private void InitBlock()
{
specialAtomIndexes = new int[JmolConstants.ATOMID_MAX];
shapes = new Shape[JmolConstants.SHAPE_MAX];
withinModelIterator = new WithinModelIterator(this);
withinAnyModelIterator = new WithinAnyModelIterator(this);
hbondMin2 = hbondMin * hbondMin;
for (int i = MAX_BONDS_LENGTH_TO_CACHE; --i > 0; )
// .GT. 0
freeBonds[i] = new Bond[MAX_NUM_TO_CACHE][];
}
public void deleteBond(int i)
{
int newLength = bonds.Length - 1;
if (newLength == 0)
{
bonds = null;
return ;
}
Bond[] bondsNew = new Bond[newLength];
int j = 0;
for (; j < i; ++j)
bondsNew[j] = bonds[j];
for (; j < newLength; ++j)
bondsNew[j] = bonds[j + 1];
bonds = bondsNew;
}
public void deleteBond(Bond bond)
{
for (int i = bonds.Length; --i >= 0; )
{
if (bonds[i] == bond)
{
deleteBond(i);
return;
}
}
}
private void addBond(Bond bond, Frame frame)
{
if (bonds == null)
{
bonds = new Bond[1];
bonds[0] = bond;
}
else
{
bonds = frame.addToBonds(bond, bonds);
}
}
public Bond bondMutually(Atom atomOther, short order, Frame frame)
{
if (isBonded(atomOther))
return null;
Bond bond = new Bond(this, atomOther, order, frame);
addBond(bond, frame);
atomOther.addBond(bond, frame);
return bond;
}
public Bond[] addToBonds(Bond newBond, Bond[] oldBonds)
{
Bond[] newBonds;
if (oldBonds == null)
{
if (numCached[1] > 0)
newBonds = freeBonds[1][--numCached[1]];
else
newBonds = new Bond[1];
newBonds[0] = newBond;
}
else
{
int oldLength = oldBonds.Length;
int newLength = oldLength + 1;
if (newLength < MAX_BONDS_LENGTH_TO_CACHE && numCached[newLength] > 0)
newBonds = freeBonds[newLength][--numCached[newLength]];
else
newBonds = new Bond[newLength];
newBonds[oldLength] = newBond;
for (int i = oldLength; --i >= 0; )
newBonds[i] = oldBonds[i];
if (oldLength < MAX_BONDS_LENGTH_TO_CACHE && numCached[oldLength] < MAX_NUM_TO_CACHE)
freeBonds[oldLength][numCached[oldLength]++] = oldBonds;
}
return newBonds;
}
private void addBond(Bond bond)
{
if (bond == null)
return;
if (bondCount == bonds.Length)
bonds = (Bond[])Util.setLength(bonds, bondCount + growthIncrement);
bonds[bondCount++] = bond;
}
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 void deleteBond(Bond bond)
{
// what a disaster ... I hate doing this
for (int i = bondCount; --i >= 0; )
{
if (bonds[i] == bond)
{
bonds[i].deleteAtomReferences();
Array.Copy(bonds, i + 1, bonds, i, bondCount - i - 1);
--bondCount;
bonds[bondCount] = null;
return;
}
}
}
