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 Model(Mmset mmset, int modelIndex, string modelTag)
{
this.mmset = mmset;
this.modelIndex = modelIndex;
this.modelTag = modelTag;
}
public override void initShape()
{
mmset = frame.mmset;
}
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 Frame(/*Viewer viewer, JmolAdapter adapter,*/ object clientFile)
{
InitBlock();
//this.viewer = viewer;
//this.adapter = adapter;
//long timeBegin = System.currentTimeMillis();
//string fileTypeName = adapter.getFileTypeName(clientFile);
// NOTE: these strings are interned and are lower case
// therefore, we can do == comparisions against string constants
// if (modelSetTypeName == "xyz") { }
//this.modelSetTypeName = String.Intern(fileTypeName.ToLower());
mmset = new Mmset(this);
//this.frameRenderer = viewer.FrameRenderer;
//this.g3d = viewer.Graphics3D;
//initializeBuild(adapter.getEstimatedAtomCount(clientFile));
/// <summary>
/// crystal cell must come first, in case atom coordinates
/// need to be transformed to fit in the crystal cell
/// </summary>
//fileCoordinatesAreFractional = adapter.coordinatesAreFractional(clientFile);
//NotionalUnitcell = adapter.getNotionalUnitcell(clientFile);
//PdbScaleMatrix = adapter.getPdbScaleMatrix(clientFile);
//PdbScaleTranslate = adapter.getPdbScaleTranslate(clientFile);
//ModelSetProperties = adapter.getAtomSetCollectionProperties(clientFile);
//currentModelIndex = - 1;
//int modelCount = adapter.getAtomSetCount(clientFile);
//ModelCount = modelCount;
//for (int i = 0; i < modelCount; ++i)
//{
// int modelNumber = adapter.getAtomSetNumber(clientFile, i);
// string modelName = adapter.getAtomSetName(clientFile, i);
// if (modelName == null)
// modelName = "" + modelNumber;
// //UPGRADE_ISSUE: Class hierarchy differences between 'java.util.Properties' and 'System.Collections.Specialized.NameValueCollection' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
// System.Collections.Specialized.NameValueCollection modelProperties = adapter.getAtomSetProperties(clientFile, i);
// setModelNameNumberProperties(i, modelName, modelNumber, modelProperties);
//}
//for (JmolAdapter.AtomIterator iterAtom = adapter.getAtomIterator(clientFile); iterAtom.hasNext(); )
//{
// sbyte elementNumber = (sbyte) iterAtom.ElementNumber;
// if (elementNumber <= 0)
// elementNumber = JmolConstants.elementNumberFromSymbol(iterAtom.ElementSymbol);
// char alternateLocation = iterAtom.AlternateLocationID;
// if (alternateLocation != '\x0000' && alternateLocation != 'A')
// continue;
// addAtom(iterAtom.AtomSetIndex, iterAtom.UniqueID, elementNumber, iterAtom.AtomName, iterAtom.FormalCharge, iterAtom.PartialCharge, iterAtom.Occupancy, iterAtom.Bfactor, iterAtom.X, iterAtom.Y, iterAtom.Z, iterAtom.IsHetero, iterAtom.AtomSerial, iterAtom.ChainID, iterAtom.Group3, iterAtom.SequenceNumber, iterAtom.InsertionCode, iterAtom.VectorX, iterAtom.VectorY, iterAtom.VectorZ, alternateLocation, iterAtom.ClientAtomReference);
//}
//fileHasHbonds = false;
//{
// JmolAdapter.BondIterator iterBond = adapter.getBondIterator(clientFile);
// if (iterBond != null)
// while (iterBond.hasNext())
// bondAtoms(iterBond.AtomUniqueID1, iterBond.AtomUniqueID2, iterBond.EncodedOrder);
//}
//JmolAdapter.StructureIterator iterStructure = adapter.getStructureIterator(clientFile);
//if (iterStructure != null)
// while (iterStructure.hasNext())
// defineStructure(iterStructure.StructureType, iterStructure.StartChainID, iterStructure.StartSequenceNumber, iterStructure.StartInsertionCode, iterStructure.EndChainID, iterStructure.EndSequenceNumber, iterStructure.EndInsertionCode);
//doUnitcellStuff();
//doAutobond();
//finalizeGroupBuild();
//buildPolymers();
//freeze();
//long msToBuild = System.currentTimeMillis() - timeBegin;
// System.out.println("Build a frame:" + msToBuild + " ms");
//adapter.finish(clientFile);
//finalizeBuild();
//dumpAtomSetNameDiagnostics(clientFile);
}
public override void initShape()
{
mmset = frame.mmset;
}
public Model(Mmset mmset, int modelIndex, string modelTag)
{
this.mmset = mmset;
this.modelIndex = modelIndex;
this.modelTag = modelTag;
}