private void pictureBox1_MouseClick(object sender, MouseEventArgs e)
{
selectedElement = null;
if (!Enabled)
{
return;
}
// test hit on element
int group = 19 * (ptWidth / (e.X - tableOrigin.Width));
int period = 8 * (ptHeight / (e.Y - tableOrigin.Height));
if (group > 1 && period > 1 && group < 20 && period < 9)
{
// look for element fitting desc
foreach (PeriodicTableElement element in ElementPTFactory.Instance)
{
if (element.Group.Length > 0)
{
if (group == int.Parse(element.Group) &&
period == int.Parse(element.Period))
{
selectedElement = element;
break;
}
}
}
}
if (OnElementSelect != null)
{
OnElementSelect(this, null);
}
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
dictRef = "";
//logger.debug("startElement: ", raw);
//logger.debug("uri: ", uri);
//logger.debug("local: ", local);
//logger.debug("raw: ", raw);
if ("elementType".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("id".Equals(atts.GetFullName(i)))
{
elementType = new PeriodicTableElement(atts.GetValue(i));
}
}
}
else if ("scalar".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
if ("cas:id".Equals(atts.GetValue(i)))
{
scalarType = LABEL_CAS;
}
else if ("cdk:name".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_NAME;
}
else if ("cdk:atomicNumber".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_ATOMICNUMBER;
}
else if ("cdk:name".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_NAME;
}
else if ("cdk:chemicalSerie".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_CHEMICALSERIE;
}
else if ("cdk:period".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_PERIOD;
}
else if ("cdk:group".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_GROUP;
}
else if ("cdk:phase".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_PHASE;
}
}
}
}
}
public AtomWrapper(IAtom atom)
{
this.atom = atom;
// rip some stats from the atom
pe = (PeriodicTableElement)atom.Properties["PeriodicTableElement"];
}
/// <summary> Configures an element. Finds the correct element type
/// by looking at the element symbol.
///
/// </summary>
/// <param name="element"> The element to be configure
/// </param>
/// <returns> The configured atom
/// </returns>
public virtual PeriodicTableElement configure(PeriodicTableElement element)
{
PeriodicTableElement elementInt = getElement(element.Symbol);
element.Symbol = elementInt.Symbol;
element.AtomicNumber = elementInt.AtomicNumber;
element.Name = elementInt.Name;
element.ChemicalSerie = elementInt.ChemicalSerie;
element.Period = elementInt.Period;
element.Group = elementInt.Group;
element.Phase = elementInt.Phase;
element.CASid = elementInt.CASid;
return(element);
}
private void CreatePreviewMolecule()
{
atoms = new IAtom[] { new Atom("O", new Point3d(0, 0, 0)), new Atom("H", new Point3d(0, 0, 1)) };
ElementPTFactory elements = ElementPTFactory.Instance;
foreach (IAtom atom in atoms)
{
PeriodicTableElement pe = elements.getElement(atom.Symbol);
if (pe != null)
{
atom.AtomicNumber = pe.AtomicNumber;
atom.Properties["PeriodicTableElement"] = pe;
atom.Properties["Period"] = int.Parse(pe.Period);
}
}
bonds = new IBond[] { new Bond(atoms[0], atoms[1], 1) };
projMat = Matrix.PerspectiveFovLH((float)Math.PI / 4.0f, Width / Height, 0.1f, 20);
viewMat = Matrix.LookAtLH(new Vector3(2, 3, -1), new Vector3(0, 0, 1), new Vector3(0, 1, 0));
}
public override void LoadModuleSettings(HashTableSettings settings)
{
//settings["Materials.Molecules.IMoleculeMaterialLookup"] = this;
// load molecule settings from xml resource
ColorConverter cc = new ColorConverter();
