public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
//MetaBlobsSchemeSettings settings = (MetaBlobsSchemeSettings)coDesc.SchemeSettings;
atomsBufferCreators = new AtomGeometryCreator[] { new AtomBlobBufferCreator() };
atomsBufferCreators[0].SetupForCreation(null);
this.coDesc = coDesc;
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
//MetaBlobsSchemeSettings settings = (MetaBlobsSchemeSettings)coDesc.SchemeSettings;
atomsBufferCreators = new AtomGeometryCreator[] { new AtomBlobBufferCreator() };
atomsBufferCreators[0].SetupForCreation(null);
this.coDesc = coDesc;
}
public void ApplySettings(CompleteOutputDescription outputDesc)
{
this.outputDesc = outputDesc;
this.outputDesc.AtomShadingDesc.MoleculeMaterials = modules[0];
this.outputDesc.BondShadingDesc.MoleculeMaterials = modules[0];
if (renderContext != null)
{
renderContext.ApplyOutputDescription(outputDesc);
renderContext.OnResize(Width, Height);
}
}
public void ApplyOutputDescription(CompleteOutputDescription desc)
{
desc.CompareAgainst(desc, true);
outputDescription = desc;
/*if (desc.GeneralShadingDesc.AntiAliasing > 0)
* presentParams.MultiSample = MultiSampleType.FourSamples;
* else
* presentParams.MultiSample = MultiSampleType.None;*/
try
{
device.Reset(presentParams);
}
catch (Exception e)
{
log.AddItem(new LogItem(string.Format("Device failed to reset with pParams={0},{1},{2},{3},{4},{5},{6}: Exception is - {7}",
presentParams.AutoDepthStencilFormat,
presentParams.BackBufferFormat,
presentParams.BackBufferHeight,
presentParams.BackBufferWidth,
presentParams.EnableAutoDepthStencil,
presentParams.MultiSample,
presentParams.SwapEffect,
e.Message),
LogItem.ItemLevel.Error));
throw;
}
sceneManager.SetScheme(desc.SchemeSettings.GetScheme(device));
sceneManager.SetOutputDesc(desc);
if (desc.GeneralShadingDesc.Wireframe)
{
device.RenderState.FillMode = FillMode.WireFrame;
}
else
{
device.RenderState.FillMode = FillMode.Solid;
}
switch (desc.GeneralShadingDesc.ShadingMode)
{
case NuGenSVisualLib.Rendering.Shading.GeneralShadingDesc.ShadingModes.Smooth:
device.RenderState.ShadeMode = ShadeMode.Phong;
break;
case NuGenSVisualLib.Rendering.Shading.GeneralShadingDesc.ShadingModes.Flat:
device.RenderState.ShadeMode = ShadeMode.Flat;
break;
}
RefreshDescription();
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
//SpriteSchemeSettings settings = (SpriteSchemeSettings)coDesc.SchemeSettings;
atomsBufferCreators = new AtomGeometryCreator[] { new AtomSpriteBufferCreator() };
atomsBufferCreators[0].SetupForCreation(null);
lightBonds = false;
lightAtoms = true;
this.coDesc = coDesc;
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
//SpriteSchemeSettings settings = (SpriteSchemeSettings)coDesc.SchemeSettings;
atomsBufferCreators = new AtomGeometryCreator[] { new AtomSpriteBufferCreator() };
atomsBufferCreators[0].SetupForCreation(null);
lightBonds = false;
lightAtoms = true;
this.coDesc = coDesc;
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
//SpaceFillSchemeSettings settings = (SpaceFillSchemeSettings)coDesc.SchemeSettings;
atomsBufferCreators = new AtomGeometryCreator[] { new AtomSphereBufferCreator(0.5f, 16, 12) };
atomsBufferCreators[0].SetupForCreation(null);
bondsBufferCreators = null;
lightAtoms = true;
this.coDesc = coDesc;
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
//SpaceFillSchemeSettings settings = (SpaceFillSchemeSettings)coDesc.SchemeSettings;
atomsBufferCreators = new AtomGeometryCreator[] { new AtomSphereBufferCreator(0.5f, 16, 12) };
atomsBufferCreators[0].SetupForCreation(null);
bondsBufferCreators = null;
lightAtoms = true;
this.coDesc = coDesc;
}
public void SetScheme(MoleculeRenderingScheme scheme, CompleteOutputDescription coDesc)
{
latestCoDesc = new CompleteOutputDescription(coDesc);
sceneManger.SetScheme(scheme);
sceneManger.SetOutputDesc(coDesc);
scheme.device = device;
// build preview via thread
if (generatorThread.ThreadState == ThreadState.Running)
{
// abort thread
generatorThread.Abort();
generatorThread.Join();
}
generatorThread = new Thread(GeneratePreviewProcess);
