public void setViewerG3dFrame(/*Viewer viewer,*/ NuGraphics3D g3d, Frame frame)
{
//this.viewer = viewer;
this.g3d = g3d;
this.frame = frame;
initShape();
}
public void setViewerFrameRenderer(/*Viewer viewer,*/ FrameRenderer frameRenderer, NuGraphics3D g3d)
{
//this.viewer = viewer;
this.frameRenderer = frameRenderer;
this.g3d = g3d;
initRenderer();
}
public virtual ShapeRenderer getRenderer(int refShape, NuGraphics3D g3d)
{
if (renderers[refShape] == null)
{
renderers[refShape] = allocateRenderer(refShape, g3d);
}
return(renderers[refShape]);
}
//UPGRADE_NOTE: ref keyword was added to struct-type parameters. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1303'"
public virtual void render(NuGraphics3D g3d, ref System.Drawing.Rectangle rectClip, Frame frame, int displayModelIndex, Shape shape)
{
this.g3d = g3d;
this.rectClip = rectClip;
this.frame = frame;
this.displayModelIndex = displayModelIndex;
this.shape = shape;
render();
}
private static int allocateColix(int argb)
{
lock (typeof(Colix))
{
// double-check to make sure that someone else did not allocate
// something of the same color while we were waiting for the lock
if ((argb & unchecked ((int)0xFF000000)) != unchecked ((int)0xFF000000))
{
throw new System.IndexOutOfRangeException();
}
for (int i = colixMax; --i >= NuGraphics3D.SPECIAL_COLIX_MAX;)
{
if (argb == argbs[i])
{
return((short)i);
}
}
if (colixMax == argbs.Length)
{
int oldSize = argbs.Length;
int newSize = oldSize * 2;
int[] t0 = new int[newSize];
Array.Copy(argbs, 0, t0, 0, oldSize);
argbs = t0;
if (argbsGreyscale != null)
{
t0 = new int[newSize];
Array.Copy(argbsGreyscale, 0, t0, 0, oldSize);
argbsGreyscale = t0;
}
int[][] t2 = new int[newSize][];
Array.Copy(ashades, 0, t2, 0, oldSize);
ashades = t2;
if (ashadesGreyscale != null)
{
t2 = new int[newSize][];
Array.Copy(ashadesGreyscale, 0, t2, 0, oldSize);
ashadesGreyscale = t2;
}
}
argbs[colixMax] = argb;
if (argbsGreyscale != null)
{
argbsGreyscale[colixMax] = NuGraphics3D.calcGreyscaleRgbFromRgb(argb);
}
colixHash.put(argb, colixMax);
return(colixMax++);
}
}
private static void calcArgbsGreyscale()
{
lock (typeof(Colix))
{
if (argbsGreyscale == null)
{
argbsGreyscale = new int[argbs.Length];
for (int i = argbsGreyscale.Length; --i >= 0;)
{
argbsGreyscale[i] = NuGraphics3D.calcGreyscaleRgbFromRgb(argbs[i]);
}
}
}
}
public virtual ShapeRenderer allocateRenderer(int refShape, NuGraphics3D g3d)
{
string classBase = JmolConstants.shapeClassBases[refShape] + "Renderer";
string className = "Org.Jmol.Viewer." + classBase;
try
{
//UPGRADE_TODO: The differences in the format of parameters for method 'java.lang.Class.forName' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
System.Type shapeClass = System.Type.GetType(className);
ShapeRenderer renderer = (ShapeRenderer)System.Activator.CreateInstance(shapeClass);
renderer.setViewerFrameRenderer(/*viewer, */ this, g3d);
return(renderer);
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.Console.Out.WriteLine("Could not instantiate renderer:" + classBase + "\n" + e);
SupportClass.WriteStackTrace(e, Console.Error);
}
return(null);
}
//UPGRADE_NOTE: ref keyword was added to struct-type parameters. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1303'"