Stream str = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenSVisualLib.Molecule.config");
XmlDocument doc = new XmlDocument();
doc.Load(str);
// load series settings
XmlNodeList series = doc.SelectNodes("configuration/chemicalSeries/chemicalSerie");
foreach (XmlNode serie in series)
{
string id = serie.Attributes["id"].InnerText;
Color baseColor = (Color)cc.ConvertFromString(serie.SelectSingleNode("color").Attributes["desc"].InnerText);
this.series[id] = new AtomMaterial(baseColor);
}
// load symbols
XmlNodeList symbols = doc.SelectNodes("configuration/chemicalSymbols/symbol");
ElementPTFactory ptElements = ElementPTFactory.Instance;
foreach (XmlNode symbol in symbols)
{
string id = symbol.Attributes["id"].InnerText;
Color baseColor = (Color)cc.ConvertFromString(symbol.SelectSingleNode("color").Attributes["desc"].InnerText);
PeriodicTableElement element = ptElements.getElement(id);
IMoleculeMaterial serie = null;
this.series.TryGetValue(element.ChemicalSerie, out serie);
elements[id] = new MoleculeMaterialTemplate(new AtomMaterial(baseColor), serie);
}
}
public Texture this[string symbol]
{
get
{
Texture tex = null;
if (symbolTextures.TryGetValue(symbol, out tex))
{
return(tex);
}
// try load
ElementPTFactory elements = ElementPTFactory.Instance;
PeriodicTableElement element = elements.getElement(symbol);
if (element != null)
{
System.Drawing.Font font = new System.Drawing.Font("Tahoma", 20);
tex = TextTexture.DrawTextToTexture(element.Symbol,
font, device, 64, 64).Texture;
return(symbolTextures[element.Symbol] = tex);
}
return(null);
}
}
private void CreatePreviewData()
{
atoms = new IAtom[] { new Atom("O", new Point3d(0, 0, 0)) };
ElementPTFactory elements = ElementPTFactory.Instance;
foreach (IAtom atom in atoms)
{
PeriodicTableElement pe = elements.getElement(atom.Symbol);
if (pe != null)
{
atom.AtomicNumber = pe.AtomicNumber;
atom.Properties["PeriodicTableElement"] = pe;
atom.Properties["Period"] = int.Parse(pe.Period);
}
}
projMat = Matrix.PerspectiveFovLH((float)Math.PI / 4.0f, Width / Height, 0.1f, 20);
viewMat = Matrix.LookAtLH(new Vector3(2, 0, 0), new Vector3(0, 0, 0), new Vector3(0, 1, 0));
latestCoDesc = CompleteOutputDescription.New();
latestCoDesc.SchemeSettings = new BallAndStickSchemeSettings();
latestCoDesc.SchemeSettings.AtomLOD = 3;
}
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 <IAtom> objs,
GeomDataBufferStream geomStream, int stream,
ref BufferedGeometryData buffer, CompleteOutputDescription coDesc)
{
// fillable fields
int positionPos = -1;
int sizePos = -1;
int diffusePos = -1;
// match field locations
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 == "DIFFUSE")
{
diffusePos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "SIZEFLOAT")
{
sizePos = geomStream.FieldPositions[gf];
}
break;
}
}
}
// 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(typeof(MetaBlobsEffect.PointVertex), objs.Count, device, Usage.None, VertexFormats.Position | VertexFormats.PointSize | VertexFormats.Diffuse, Pool.SystemMemory);
/*new VertexBuffer(device, geomStream.Stride * objs.Count,
* Usage.WriteOnly, geomStream.Format, Pool.SystemMemory);*/
buffer.vBuffers[0].Stride = geomStream.Stride;
buffer.vBuffers[0].NumElements = objs.Count;
buffer.vBuffers[0].Format = geomStream.Format;
buffer.DataValidity = BufferedGeometryData.DataValidityType.Source;
buffer.Target = BufferedGeometryData.DataTarget.Geometry;
// lock stream
GraphicsStream data = buffer.vBuffers[0].Buffer.Lock(0, 0, LockFlags.None);
// fill fields
// create points
AtomShadingDesc aShading = coDesc.AtomShadingDesc;
