public CompleteOutputDescription(CompleteOutputDescription toClone)
{
generalShadingDesc = new GeneralShadingDesc(toClone.GeneralShadingDesc);
generalLightingDesc = new GeneralLightingDesc(toClone.GeneralLightingDesc);
atomShadingDesc = new AtomShadingDesc(toClone.AtomShadingDesc);
bondShadingDesc = new BondShadingDesc(toClone.BondShadingDesc);
//structuresShadingDesc = new GeneralStructuresShadingDesc(toClone.GeneralStructuresShadingDesc);
schemeSettings = (MoleculeSchemeSettings)toClone.schemeSettings.Clone();
}
public BondShadingDesc(BondShadingDesc toClone)
{
this.wireframe = toClone.wireframe;
this.moleculeMaterials = toClone.moleculeMaterials;
this.shadeBothColors = toClone.shadeBothColors;
this.bondOrderAsMultipleBonds = toClone.bondOrderAsMultipleBonds;
this.width = toClone.width;
this.draw = toClone.draw;
}
public BondShadingDesc(BondShadingDesc toClone)
{
this.wireframe = toClone.wireframe;
this.moleculeMaterials = toClone.moleculeMaterials;
this.shadeBothColors = toClone.shadeBothColors;
this.bondOrderAsMultipleBonds = toClone.bondOrderAsMultipleBonds;
this.width = toClone.width;
this.draw = toClone.draw;
}
public static void GenericBondCalcPositions(IBond bond, BondShadingDesc bShading, Vector3 direction,
Vector3 directionUV, IAtom[] atoms, Vector3[] atomsPos,
float orderSpacing, out Vector3[] bondInstances, out float midPos,
bool ignoreEnds)
{
float orderSpace = ((float)bond.Order - 1f) * orderSpacing;
Vector3 bondCross = Vector3.Normalize(Vector3.Cross(direction, new Vector3(0, 1, 0)));
// calc A->B spacing positions
Vector3 startPosA = atomsPos[0] -
(bondCross * (orderSpace / 2f));
Vector3 startPosB = atomsPos[1] -
(bondCross * (orderSpace / 2f));
// determine weighting of the 2 atoms
int periodA = 1;
if (atoms[0].Properties.ContainsKey("Period"))
{
periodA = (int)atoms[0].Properties["Period"];
}
int periodB = 1;
if (atoms[1].Properties.ContainsKey("Period"))
{
periodB = (int)atoms[1].Properties["Period"];
}
float periodDif = periodA - periodB;
float sizeA = 0.2f * periodA;
float sizeB = 0.2f * periodB;
// adjust for ends
if (!ignoreEnds)
{
Vector3 endShift;
switch (bShading.EndType)
{
case BondShadingDesc.BondEndTypes.Point:
endShift = directionUV * 0.05f;
startPosA += endShift;
startPosB -= endShift;
break;
case BondShadingDesc.BondEndTypes.Rounded:
endShift = directionUV * 0.075f;
startPosA += endShift;
startPosB -= endShift;
break;
}
}
// calc point exactly between both atoms
float midLen = ((startPosB - startPosA).Length() /*direction.Length()*/ - sizeA - sizeB) / 2f;
midPos = sizeA + midLen;
// adjust for spacing
switch (bShading.Spacing)
{
case BondShadingDesc.BondSpacings.CenterSpace:
startPosA += directionUV * sizeA;
startPosB -= directionUV * sizeB;
// recalc
midLen = (startPosB - startPosA).Length() / 2;
midPos = midLen;
break;
}
// calc instances for both ends
bondInstances = new Vector3[(int)(bond.Order * 2f)];
int bondIdx = 0;
float shift = 0;
for (int order = 0; order < bond.Order; order++)
{
bondInstances[bondIdx] = startPosA + (bondCross * shift);
bondInstances[bondIdx + 1] = startPosB + (bondCross * shift);
bondIdx += 2;
shift += orderSpacing;
}
}
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;
}
int numVerts = 0;
if (coDesc.BondShadingDesc.BlendEndClrs)
{
numVerts = numActualBonds * 2;
}
else
{
numVerts = numActualBonds * 4;
}
// 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 = 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 = numVerts / 2;
buffer.iBuffers[0].PrimType = PrimitiveType.LineList;
buffer.vBuffers[0].NumElements = numVerts;
buffer.vBuffers[0].Buffer = new VertexBuffer(device, geomStream.Stride * numVerts,