public virtual void render(NuGraphics3D g3d, ref System.Drawing.Rectangle rectClip, Frame frame, int displayModelIndex, int shapeType)
{
if (frame == null || frame.atomCount <= 0)
{
return;
}
//viewer.calcTransformMatrices();
//for (int i = 0; i < JmolConstants.SHAPE_MAX; ++i)
//{
Shape shape = frame.shapes[shapeType /*i*/];
//if (shape == null)
// continue;
if (shape != null)
{
getRenderer(shapeType /*i*/, g3d).render(g3d, ref rectClip, frame, displayModelIndex, shape);
}
//}
g3d.Flush();
}
public static int[] getShades(int rgb, bool greyScale)
{
int[] shades = new int[shadeMax];
int red = (rgb >> 16) & 0xFF;
int grn = (rgb >> 8) & 0xFF;
int blu = rgb & 0xFF;
float ambientRange = 1 - ambientFraction;
shades[shadeNormal] = Shade3D.rgb(red, grn, blu);
for (int i = 0; i < shadeNormal; ++i)
{
float fraction = ambientFraction + ambientRange * i / shadeNormal;
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
shades[i] = Shade3D.rgb((int)(red * fraction + 0.5f), (int)(grn * fraction + 0.5f), (int)(blu * fraction + 0.5f));
}
int nSteps = shadeMax - shadeNormal - 1;
float redRange = (255 - red) * intenseFraction;
float grnRange = (255 - grn) * intenseFraction;
float bluRange = (255 - blu) * intenseFraction;
for (int i = 1; i <= nSteps; ++i)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
shades[shadeNormal + i] = Shade3D.rgb(red + (int)(redRange * i / nSteps + 0.5f), grn + (int)(grnRange * i / nSteps + 0.5f), blu + (int)(bluRange * i / nSteps + 0.5f));
}
if (greyScale)
{
for (int i = shadeMax; --i >= 0;)
{
shades[i] = NuGraphics3D.calcGreyscaleRgbFromRgb(shades[i]);
}
}
return(shades);
}
public /*Chem*/ Frame(Org.OpenScience.CDK.Interfaces.IChemFile chemFile, Device graphicsDevice)
{
shapes = new Shape[JmolConstants.SHAPE_MAX];
this.g3d = new NuGraphics3D(graphicsDevice);
this.frameRenderer = new FrameRenderer();
for (int i = MAX_BONDS_LENGTH_TO_CACHE; --i > 0;) // .GT. 0
{
freeBonds[i] = new Bond[MAX_NUM_TO_CACHE][];
}
// convert to jmol native
mmset = new Mmset(this);
// set properties
mmset.ModelSetProperties = new System.Collections.Specialized.NameValueCollection();
// init build
currentModelIndex = -1;
currentModel = null;
currentChainID = '\uFFFF';
currentChain = null;
currentGroupSequenceNumber = -1;
currentGroupInsertionCode = '\uFFFF';
int atomCountEstimate = 0;
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
for (int atomC = 0; atomC < chemModel.SetOfMolecules.AtomContainerCount; atomC++)
{
atomCountEstimate += chemModel.SetOfMolecules.AtomContainers[atomC].AtomCount;
}
}
}
if (atomCountEstimate <= 0)
{
atomCountEstimate = ATOM_GROWTH_INCREMENT;
}
atoms = new Atom[atomCountEstimate];
bonds = new Bond[2 * atomCountEstimate];
htAtomMap.Clear();
// translate IChemSequence[] into Model[]
mmset.ModelCount = chemFile.ChemSequenceCount;
for (int seq = 0; seq < chemFile.ChemSequenceCount; ++seq)
{
int modelNumber = seq + 1;
string modelName = modelNumber.ToString();
NameValueCollection modelProperties = new NameValueCollection(); // FIXME: Loading property values
mmset.setModelNameNumberProperties(seq, modelName, modelNumber, modelProperties);
}
// translate Atoms
Dictionary <Org.OpenScience.CDK.Interfaces.IAtom, Atom> atomsList = new Dictionary <Org.OpenScience.CDK.Interfaces.IAtom, Atom>();
//try
//{
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
