/// <summary> Converts a Jmol <i>model</i> to a CDK AtomContainer.
///
/// </summary>
/// <param name="model">A Jmol model as returned by the method ModelAdapter.openBufferedReader()
/// </param>
public virtual IAtomContainer convert(System.Object model)
{
IAtomContainer atomContainer = builder.newAtomContainer();
SmarterJmolAdapter adapter = new SmarterJmolAdapter();
// use this hashtable to map the ModelAdapter Unique IDs to
// our CDK Atom's
System.Collections.Hashtable htMapUidsToAtoms = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
Org.Jmol.Api.JmolAdapter.AtomIterator atomIterator = adapter.getAtomIterator(model);
while (atomIterator.hasNext())
{
IAtom atom = builder.newAtom(atomIterator.ElementSymbol);
atom.X3d = atomIterator.X;
atom.Y3d = atomIterator.Y;
atom.Z3d = atomIterator.Z;
htMapUidsToAtoms[atomIterator.UniqueID] = atom;
atomContainer.addAtom(atom);
}
Org.Jmol.Api.JmolAdapter.BondIterator bondIterator = adapter.getBondIterator(model);
while (bondIterator.hasNext())
{
System.Object uid1 = bondIterator.AtomUniqueID1;
System.Object uid2 = bondIterator.AtomUniqueID2;
int order = bondIterator.EncodedOrder;
// now, look up the uids in our atom map.
IAtom atom1 = (IAtom)htMapUidsToAtoms[uid1];
IAtom atom2 = (IAtom)htMapUidsToAtoms[uid2];
IBond bond = builder.newBond(atom1, atom2, (double)order);
atomContainer.addBond(bond);
}
return atomContainer;
}
internal StructureIterator(SmarterJmolAdapter enclosingInstance, AtomSetCollection atomSetCollection)
{
InitBlock(enclosingInstance);
structureCount = atomSetCollection.structureCount;
structures = atomSetCollection.structures;
istructure = 0;
}
internal BondIterator(SmarterJmolAdapter enclosingInstance, AtomSetCollection atomSetCollection)
{
InitBlock(enclosingInstance);
this.atomSetCollection = atomSetCollection;
atoms = atomSetCollection.atoms;
bonds = atomSetCollection.bonds;
ibond = 0;
}
internal StructureIterator(SmarterJmolAdapter enclosingInstance, AtomSetCollection atomSetCollection)
{
InitBlock(enclosingInstance);
structureCount = atomSetCollection.structureCount;
structures = atomSetCollection.structures;
istructure = 0;
}
private void InitBlock(SmarterJmolAdapter enclosingInstance)
{
this.enclosingInstance = enclosingInstance;
}
internal BondIterator(SmarterJmolAdapter enclosingInstance, AtomSetCollection atomSetCollection)
{
InitBlock(enclosingInstance);
this.atomSetCollection = atomSetCollection;
atoms = atomSetCollection.atoms;
bonds = atomSetCollection.bonds;
ibond = 0;
}
private void InitBlock(SmarterJmolAdapter enclosingInstance)
{
this.enclosingInstance = enclosingInstance;
}
private IMolecule readMolecule(IMolecule molecule)
{
JmolAdapter adapter = new SmarterJmolAdapter();
// note that it actually let's the adapter detect the format!
System.Object model = adapter.openBufferedReader("", input);
molecule.add(new Convertor(molecule.Builder).convert(model));
return molecule;
}