Usage.WriteOnly, geomStream.Format, Pool.Managed);
// write bonds to buffer
Vector3 direction, directionUV;
IAtom[] atoms;
Vector3[] atomsPos;
IMoleculeMaterial materialA, materialB;
Vector3[] bondInstances = null;
float midPos;
BondShadingDesc bShading = coDesc.BondShadingDesc;
// lock stream
GraphicsStream data = buffer.vBuffers[0].Buffer.Lock(0, 0, LockFlags.None);
long pos = 0;
foreach (IBond bond in objs)
{
GenericBondSetup(bond, false, bShading, out direction, out directionUV,
out atoms, out atomsPos, out materialA, out materialB);
// calc bond positioning / instances
GenericBondCalcPositions(bond, bShading, direction, directionUV,
atoms, atomsPos, 0.1f, out bondInstances,
out midPos, true);
// draw bond instances
for (int bInst = 0; bInst < bondInstances.Length; bInst += 2)
{
if (bShading.BlendEndClrs)
{
GenericDrawBondSolidBlended(bondInstances[bInst], bondInstances[bInst + 1],
materialA, materialB, data, ref pos, geomStream.Stride, positionPos, diffusePos);
//GenericDrawBondDashedBlended(bondInstances[bInst], bondInstances[bInst + 1],
// materialA, materialB);
}
else
{
Vector3 sectA = directionUV * midPos;
// convert into points (2 lines)
if (positionPos != -1)
{
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write(bondInstances[bInst].X);
data.Write(bondInstances[bInst].Y);
data.Write(bondInstances[bInst].Z);
data.Seek(pos + geomStream.Stride + positionPos, SeekOrigin.Begin);
Vector3 p = bondInstances[bInst] + sectA;
data.Write(p.X);
data.Write(p.Y);
data.Write(p.Z);
data.Seek(pos + geomStream.Stride + geomStream.Stride + positionPos, SeekOrigin.Begin);
data.Write(p.X);
data.Write(p.Y);
data.Write(p.Z);
data.Seek(pos + geomStream.Stride + geomStream.Stride + geomStream.Stride + positionPos, SeekOrigin.Begin);
data.Write(bondInstances[bInst + 1].X);
data.Write(bondInstances[bInst + 1].Y);
data.Write(bondInstances[bInst + 1].Z);
}
if (diffusePos != -1)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
int clr = materialA.BaseColor.ToArgb();
data.Write(clr);
data.Seek(pos + geomStream.Stride + diffusePos, SeekOrigin.Begin);
data.Write(clr);
clr = materialB.BaseColor.ToArgb();
data.Seek(pos + geomStream.Stride + geomStream.Stride + diffusePos, SeekOrigin.Begin);
data.Write(clr);
data.Seek(pos + geomStream.Stride + geomStream.Stride + geomStream.Stride + diffusePos, SeekOrigin.Begin);
data.Write(clr);
}
pos += geomStream.Stride * 4;
}
}
}
buffer.vBuffers[0].Buffer.Unlock();
}
public static void GenericBondSetup(IBond bond, bool sort, BondShadingDesc bShading,
out Vector3 direction, out Vector3 directionUV,
out IAtom[] atoms, out Vector3[] atomsPos,
out IMoleculeMaterial matA, out IMoleculeMaterial matB)
{
atoms = bond.getAtoms();
Vector3 v1 = new Vector3((float)atoms[0].X3d, (float)atoms[0].Y3d, (float)atoms[0].Z3d);
Vector3 v2 = new Vector3((float)atoms[1].X3d, (float)atoms[1].Y3d, (float)atoms[1].Z3d);
direction = v2 - v1;
atomsPos = new Vector3[2];
if (sort)
{
if (direction.Z < (v1 - v2).Z)
{
IAtom temp = atoms[0];
atoms[0] = atoms[1];
atoms[1] = temp;
atomsPos[0] = v2;
atomsPos[1] = v1;
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
direction = Vector3.Normalize(atomsPos[1] - atomsPos[0]);
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
directionUV = Vector3.Normalize(direction);
IMoleculeMaterialLookup lookup = bShading.MoleculeMaterials;
IMoleculeMaterialTemplate matTemp = lookup.ResolveBySymbol(atoms[0].Symbol);
if (matTemp != null)
{
matA = matTemp.BySymbol;
}
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[0].Properties["PeriodicTableElement"];
matA = lookup.GetBySeries(pe.ChemicalSerie);
}
