fields[i].Format == geomStream.Fields[gf])
{
if (fields[i].Usage == "POSITION")
{
positionPos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "NORMAL")
{
normalPos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "DIFFUSE")
{
diffusePos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "TEXTURE0")
{
texPos = geomStream.FieldPositions[gf];
}
//fieldsPos[i] = geomStream.FieldPositions[gf];
break;
}
}
}
int numVerts = sphereDetail1 * sphereDetail2 * 6;
int numTris = sphereDetail1 * sphereDetail2 * 2;
// create buffers
buffer = new BufferedGeometryData(device, objs.Count);
buffer.vBuffers = new BufferedGeometryData.VertexData[1];
buffer.vBuffers[0] = new BufferedGeometryData.VertexData();
buffer.vBuffers[0].Buffer = new VertexBuffer(device, geomStream.Stride * numVerts * objs.Count,
Usage.WriteOnly, geomStream.Format, Pool.Managed);
buffer.vBuffers[0].Stride = geomStream.Stride;
buffer.vBuffers[0].NumElements = objs.Count * numVerts;
buffer.vBuffers[0].Format = geomStream.Format;
buffer.iBuffers = new BufferedGeometryData.IndexData[1];
buffer.iBuffers[0] = new BufferedGeometryData.IndexData();
buffer.iBuffers[0].Desc = BufferedGeometryData.IndexData.Description.Geometry;
buffer.iBuffers[0].NumPrimitives = objs.Count * numTris;
buffer.iBuffers[0].PrimType = PrimitiveType.TriangleList;
// lock stream
GraphicsStream data = buffer.vBuffers[0].Buffer.Lock(0, 0, LockFlags.None);
// fill fields
bool newWay = true;
if (!newWay)
{
// create template sphere
SphereMathHelper.SphereN sphere = SphereMathHelper.CalcSphereWNormals(sphereDetail1, sphereDetail2, 1.0f, new Vector3(), true);
// clone and scale template for each size required
Vector3 center = new Vector3();
Dictionary <int, Vector3[]> spheres = new Dictionary <int, Vector3[]>();
AtomShadingDesc aShading = coDesc.AtomShadingDesc;
//int vertsIdx = 0;
long pos = 0;
foreach (IAtom atom in objs)
{
int period = 1;
if (atom.Properties.ContainsKey("Period"))
{
period = (int)atom.Properties["Period"];
}
// check for existing
if (!spheres.ContainsKey(period))
{
// scale template
float size = period * _Scaling;
Vector4[] vertices = Vector3.Transform(sphere.Positions, Matrix.Scaling(size, size, size));
Vector3[] vertices3 = new Vector3[vertices.Length];
for (int i = 0; i < vertices.Length; i++)
{
vertices3[i] = new Vector3(vertices[i].X, vertices[i].Y, vertices[i].Z);
}
spheres.Add(period, vertices3);
}
Vector3[] sphereData = spheres[period];
// write to buffer
IMoleculeMaterialLookup lookup = aShading.MoleculeMaterials;
IMoleculeMaterialTemplate matTemp = lookup.ResolveBySymbol(atom.Symbol);
IMoleculeMaterial material = null;
if (matTemp != null)
{
material = matTemp.BySymbol;
}
else
{
PeriodicTableElement pe = (PeriodicTableElement)atom.Properties["PeriodicTableElement"];
if (pe != null)
{
material = lookup.GetBySeries(pe.ChemicalSerie);
}
}
// copy sphere
Vector3 atomSpace = new Vector3((float)atom.X3d, (float)atom.Y3d, (float)atom.Z3d);
/*Vector4 clr = new Vector4((float)material.BaseColor.R / 255f, (float)material.BaseColor.G / 255f,
* (float)material.BaseColor.B / 255f, (float)material.BaseColor.A / 255f);*/
int clr = material.BaseColor.ToArgb();
for (int v = 0; v < sphereData.Length; v++)
{
if (positionPos != -1)
{
Vector3 position = sphereData[v] + atomSpace;
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write(position.X);
data.Write(position.Y);
data.Write(position.Z);
}
if (texPos != -1)
{
data.Seek(pos + texPos, SeekOrigin.Begin);