long pos = 0;
foreach (IAtom atom in objs)
{
int period = 1;
if (atom.Properties.ContainsKey("Period"))
{
period = (int)atom.Properties["Period"];
}
if (positionPos != -1)
{
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write((float)atom.X3d);
data.Write((float)atom.Y3d);
data.Write((float)atom.Z3d);
}
if (sizePos != -1)
{
data.Seek(pos + sizePos, SeekOrigin.Begin);
data.Write((float)period);
}
if (diffusePos != -1)
{
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);
}
}
if (material != null)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
//data.Write((float)material.BaseColor.ToArgb());
if (material.BaseColor.R > 0)
{
data.Write(255f / material.BaseColor.R);
}
else
{
data.Write((float)0);
}
if (material.BaseColor.G > 0)
{
data.Write(255f / material.BaseColor.G);
}
else
{
data.Write((float)0);
}
if (material.BaseColor.B > 0)
{
data.Write(255f / material.BaseColor.B);
}
else
{
data.Write((float)0);
}
}
}
pos += geomStream.Stride;
}
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);
}
}
// SAX Parser methods
public override void startDocument()
{
elements = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
scalarType = SCALAR_UNSET;
elementType = null;
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
dictRef = "";
//logger.debug("startElement: ", raw);
//logger.debug("uri: ", uri);
//logger.debug("local: ", local);
//logger.debug("raw: ", raw);
if ("elementType".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("id".Equals(atts.GetFullName(i)))
{
elementType = new PeriodicTableElement(atts.GetValue(i));
}
}
}
else if ("scalar".Equals(local))
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
if ("cas:id".Equals(atts.GetValue(i)))
{
scalarType = LABEL_CAS;
}
else if ("cdk:name".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_NAME;
}
else if ("cdk:atomicNumber".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_ATOMICNUMBER;
}
else if ("cdk:name".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_NAME;
}
else if ("cdk:chemicalSerie".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_CHEMICALSERIE;
}
else if ("cdk:period".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_PERIOD;
}
else if ("cdk:group".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_GROUP;
}
else if ("cdk:phase".Equals(atts.GetValue(i)))
{
scalarType = SCALAR_PHASE;
}
}
}
}
private static void ProcessChemModel(IChemModel chemModel, ISettings settings, FileUsage usage,
MoleculeLoadingResults results, MoleculeProcessingProgress progress,
float sectionSz)
{
//if (ChemModelManipulator.getAllInOneContainer(chemModel).getBondCount() == 0)
//{
// return;
//}
// check for coordinates
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))//
{
results.Num2DCoords++;
}
// usage == FileUsage.TwoD)
//{
// throw new UserLevelException("File has no 2D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))// &&
{
results.Num3DCoords++;
}
// usage == FileUsage.ThreeD)
//{
// throw new UserLevelException("File has no 3D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
ElementPTFactory elements = ElementPTFactory.Instance;
// calc item sz
int numItems = 0;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
numItems += chemModel.SetOfMolecules.Molecules[mol].Atoms.Length;
//numItems += chemModel.SetOfMolecules.Molecules[mol].Bonds.Length;
}
}
float itemSz = sectionSz / (float)numItems;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
IMolecule molecule = chemModel.SetOfMolecules.Molecules[mol];
results.NumAtoms += molecule.Atoms.Length;
results.NumBonds += molecule.Bonds.Length;
