/// <summary> Partitions the atoms in an AtomContainer into covalently connected components.
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be partitioned into connected components, i.e. molecules
/// </param>
/// <returns> A SetOfMolecules.
///
/// </returns>
/// <cdk.dictref> blue-obelisk:graphPartitioning </cdk.dictref>
public static ISetOfMolecules partitionIntoMolecules(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IElectronContainer eContainer = null;
IMolecule molecule = null;
ISetOfMolecules molecules = atomContainer.Builder.newSetOfMolecules();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atom.setFlag(CDKConstants.VISITED, false);
ac.addAtom(atom);
}
IElectronContainer[] eContainers = atomContainer.ElectronContainers;
for (int f = 0; f < eContainers.Length; f++)
{
eContainer = eContainers[f];
eContainer.setFlag(CDKConstants.VISITED, false);
ac.addElectronContainer(eContainer);
}
while (ac.AtomCount > 0)
{
atom = ac.getAtomAt(0);
molecule = atomContainer.Builder.newMolecule();
sphere.Clear();
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
molecules.addMolecule(molecule);
ac.remove(molecule);
}
return(molecules);
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void setObjectProperty(System.String objectType, System.String propertyType, System.String propertyValue)
{
//logger.debug("objectType: " + objectType);
//logger.debug("propType: " + propertyType);
//logger.debug("property: " + propertyValue);
if (objectType == null)
{
//logger.error("Cannot add property for null object");
return;
}
if (propertyType == null)
{
//logger.error("Cannot add property for null property type");
return;
}
if (propertyValue == null)
{
//logger.warn("Will not add null property");
return;
}
if (objectType.Equals("Molecule"))
{
if (propertyType.Equals("id"))
{
currentMolecule.ID = propertyValue;
}
else if (propertyType.Equals("inchi"))
{
currentMolecule.setProperty("iupac.nist.chemical.identifier", propertyValue);
}
else if (propertyType.Equals("pdb:residueName"))
{
currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue);
}
else if (propertyType.Equals("pdb:oneLetterCode"))
{
currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue);
}
else if (propertyType.Equals("pdb:id"))
{
currentMolecule.setProperty(new DictRef(propertyType, propertyValue), propertyValue);
}
else
{
//logger.warn("Not adding molecule property!");
}
}
else if (objectType.Equals("PseudoAtom"))
{
if (propertyType.Equals("label"))
{
if (!(currentAtom is IPseudoAtom))
{
currentAtom = currentChemFile.Builder.newPseudoAtom(currentAtom);
}
((IPseudoAtom)currentAtom).Label = propertyValue;
}
}
else if (objectType.Equals("Atom"))
{
if (propertyType.Equals("type"))
{
if (propertyValue.Equals("R") && !(currentAtom is IPseudoAtom))
{
currentAtom = currentChemFile.Builder.newPseudoAtom(currentAtom);
}
currentAtom.Symbol = propertyValue;
}
else if (propertyType.Equals("x2"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.X2d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("y2"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.Y2d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("x3"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.X3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("y3"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.Y3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("z3"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.Z3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("xFract"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.FractX3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("yFract"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.FractY3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("zFract"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.FractZ3d = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("formalCharge"))
{
currentAtom.setFormalCharge(System.Int32.Parse(propertyValue));
}
else if (propertyType.Equals("charge") || propertyType.Equals("partialCharge"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.setCharge(System.Double.Parse(propertyValue));
}
else if (propertyType.Equals("hydrogenCount"))
{
currentAtom.setHydrogenCount(System.Int32.Parse(propertyValue));
}
else if (propertyType.Equals("dictRef"))
{
currentAtom.setProperty("org.openscience.cdk.dict", propertyValue);
}
else if (propertyType.Equals("atomicNumber"))
{
currentAtom.AtomicNumber = System.Int32.Parse(propertyValue);
}
else if (propertyType.Equals("massNumber"))
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
currentAtom.MassNumber = (int)(System.Double.Parse(propertyValue));
}
else if (propertyType.Equals("spinMultiplicity"))
{
int unpairedElectrons = System.Int32.Parse(propertyValue) - 1;
for (int i = 0; i < unpairedElectrons; i++)
{
currentMolecule.addElectronContainer(currentChemFile.Builder.newSingleElectron(currentAtom));
}
}
else if (propertyType.Equals("id"))
{
//logger.debug("id: ", propertyValue);
currentAtom.ID = propertyValue;
atomEnumeration[propertyValue] = (System.Int32)numberOfAtoms;
}
}
else if (objectType.Equals("Bond"))
{
if (propertyType.Equals("atom1"))
{
bond_a1 = System.Int32.Parse(propertyValue);
}
else if (propertyType.Equals("atom2"))
{
bond_a2 = System.Int32.Parse(propertyValue);
}
else if (propertyType.Equals("id"))
{
//logger.debug("id: " + propertyValue);
bond_id = propertyValue;
}
else if (propertyType.Equals("order"))
{
try
{
bond_order = System.Double.Parse(propertyValue);
}
catch (System.Exception e)
{
//logger.error("Cannot convert to double: " + propertyValue);
bond_order = 1.0;
}
}
else if (propertyType.Equals("stereo"))
{
if (propertyValue.Equals("H"))
{
bond_stereo = CDKConstants.STEREO_BOND_DOWN;
}
else if (propertyValue.Equals("W"))
{
bond_stereo = CDKConstants.STEREO_BOND_UP;
}
}
}
else if (objectType.Equals("Reaction"))
{
if (propertyType.Equals("id"))
{
currentReaction.ID = propertyValue;
}
}
else if (objectType.Equals("SetOfReactions"))
{
if (propertyType.Equals("id"))
{
currentSetOfReactions.ID = propertyValue;
}
}
else if (objectType.Equals("Reactant"))
{
if (propertyType.Equals("id"))
{
currentMolecule.ID = propertyValue;
}
}
else if (objectType.Equals("Product"))
{
if (propertyType.Equals("id"))
{
currentMolecule.ID = propertyValue;
}
}
else if (objectType.Equals("Crystal"))
{
// set these variables
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
if (propertyType.Equals("spacegroup"))
{
//logger.debug("Setting crystal spacegroup to: " + propertyValue);
current.SpaceGroup = propertyValue;
}
else if (propertyType.Equals("z"))
{
try
{
//logger.debug("Setting z to: " + propertyValue);
current.Z = System.Int32.Parse(propertyValue);
}
catch (System.FormatException exception)
{
//logger.error("Error in format of Z value");
}
}
}
else
{
//logger.warn("Cannot add crystal cell parameters to a non " + "Crystal class!");
}
}
else if (objectType.Equals("a-axis") || objectType.Equals("b-axis") || objectType.Equals("c-axis"))
{
// set these variables
if (currentMolecule is ICrystal)
{
//logger.debug("Setting axis (" + objectType + "): " + propertyValue);
if (propertyType.Equals("x"))
{
crystal_axis_x = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("y"))
{
crystal_axis_y = System.Double.Parse(propertyValue);
}
else if (propertyType.Equals("z"))
{
crystal_axis_z = System.Double.Parse(propertyValue);
}
}
else
{
//logger.warn("Cannot add crystal cell parameters to a non " + "Crystal class!");
}
}
//logger.debug("Object property set...");
}