data.Write(0f); //sphere.TexCoords[v].X);
data.Write(0f); //sphere.TexCoords[v].Y);
}
if (normalPos != -1)
{
data.Seek(pos + normalPos, SeekOrigin.Begin);
data.Write(sphere.Normals[v].X);
data.Write(sphere.Normals[v].Y);
data.Write(sphere.Normals[v].Z);
}
if (diffusePos != -1)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
/*data.Write(clr.X);
* data.Write(clr.Y);
* data.Write(clr.Z);
* data.Write(clr.W);*/
data.Write((Int32)clr);
}
pos += geomStream.Stride;
}
}
}
else
{
Vector3[] Positions, normals;
Vector2[] texCoords;
SphereMathHelper.CreateSphereTriangles(new Vector3(), 1, sphereDetail1, out Positions,
out normals, out texCoords);
// clone and scale template for each size required
Vector3 center = new Vector3();
Dictionary <int, Vector3[]> spheres = new Dictionary <int, Vector3[]>();
AtomShadingDesc aShading = coDesc.AtomShadingDesc;
int vertsIdx = 0;
long pos = 0;
foreach (IAtom atom in objs)
{
int period = 1;
if (atom.Properties.ContainsKey("Period"))
{
period = (int)atom.Properties["Period"];
}
// check for existing
if (!spheres.ContainsKey(period))
{
// scale template
float size = period * _Scaling;
Vector4[] vertices = Vector3.Transform(Positions, Matrix.Scaling(size, size, size));
Vector3[] vertices3 = new Vector3[vertices.Length];
for (int i = 0; i < vertices.Length; i++)
{
vertices3[i] = new Vector3(vertices[i].X, vertices[i].Y, vertices[i].Z);
}
spheres.Add(period, vertices3);
}
Vector3[] sphereData = spheres[period];
// write to buffer
IMoleculeMaterialLookup lookup = aShading.MoleculeMaterials;
IMoleculeMaterialTemplate matTemp = lookup.ResolveBySymbol(atom.Symbol);
IMoleculeMaterial material = null;
if (matTemp != null)
{
material = matTemp.BySymbol;
}
else
{
PeriodicTableElement pe = (PeriodicTableElement)atom.Properties["PeriodicTableElement"];
if (pe != null)
{
material = lookup.GetBySeries(pe.ChemicalSerie);
}
}
// copy sphere
Vector3 atomSpace = new Vector3((float)atom.X3d, (float)atom.Y3d, (float)atom.Z3d);
int clr = material.BaseColor.ToArgb();
for (int v = 0; v < sphereData.Length; v++)
{
if (positionPos != -1)
{
Vector3 position = sphereData[v] + atomSpace;
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write(position.X);
data.Write(position.Y);
data.Write(position.Z);
}
if (texPos != -1)
{
data.Seek(pos + texPos, SeekOrigin.Begin);
data.Write(texCoords[v].X);
data.Write(texCoords[v].Y);
}
if (normalPos != -1)
{
data.Seek(pos + normalPos, SeekOrigin.Begin);
data.Write(normals[v].X);
data.Write(normals[v].Y);
data.Write(normals[v].Z);
}
if (diffusePos != -1)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
/*data.Write(clr.X);
* data.Write(clr.Y);
* data.Write(clr.Z);
* data.Write(clr.W);*/
data.Write((Int32)clr);
}
pos += geomStream.Stride;
}
}
}
buffer.vBuffers[0].Buffer.Unlock();
}
public override void CreateGeometryForObjects(Device device, ICollection <IBond> objs,
GeomDataBufferStream geomStream, int stream,
ref BufferedGeometryData buffer, CompleteOutputDescription coDesc)
{
// fillable fields
int positionPos = -1;
int normalPos = -1;
int diffusePos = -1;
int texPos = -1;
// match field locations
//int[] fieldsPos = new int[fields.Length];
for (int i = 0; i < fields.Length; i++)
{
for (int gf = 0; gf < geomStream.Fields.Length; gf++)
{
if (fields[i].Format == geomStream.Fields[gf])
{
if (fields[i].Usage == "POSITION")
{
positionPos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "NORMAL")
{