foreach (IAtom atom in molecule.Atoms)
{
PeriodicTableElement pe = elements.getElement(atom.Symbol);
if (pe != null)
{
atom.AtomicNumber = pe.AtomicNumber;
atom.Properties["PeriodicTableElement"] = pe;
atom.Properties["Period"] = int.Parse(pe.Period);
}
else
{
progress.Log(string.Format("Failed to find periodic element: {0}", atom.Symbol), LogItem.ItemLevel.Failure);
}
progress.UpdateProgress(itemSz);
}
progress.Log(string.Format("Processed {0} atoms", molecule.Atoms.Length), LogItem.ItemLevel.Info);
}
}
progress.Log("Processed Model", LogItem.ItemLevel.Success);
}
// SAX Parser methods
public override void startDocument()
{
elements = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
scalarType = SCALAR_UNSET;
elementType = null;
}
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;
// match field locations
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];
}
break;
}
}
}
// actually create the metaball triangles or points
IVolume[] volumes = new IVolume[objs.Count];
int sIdx = 0;
AtomShadingDesc aShading = coDesc.AtomShadingDesc;
IMoleculeMaterialLookup lookup = aShading.MoleculeMaterials;
foreach (IAtom atom in objs)
{
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);
}
}
volumes[sIdx++] = new Metaball(new Vector3((float)atom.X3d, (float)atom.Y3d, (float)atom.Z3d), 0.17f, material.BaseColor);
}
// process volume into triangles
GenericVolumeScene scene = new GenericVolumeScene(volumes);
int[] triangles = null;
Vector3[] vertices;
Color[] colours;
Vector3[] normals = null;
if (!pointsOnly)
{
IsosurfaceGenerator3D.GenerateSimpleMesh(scene, new Vector3(), scene.EstimateVolumeMaxSize(), 40, false, out triangles, out vertices, out colours);
MeshOptimzer.GenerateTriPointNormals(triangles, vertices, out normals);
}
else
{
IsosurfaceGenerator3D.GenerateSimplePointOutline(scene, new Vector3(), scene.EstimateVolumeMaxSize(), 40, out vertices, out colours);
}
// 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 * vertices.Length,
Usage.WriteOnly, geomStream.Format, Pool.Managed);
buffer.vBuffers[0].Stride = geomStream.Stride;
buffer.vBuffers[0].NumElements = vertices.Length;
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;
if (pointsOnly)
{
buffer.iBuffers[0].NumPrimitives = vertices.Length;
buffer.iBuffers[0].PrimType = PrimitiveType.PointList;
buffer.Light = false;
}
else
{
buffer.iBuffers[0].NumPrimitives = triangles.Length / 3;
buffer.iBuffers[0].PrimType = PrimitiveType.TriangleList;
buffer.iBuffers[0].Buffer = new IndexBuffer(typeof(int), triangles.Length, device, Usage.WriteOnly, Pool.Managed);
}
// lock stream
GraphicsStream data = buffer.vBuffers[0].Buffer.Lock(0, 0, LockFlags.None);
// fill fields
int clr = Color.FromArgb(255, 255, 255).ToArgb();
long pos = 0;
for (int i = 0; i < vertices.Length; i++)
{
if (positionPos != -1)
{
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write(vertices[i].X);
data.Write(vertices[i].Y);
data.Write(vertices[i].Z);
}
if (normalPos != -1 && !pointsOnly)
{
data.Seek(pos + normalPos, SeekOrigin.Begin);
data.Write(normals[i].X);
data.Write(normals[i].Y);
data.Write(normals[i].Z);
}
if (diffusePos != -1)
{
data.Seek(pos + diffusePos, SeekOrigin.Begin);
data.Write(colours[i].ToArgb());
}
//verts[i].Color = colours[i].ToArgb();
pos += geomStream.Stride;
}
buffer.vBuffers[0].Buffer.Unlock();
if (!pointsOnly)
{
buffer.iBuffers[0].Buffer.SetData(triangles, 0, LockFlags.None);
}
// dispose of temp data
}
/// <summary> Configures an element. Finds the correct element type
/// by looking at the element symbol.