matTemp = lookup.ResolveBySymbol(atoms[1].Symbol);
if (matTemp != null)
{
matB = matTemp.BySymbol;
}
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[1].Properties["PeriodicTableElement"];
matB = lookup.GetBySeries(pe.ChemicalSerie);
}
}
public static void GenericBondCalcPositions(IBond bond, BondShadingDesc bShading, Vector3 direction,
Vector3 directionUV, IAtom[] atoms, Vector3[] atomsPos,
float orderSpacing, out Vector3[] bondInstances, out float midPos,
bool ignoreEnds)
{
float orderSpace = ((float)bond.Order - 1f) * orderSpacing;
Vector3 bondCross = Vector3.Normalize(Vector3.Cross(direction, new Vector3(0, 1, 0)));
// calc A->B spacing positions
Vector3 startPosA = atomsPos[0] -
(bondCross * (orderSpace / 2f));
Vector3 startPosB = atomsPos[1] -
(bondCross * (orderSpace / 2f));
// determine weighting of the 2 atoms
int periodA = 1;
if (atoms[0].Properties.ContainsKey("Period"))
periodA = (int)atoms[0].Properties["Period"];
int periodB = 1;
if (atoms[1].Properties.ContainsKey("Period"))
periodB = (int)atoms[1].Properties["Period"];
float periodDif = periodA - periodB;
float sizeA = 0.2f * periodA;
float sizeB = 0.2f * periodB;
// adjust for ends
if (!ignoreEnds)
{
Vector3 endShift;
switch (bShading.EndType)
{
case BondShadingDesc.BondEndTypes.Point:
endShift = directionUV * 0.05f;
startPosA += endShift;
startPosB -= endShift;
break;
case BondShadingDesc.BondEndTypes.Rounded:
endShift = directionUV * 0.075f;
startPosA += endShift;
startPosB -= endShift;
break;
}
}
// calc point exactly between both atoms
float midLen = ((startPosB - startPosA).Length()/*direction.Length()*/ - sizeA - sizeB) / 2f;
midPos = sizeA + midLen;
// adjust for spacing
switch (bShading.Spacing)
{
case BondShadingDesc.BondSpacings.CenterSpace:
startPosA += directionUV * sizeA;
startPosB -= directionUV * sizeB;
// recalc
midLen = (startPosB - startPosA).Length() / 2;
midPos = midLen;
break;
}
// calc instances for both ends
bondInstances = new Vector3[(int)(bond.Order * 2f)];
int bondIdx = 0;
float shift = 0;
for (int order = 0; order < bond.Order; order++)
{
bondInstances[bondIdx] = startPosA + (bondCross * shift);
bondInstances[bondIdx + 1] = startPosB + (bondCross * shift);
bondIdx += 2;
shift += orderSpacing;
}
}
public static void GenericBondSetup(IBond bond, bool sort, BondShadingDesc bShading,
out Vector3 direction, out Vector3 directionUV,
out IAtom[] atoms, out Vector3[] atomsPos,
out IMoleculeMaterial matA, out IMoleculeMaterial matB)
{
atoms = bond.getAtoms();
Vector3 v1 = new Vector3((float)atoms[0].X3d, (float)atoms[0].Y3d, (float)atoms[0].Z3d);
Vector3 v2 = new Vector3((float)atoms[1].X3d, (float)atoms[1].Y3d, (float)atoms[1].Z3d);
direction = v2 - v1;
atomsPos = new Vector3[2];
if (sort)
{
if (direction.Z < (v1 - v2).Z)
{
IAtom temp = atoms[0];
atoms[0] = atoms[1];
atoms[1] = temp;
atomsPos[0] = v2;
atomsPos[1] = v1;
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
direction = Vector3.Normalize(atomsPos[1] - atomsPos[0]);
}
else
{
atomsPos[0] = v1;
atomsPos[1] = v2;
}
directionUV = Vector3.Normalize(direction);
IMoleculeMaterialLookup lookup = bShading.MoleculeMaterials;
IMoleculeMaterialTemplate matTemp = lookup.ResolveBySymbol(atoms[0].Symbol);
if (matTemp != null)
matA = matTemp.BySymbol;
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[0].Properties["PeriodicTableElement"];
matA = lookup.GetBySeries(pe.ChemicalSerie);
}
matTemp = lookup.ResolveBySymbol(atoms[1].Symbol);
if (matTemp != null)
matB = matTemp.BySymbol;
else
{
PeriodicTableElement pe = (PeriodicTableElement)atoms[1].Properties["PeriodicTableElement"];
matB = lookup.GetBySeries(pe.ChemicalSerie);
}
}