normalPos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "DIFFUSE")
{
diffusePos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "TEXTURE0")
{
texPos = geomStream.FieldPositions[gf];
}
//fieldsPos[i] = geomStream.FieldPositions[gf];
break;
}
}
}
// count bond orders via preview data
int numActualBonds = 0;
foreach (IBond bond in objs)
{
numActualBonds += (int)bond.Order;
}
if (!coDesc.BondShadingDesc.BlendEndClrs)
{
numActualBonds *= 2;
}
int numTriangles = objs.Count * (numSides * 2);
SphereMathHelper.EndType endType = SphereMathHelper.EndType.Open;
float offset = 0.0f;
switch (coDesc.BondShadingDesc.EndType)
{
case BondShadingDesc.BondEndTypes.Open:
break;
case BondShadingDesc.BondEndTypes.Closed:
numTriangles += numActualBonds * (numSides * 2);
endType = SphereMathHelper.EndType.Flat;
break;
case BondShadingDesc.BondEndTypes.Point:
offset = 0.05f;
numTriangles += numActualBonds * (numSides * 2);
endType = SphereMathHelper.EndType.Flat;
break;
case BondShadingDesc.BondEndTypes.Rounded:
offset = 0.075f;
numTriangles += numActualBonds * (numSides * 6);
endType = SphereMathHelper.EndType.Rounded;
break;
}
// build template bond
Vector3[] tCylinderPoints, tCylinderEndPoints1, tCylinderEndPoints2;
Vector3[] tCylinderNormals, tCylinderEndNormals1, tCylinderEndNormals2;
int[] tCylinderTris, tCylinderEndTris1, tCylinderEndTris2;
SphereMathHelper.CalcCylinderTriangles(numSides, 1, 1.0f, new Vector3(0, 0, 0), new Vector3(0, 0, 1),
true, endType, offset, out tCylinderPoints,
out tCylinderNormals, out tCylinderTris, out tCylinderEndPoints1,
out tCylinderEndNormals1, out tCylinderEndTris1,
out tCylinderEndPoints2, out tCylinderEndNormals2,
out tCylinderEndTris2);
int numActualVerts = tCylinderPoints.Length + tCylinderEndPoints1.Length + tCylinderEndPoints2.Length;
int numActualTris = tCylinderTris.Length + tCylinderEndTris1.Length + tCylinderEndTris2.Length;
// create buffers
buffer = new BufferedGeometryData(device, objs.Count);
buffer.vBuffers = new BufferedGeometryData.VertexData[1];
buffer.vBuffers[0] = new BufferedGeometryData.VertexData();
buffer.vBuffers[0].Stride = geomStream.Stride;
buffer.vBuffers[0].NumElements = numActualVerts;
buffer.vBuffers[0].Format = geomStream.Format;
buffer.vBuffers[0].NumElements = numActualVerts * numActualBonds;
buffer.vBuffers[0].Buffer = new VertexBuffer(device, geomStream.Stride * numActualTris * numActualBonds * 3,
Usage.WriteOnly, geomStream.Format, Pool.Managed);
buffer.iBuffers = new BufferedGeometryData.IndexData[1];
buffer.iBuffers[0] = new BufferedGeometryData.IndexData();
buffer.iBuffers[0].Desc = BufferedGeometryData.IndexData.Description.Geometry;
buffer.iBuffers[0].NumPrimitives = numActualTris;
buffer.iBuffers[0].PrimType = PrimitiveType.TriangleList;
buffer.iBuffers[0].NumPrimitives = (numActualTris * numActualBonds) / 3;
/*buffer.iBuffers[0].Buffer = new IndexBuffer(typeof(int), numActualTris * numActualBonds, device,
* Usage.WriteOnly, Pool.Managed);*/
// lock stream
GraphicsStream data = buffer.vBuffers[0].Buffer.Lock(0, 0, LockFlags.None);
// write bonds to buffer
Vector3 direction, directionUV;
IAtom[] atoms;
Vector3[] atomsPos;
IMoleculeMaterial matA, matB;
foreach (IBond bond in objs)
{
BondLinesBufferCreator.GenericBondSetup(bond, true, coDesc.BondShadingDesc, out direction,
out directionUV, out atoms, out atomsPos, out matA,
out matB);
// calc bond positioning / instances
Vector3[] bondInstances = null;
float midPos;