///
/// </summary>
/// <param name="element"> The element to be configure
/// </param>
/// <returns> The configured atom
/// </returns>
public virtual PeriodicTableElement configure(PeriodicTableElement element)
{
PeriodicTableElement elementInt = getElement(element.Symbol);
element.Symbol = elementInt.Symbol;
element.AtomicNumber = elementInt.AtomicNumber;
element.Name = elementInt.Name;
element.ChemicalSerie = elementInt.ChemicalSerie;
element.Period = elementInt.Period;
element.Group = elementInt.Group;
element.Phase = elementInt.Phase;
element.CASid = elementInt.CASid;
return element;
}
public override void CreateGeometryForObjects(Device device, ICollection <IAtom> objs,
GeomDataBufferStream geomStream, int stream,
ref BufferedGeometryData buffer, CompleteOutputDescription coDesc)
{
if (spriteTexture == null)
{
Stream texstm = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenSVisualLib.Resources.Atom.PNG");
spriteTexture = TextureLoader.FromStream(device, texstm);
}
// fillable fields
int positionPos = -1;
int sizePos = -1;
int diffusePos = -1;
// match field locations
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 == "DIFFUSE")
{
diffusePos = geomStream.FieldPositions[gf];
}
else if (fields[i].Usage == "POINTSIZE")
{
sizePos = geomStream.FieldPositions[gf];
}
break;
}
}
}
// 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(typeof(PointSprite), objs.Count, device, Usage.WriteOnly,
geomStream.Format, Pool.Managed);
/*new VertexBuffer(device, geomStream.Stride * objs.Count,
* Usage.None, geomStream.Format, Pool.Managed);*/
buffer.vBuffers[0].Stride = geomStream.Stride;
buffer.vBuffers[0].NumElements = objs.Count;
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.Sprites;
buffer.iBuffers[0].NumPrimitives = objs.Count;
buffer.iBuffers[0].PrimType = PrimitiveType.PointList;
buffer.iBuffers[0].Textures = new Texture[] { spriteTexture };
// lock stream
GraphicsStream data = buffer.vBuffers[0].Buffer.Lock(0, 0, LockFlags.None);
AtomShadingDesc aShading = coDesc.AtomShadingDesc;
long pos = 0;
foreach (IAtom atom in objs)
{
if (positionPos != -1)
{
data.Seek(pos + positionPos, SeekOrigin.Begin);
data.Write((float)atom.X3d);
data.Write((float)atom.Y3d);
data.Write((float)atom.Z3d);
}
if (sizePos != -1)
{
data.Seek(pos + sizePos, SeekOrigin.Begin);
int period = 1;
if (atom.Properties.ContainsKey("Period"))
{
period = (int)atom.Properties["Period"];
}
data.Write((float)period * 0.4f);
}
if (diffusePos != -1)
{
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);
}
}
data.Seek(pos + diffusePos, SeekOrigin.Begin);
data.Write(material.BaseColor.ToArgb());
}
pos += geomStream.Stride;
}
/*Dictionary<int, List<int>> atomSizeGroups = new Dictionary<int, List<int>>();
* // first split into group counts
* int aIdx = 0;
* foreach (IAtom[] atoms in atomSets)
* {
* foreach (IAtom atom in atoms)
* {
* int period = 1;
* if (atom.Properties.ContainsKey("Period"))
* period = (int)atom.Properties["Period"];
*
* List<int> groupAtoms = null;
* if (!atomSizeGroups.TryGetValue(period, out groupAtoms))
* atomSizeGroups.Add(period, groupAtoms = new List<int>());
*
* groupAtoms.Add(aIdx++);
* }
* }
*
* int vertsIdx = 0;
* Dictionary<int, List<int>>.Enumerator group = atomSizeGroups.GetEnumerator();
* sBuffer.groupLengths = new int[atomSizeGroups.Count];
* sBuffer.groupSizes = new int[atomSizeGroups.Count];
* sBuffer.groupStarts = new int[atomSizeGroups.Count];
* int bIdx = 0;
* while (group.MoveNext())
* {
* int groupPeriod = group.Current.Key;
* List<int> groupMembers = group.Current.Value;
* aIdx = 0;
* int gIdx = 0;
* sBuffer.groupSizes[bIdx] = groupPeriod;
* sBuffer.groupStarts[bIdx] = vertsIdx;
* sBuffer.groupLengths[bIdx] = groupMembers.Count;
* foreach (IAtom[] atoms in atomSets)
* {
* foreach (IAtom atom in atoms)
* {
* if (aIdx == groupMembers[gIdx])
* {
* 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);
* }
*
* atomVerts[vertsIdx].Position = new Vector3((float)atom.X3d, (float)atom.Y3d, (float)atom.Z3d);
* atomVerts[vertsIdx].Color = material.BaseColor.ToArgb();
* vertsIdx++;
* gIdx++;
* }
* if (gIdx == groupMembers.Count)
* break;
* aIdx++;
* }
* if (gIdx == groupMembers.Count)
* break;
* }
* bIdx++;
* }*/
buffer.vBuffers[0].Buffer.Unlock();
}