generatorThread.Start();
wantPreview = true;
}
public void UpdateBonds(CompleteOutputDescription latestCoDesc, IBond[] bonds)
{
if (scheme.HandlesBonds)
{
scheme.SetOutputDescription(coDesc);
DataFields[][] allStreams = new DataFields[1][];
IGeometryCreator[] schStreams = scheme.GetBondStreams();
GeomDataBufferStream[] geomStream = new GeomDataBufferStream[schStreams.Length];
for (int i = 0; i < geomStream.Length; i++)
{
allStreams[0] = schStreams[i].Fields;
GeomDataTransformer.CreateBufferStream(allStreams, out geomStream[i]);
}
// fill buffer stream
scheme.SetBondData(bonds, geomStream);
}
}
public MoleculeSchemeDlg(HashTableSettings settings, OutputCaps outCaps, Device device, CompleteOutputDescription coDesc)
{
InitializeComponent();
currentEffects = new List <Effect>();
this.settings = settings;
LoadLocalResources();
this.refDevice = device;
this.outCaps = outCaps;
this.refcoDesc = coDesc;
this.coDesc = new CompleteOutputDescription(coDesc);
using (Stream stream = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenSVisualLib.LightingPresets.config"))
{
LoadLightingPresets(stream);
}
SetupLightingPreview();
SetupEffectPreview();
schemePreviewControl.OnNewPreview += new EventHandler(schemePreviewControl_OnNewPreview);
using (Stream stream = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenSVisualLib.MoleculeSchemes.config"))
{
if (stream != null)
{
XmlDocument xml = new XmlDocument();
xml.Load(stream);
LoadSchemes(xml);
LoadEffects(xml);
LoadMaterials(xml);
}
}
previewReady = true;
updateThread = new Thread(this.UpdatePreviewsProcess);
updateThread.Start();
}
public void UpdateAtoms(CompleteOutputDescription coDesc, IAtom[] atoms)
{
if (scheme.HandlesAtoms)
{
scheme.SetOutputDescription(coDesc);
// pass throught scheme & effects
IGeometryCreator[] schStreams = scheme.GetAtomStreams();
DataFields[][] allStreams = new DataFields[1][];
GeomDataBufferStream[] geomStream = new GeomDataBufferStream[schStreams.Length];
for (int i = 0; i < geomStream.Length; i++)
{
allStreams[0] = schStreams[i].Fields;
GeomDataTransformer.CreateBufferStream(allStreams, out geomStream[i]);
}
// fill buffer stream
scheme.SetAtomData(atoms, geomStream);
}
}
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 void Init(HashTableSettings settings, ICommonDeviceInterface cdi)
{
this.settings = settings;
settings["Molecule.Shading.Material.Type"] = "BySerie";
// load settings
BackColor = (Color)settings["View3D.BgClr"];
// load local modules
foreach (ISettingsModule module in modules)
{
module.LoadModuleSettings(settings);
}
renderContext = new ChemRenderingContext3DDX9(settings, this, (CommonDeviceInterface)cdi);
renderContext.BackColor = BackColor;
// load default output settings
CompleteOutputDescription desc = CompleteOutputDescription.LoadDescription(Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenSVisualLib.defaultOutput.xml"));
desc.SchemeSettings = new BallAndStickSchemeSettings();
desc.SchemeSettings.AtomLOD = 2;
ApplySettings(desc);
}
private void LoadOutputSettings()
{
outputDesc = CompleteOutputDescription.LoadDescription(outputSettingsXmlFile);
outputDesc.SchemeSettings = new BallAndStickSchemeSettings();
ApplySettings(outputDesc);
}
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
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
bool updateAtomLOD = true;
bool updateBondLOD = true;
bool updateSymbols = true;
bool updateGlow = true;
bool updateBondSize = true;
bool updateBonds = true;
bool updateAtoms = true;
bool updateScheme = true;
if (this.coDesc != null)
{
this.coDesc = coDesc;
updateAtoms = coDesc.CheckChange("AtomShadingDesc.");
if (updateAtoms)
{
updateSymbols = coDesc.CheckChange("AtomShadingDesc.", "SymbolText");
updateGlow = coDesc.CheckChange("SchemeSettings.", "Glow");
}
updateBonds = coDesc.CheckChange("BondShadingDesc.");
updateScheme = coDesc.CheckChange("SchemeSettings.");
if (updateScheme)
{
updateAtomLOD = coDesc.CheckChange("SchemeSettings.", "AtomLOD");
updateBondLOD = coDesc.CheckChange("SchemeSettings.", "BondLOD");
updateBondSize = coDesc.CheckChange("SchemeSettings.", "StickThickness");