BondLinesBufferCreator.GenericBondCalcPositions(bond, coDesc.BondShadingDesc, direction,
directionUV, atoms, atomsPos, 0.15f,
out bondInstances, out midPos, false);
long pos = 0;
for (int bInst = 0; bInst < bondInstances.Length; bInst += 2)
{
// translation
Matrix translate = Matrix.Translation(bondInstances[bInst]);
// rotation
double x = direction.X;
double y = direction.Y;
double z = direction.Z;
double alpha = (z == 0) ? Math.PI / 2 : Math.Atan(x / z);
double r = (alpha == 0) ? z : x / Math.Sin(alpha);
float sign = 1f;
if (z != 0)
{
sign *= Math.Sign(z);
}
else if (x != 0)
{
sign *= Math.Sign(x);
}
if (y != 0)
{
sign *= Math.Sign(y);
}
double theta = -sign *Math.Abs((r == 0)?Math.PI / 2 : Math.Atan(y / r));
Matrix rotation = Matrix.RotationX((float)theta) * Matrix.RotationY((float)alpha);
// scaling
float zScale;
if (coDesc.BondShadingDesc.BlendEndClrs)
{
zScale = (bondInstances[1] - bondInstances[0]).Length();//(atomsPos[1] - atomsPos[0]).Length();//direction.Length();
}
else
{
zScale = midPos;
}
float xyScale = 0.05f; // thickness
Matrix scale = Matrix.Scaling(xyScale, xyScale, zScale);
// rotate & translate ends
if (tCylinderEndPoints1 != null)
{
Matrix endFinal = Matrix.Scaling(xyScale, xyScale, 1f) * rotation * translate;
Vector4[] tfEndTriangles = Vector3.Transform(tCylinderEndPoints1, endFinal);
// first end
for (int point = 0; point < tCylinderEndTris1.Length; point++)
{
int pointIdx = tCylinderEndTris1[point];
if (positionPos != -1)
{
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write(tfEndTriangles[pointIdx].X);
data.Write(tfEndTriangles[pointIdx].Y);
data.Write(tfEndTriangles[pointIdx].Z);
}
if (normalPos != -1)
{
data.Seek(pos + normalPos, SeekOrigin.Begin);
data.Write(tCylinderEndNormals1[pointIdx].X);
data.Write(tCylinderEndNormals1[pointIdx].Y);
data.Write(tCylinderEndNormals1[pointIdx].Z);
}
if (diffusePos != -1)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
data.Write(matA.BaseColor.ToArgb());
}
pos += geomStream.Stride;
}
// second end
endFinal = Matrix.Scaling(xyScale, xyScale, 1f) * rotation *
Matrix.Translation(bondInstances[bInst + 1]);
tfEndTriangles = Vector3.Transform(tCylinderEndPoints2, endFinal);
// first end
for (int point = 0; point < tCylinderEndTris2.Length; point++)
{
int pointIdx = tCylinderEndTris2[point];
if (positionPos != -1)
{
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write(tfEndTriangles[pointIdx].X);
data.Write(tfEndTriangles[pointIdx].Y);
data.Write(tfEndTriangles[pointIdx].Z);
}
if (normalPos != -1)
{
data.Seek(pos + normalPos, SeekOrigin.Begin);
data.Write(tCylinderEndNormals2[pointIdx].X);
data.Write(tCylinderEndNormals2[pointIdx].Y);
data.Write(tCylinderEndNormals2[pointIdx].Z);
}
if (diffusePos != -1)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
data.Write(matB.BaseColor.ToArgb());
}
pos += geomStream.Stride;
}
}
Matrix final = scale * rotation * translate;
if (coDesc.BondShadingDesc.BlendEndClrs)
{
DrawSolidBondBlended(tCylinderPoints, tCylinderNormals, tCylinderTris,
matA, matB, final, data, positionPos, normalPos,
diffusePos, ref pos, geomStream.Stride, rotation);
}
else
{
float bLen2 = (bondInstances[bInst + 1] - (bondInstances[bInst] + (directionUV * midPos))).Length();
DrawSolidBondDistinct(tCylinderPoints, tCylinderNormals, tCylinderTris,
matA, matB, final, data, xyScale, bLen2, rotation,
bondInstances[bInst], directionUV, midPos, positionPos,
normalPos, diffusePos, ref pos, geomStream.Stride);
}
}
}
}