for (int atomC = 0; atomC < chemModel.SetOfMolecules.AtomContainerCount; atomC++)
{
for (int atomIdx = 0; atomIdx < chemModel.SetOfMolecules.AtomContainers[atomC].AtomCount; atomIdx++)
{
Org.OpenScience.CDK.Interfaces.IAtom atom = chemModel.SetOfMolecules.AtomContainers[atomC].Atoms[atomIdx];
sbyte elementNumber = (sbyte)atom.AtomicNumber;
if (elementNumber <= 0)
{
elementNumber = JmolConstants.elementNumberFromSymbol(atom.Symbol);
}
char alternateLocation = '\0';
int sequenceNumber = int.MinValue;
char groupInsertionCode = '\0';
string atomName = null;
string group3Name = null;
char chainID = '\0';
if (atom is PDBAtom)
{
PDBAtom pdbAtom = (PDBAtom)atom;
if (pdbAtom.ResSeq != null && pdbAtom.ResSeq.Length > 0)
{
sequenceNumber = int.Parse(pdbAtom.ResSeq);
}
if (pdbAtom.ICode != null && pdbAtom.ICode.Length > 0)
{
groupInsertionCode = pdbAtom.ICode[0];
}
atomName = pdbAtom.Name;
group3Name = pdbAtom.ResName;
if (pdbAtom.ChainID != null && pdbAtom.ChainID.Length >= 1)
{
chainID = pdbAtom.ChainID[0];
}
}
else
{
atomName = atom.AtomTypeName;
}
atomsList[atom] = AddAtom(model, atom, elementNumber, atomName, atom.getFormalCharge(),
(float)atom.getCharge(), 100, float.NaN, (float)atom.X3d, (float)atom.Y3d,
(float)atom.Z3d, false, int.MinValue, chainID, group3Name, sequenceNumber,
groupInsertionCode, float.NaN, float.NaN, float.NaN, alternateLocation, null);
}
}
}
}
//}
//catch (Exception e)
//{
// throw new ApplicationException("Problem translating atoms", e);
//}
fileHasHbonds = false;
// translate bonds
try
{
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
for (int atomC = 0; atomC < chemModel.SetOfMolecules.AtomContainerCount; atomC++)
{
for (int bondIdx = 0; bondIdx < chemModel.SetOfMolecules.AtomContainers[atomC].Bonds.Length; bondIdx++)
{
Org.OpenScience.CDK.Interfaces.IBond bond = chemModel.SetOfMolecules.AtomContainers[atomC].Bonds[bondIdx];
Org.OpenScience.CDK.Interfaces.IAtom[] cdkAtoms = bond.getAtoms();
// locate translated atoms
Atom atom1, atom2;
atomsList.TryGetValue(cdkAtoms[0], out atom1);
atomsList.TryGetValue(cdkAtoms[1], out atom2);
bondAtoms(atom1, atom2, (int)bond.Order);
}
}
}
}
}
catch (Exception e)
{
throw new ApplicationException("Problem translating bonds", e);
}
atomsList.Clear();
// translate structures of PDBPolymer only
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
foreach (Org.OpenScience.CDK.Interfaces.IMolecule molecule in chemModel.SetOfMolecules.Molecules)
{
if (molecule is PDBPolymer)
{
PDBPolymer pdbPolymer = (PDBPolymer)molecule;
if (pdbPolymer.Structures != null && pdbPolymer.Structures.Count > 0)
{
structuresDefined = true;
foreach (PDBStructure pdbStruct in pdbPolymer.Structures)
{
structuresDefined = true;
mmset.defineStructure(pdbStruct.StructureType, pdbStruct.StartChainID,
pdbStruct.StartSequenceNumber, pdbStruct.StartInsertionCode,
pdbStruct.EndChainID, pdbStruct.EndSequenceNumber, pdbStruct.EndInsertionCode);
}
}
}
}
}
}
autoBond(null, null);
// build groups
FinalizeGroupBuild();
BuildPolymers();
Freeze();
finalizeBuild();
// create ribbon shapes
try
{
setShapeSize(JmolConstants.SHAPE_RIBBONS, -1, new BitArray(0));
setShapeSize(JmolConstants.SHAPE_CARTOON, -1, new BitArray(0));
}
catch (Exception) { }
}
public Cylinder3D(NuGraphics3D g3d)
{
this.g3d = g3d;
}