}
}
else
{
this.coDesc = coDesc;
}
BallAndStickSchemeSettings settings = (BallAndStickSchemeSettings)coDesc.SchemeSettings;
int atomDetail1 = 4;
int atomDetail2 = 1;
if (updateAtoms || updateScheme)
{
/*if (updateAtomLOD)
* {*/
switch (settings.AtomLOD)
{
case 0:
atomDetail1 = 4;
atomDetail2 = 1;
break;
case 1:
atomDetail1 = 8;
atomDetail2 = 6;
break;
case 2:
atomDetail1 = 12;
atomDetail2 = 9;
break;
case 3:
atomDetail1 = 16;
atomDetail2 = 12;
break;
case 4:
atomDetail1 = 24;
atomDetail2 = 18;
break;
case 5:
atomDetail1 = 32;
atomDetail2 = 26;
break;
}
//}
int bufCount = 1;
if (settings.ElectronChargeCloud)
{
bufCount++;
}
if (settings.Glow > 0)
{
bufCount++;
}
if (coDesc.AtomShadingDesc.SymbolText)
{
bufCount++;
}
// TODO: Reconfigure previous creators
atomsBufferCreators = new AtomGeometryCreator[bufCount];
atomsBufferCreators[0] = new AtomSphereBufferCreator(0.2f, atomDetail1, atomDetail2);
bufCount = 1;
if (settings.Glow > 0)
{
atomsBufferCreators[bufCount++] = new AtomSpriteBufferCreator();
}
if (settings.ElectronChargeCloud)
{
atomsBufferCreators[bufCount++] = new AtomMetaballsBufferCreator(true);
}
if (coDesc.AtomShadingDesc.SymbolText)
{
atomsBufferCreators[bufCount++] = new AtomSymbolSpriteBufferCreator();
}
foreach (AtomGeometryCreator creator in atomsBufferCreators)
{
creator.SetupForCreation(null);
}
}
if (updateBonds || updateScheme)
{
if (updateBondSize)
{
if (settings.StickThickness == 0 && (bondsBufferCreators == null || !(bondsBufferCreators[0] is BondLinesBufferCreator)))
{
bondsBufferCreators = new BondGeometryCreator[] { new BondLinesBufferCreator() }
}
;
else if (settings.StickThickness > 0 && (bondsBufferCreators == null || !(bondsBufferCreators[0] is BondThickLinesBufferCreator)))
{
bondsBufferCreators = new BondGeometryCreator[] { new BondThickLinesBufferCreator(5) }
}
;
bondsBufferCreators[0].SetupForCreation(null);
}
}
lightBonds = false;
lightAtoms = true;
this.coDesc = coDesc;
}
}
public override void SetOutputDescription(CompleteOutputDescription coDesc)
{
bool updateAtomLOD = true;
bool updateBondLOD = true;
bool updateSymbols = true;
bool updateGlow = true;
bool updateBondSize = true;
bool updateBonds = true;
bool updateAtoms = true;
bool updateScheme = true;
if (this.coDesc != null)
{
this.coDesc = coDesc;
updateAtoms = coDesc.CheckChange("AtomShadingDesc.");
if (updateAtoms)
{
updateSymbols = coDesc.CheckChange("AtomShadingDesc.", "SymbolText");
updateGlow = coDesc.CheckChange("SchemeSettings.", "Glow");
}
updateBonds = coDesc.CheckChange("BondShadingDesc.");
updateScheme = coDesc.CheckChange("SchemeSettings.");
if (updateScheme)
{
updateAtomLOD = coDesc.CheckChange("SchemeSettings.", "AtomLOD");
updateBondLOD = coDesc.CheckChange("SchemeSettings.", "BondLOD");
updateBondSize = coDesc.CheckChange("SchemeSettings.", "StickThickness");
}
}
else
this.coDesc = coDesc;
BallAndStickSchemeSettings settings = (BallAndStickSchemeSettings)coDesc.SchemeSettings;
int atomDetail1 = 4;
int atomDetail2 = 1;
if (updateAtoms || updateScheme)
{
/*if (updateAtomLOD)
{*/
switch (settings.AtomLOD)
{
case 0:
atomDetail1 = 4;
atomDetail2 = 1;
break;
case 1:
atomDetail1 = 8;
atomDetail2 = 6;
break;
case 2:
atomDetail1 = 12;
atomDetail2 = 9;
break;
case 3:
atomDetail1 = 16;
atomDetail2 = 12;
break;
case 4:
atomDetail1 = 24;
atomDetail2 = 18;
break;
case 5:
atomDetail1 = 32;
atomDetail2 = 26;
break;
}
//}
int bufCount = 1;
if (settings.ElectronChargeCloud)
bufCount++;
if (settings.Glow > 0)
bufCount++;
if (coDesc.AtomShadingDesc.SymbolText)
bufCount++;
// TODO: Reconfigure previous creators
atomsBufferCreators = new AtomGeometryCreator[bufCount];
atomsBufferCreators[0] = new AtomSphereBufferCreator(0.2f, atomDetail1, atomDetail2);
bufCount = 1;
if (settings.Glow > 0)
atomsBufferCreators[bufCount++] = new AtomSpriteBufferCreator();
if (settings.ElectronChargeCloud)
atomsBufferCreators[bufCount++] = new AtomMetaballsBufferCreator(true);
if (coDesc.AtomShadingDesc.SymbolText)
atomsBufferCreators[bufCount++] = new AtomSymbolSpriteBufferCreator();
foreach (AtomGeometryCreator creator in atomsBufferCreators)
{
creator.SetupForCreation(null);
}
}
if (updateBonds || updateScheme)
{
if (updateBondSize)
{
if (settings.StickThickness == 0 && (bondsBufferCreators == null || !(bondsBufferCreators[0] is BondLinesBufferCreator)))
bondsBufferCreators = new BondGeometryCreator[] { new BondLinesBufferCreator() };
else if (settings.StickThickness > 0 && (bondsBufferCreators == null || !(bondsBufferCreators[0] is BondThickLinesBufferCreator)))
bondsBufferCreators = new BondGeometryCreator[] { new BondThickLinesBufferCreator(5) };
bondsBufferCreators[0].SetupForCreation(null);
}
}
lightBonds = false;
lightAtoms = true;
this.coDesc = coDesc;
}
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();
}
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 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 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 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();
}
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);
}
}
}
}
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;
// 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 == "POINTSIZE")
{
sizePos = geomStream.FieldPositions[gf];
}
break;
}
}
}
// pre-scan for index groups
Dictionary <string, List <int> > groups = new Dictionary <string, List <int> >();
int aIdx = 0;
foreach (IAtom atom in objs)
{
if (!groups.ContainsKey(atom.Symbol))
{
groups[atom.Symbol] = new List <int>();
}
groups[atom.Symbol].Add(aIdx++);
}
// 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);
buffer.vBuffers[0].Stride = geomStream.Stride;
buffer.vBuffers[0].NumElements = objs.Count;
buffer.vBuffers[0].Format = geomStream.Format;
buffer.DataValidity = BufferedGeometryData.DataValidityType.View;
ChemSymbolTextures cTex = ChemSymbolTextures.Instance;
buffer.iBuffers = new BufferedGeometryData.IndexData[groups.Count];
int gIdx = 0;
foreach (KeyValuePair <string, List <int> > group in groups)
{
buffer.iBuffers[gIdx] = new BufferedGeometryData.IndexData();
buffer.iBuffers[gIdx].Desc = BufferedGeometryData.IndexData.Description.Sprites;
buffer.iBuffers[gIdx].NumPrimitives = group.Value.Count;
buffer.iBuffers[gIdx].PrimType = PrimitiveType.PointList;
buffer.iBuffers[gIdx].Textures = new Texture[] { cTex[group.Key] };
buffer.iBuffers[gIdx].Buffer = new IndexBuffer(typeof(int), group.Value.Count, device,
Usage.WriteOnly, Pool.Managed);
int[] indices = (int[])buffer.iBuffers[gIdx].Buffer.Lock(0, LockFlags.None);
for (int i = 0; i < indices.Length; i++)
{
indices[i] = group.Value[i];
}
buffer.iBuffers[gIdx].Buffer.Unlock();
gIdx++;
}
// 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 * 0.2f);
}
pos += geomStream.Stride;
}
buffer.vBuffers[0].Buffer.Unlock();
}
public void SetOutputDesc(CompleteOutputDescription desc)
{
this.coDesc = new CompleteOutputDescription(desc);
scheme.SetOutputDescription(desc);
}
public abstract void SetOutputDescription(CompleteOutputDescription coDesc);
private void LoadOutputSettings()
{
outputDesc = CompleteOutputDescription.LoadDescription(outputSettingsXmlFile);
outputDesc.SchemeSettings = new BallAndStickSchemeSettings();
ApplySettings(outputDesc);
}
public void ApplySettings(CompleteOutputDescription outputDesc)
{
this.outputDesc = outputDesc;
this.outputDesc.AtomShadingDesc.MoleculeMaterials = modules[0];
this.outputDesc.BondShadingDesc.MoleculeMaterials = modules[0];
if (renderContext != null)
{
renderContext.ApplyOutputDescription(outputDesc);
renderContext.OnResize(Width, Height);
}
}
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;
}
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 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
}
public abstract void SetOutputDescription(CompleteOutputDescription coDesc);
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 abstract void CreateGeometryForObjects(Device device, ICollection <IBond> objs,
GeomDataBufferStream geomStream, int stream,
ref BufferedGeometryData buffer,
CompleteOutputDescription coDesc);
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);
}
}
}
}
