public virtual void saturateRingSystems(IAtomContainer atomContainer)
{
IRingSet rs = new SSSRFinder(atomContainer.Builder.newMolecule(atomContainer)).findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(rs);
IAtomContainer ac = null;
IAtom atom = null;
int[] temp;
for (int f = 0; f < ringSets.Count; f++)
{
rs = (IRingSet)ringSets[f];
ac = RingSetManipulator.getAllInOneContainer(rs);
temp = new int[ac.AtomCount];
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
temp[g] = atom.getHydrogenCount();
atom.setHydrogenCount(atomContainer.getBondCount(atom) - ac.getBondCount(atom) - temp[g]);
}
saturate(ac);
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
atom.setHydrogenCount(temp[g]);
}
}
}
/// <summary> Method that saturates an atom in a molecule by adding implicit hydrogens.
///
/// </summary>
/// <param name="container"> Molecule to saturate
/// </param>
/// <param name="atom"> Atom to satureate.
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> implicit hydrogen </cdk.keyword>
public virtual int[] addImplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom)
{
int formerHydrogens = atom.getHydrogenCount();
int missingHydrogens = valencyChecker.calculateNumberOfImplicitHydrogens(atom, container);
atom.setHydrogenCount(missingHydrogens);
int[] hydrogens = new int[2];
hydrogens[0] = formerHydrogens;
hydrogens[1] = missingHydrogens;
return(hydrogens);
}
/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="count"> Number of hydrogens to add
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer)
{
//boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
IIsotope isotope = IsotopeFactory.getInstance(container.Builder).getMajorIsotope("H");
atom.setHydrogenCount(0);
IAtomContainer changedAtomsAndBonds = container.Builder.newAtomContainer();
for (int i = 1; i <= count; i++)
{
IAtom hydrogen = container.Builder.newAtom("H");
IsotopeFactory.getInstance(container.Builder).configure(hydrogen, isotope);
totalContainer.addAtom(hydrogen);
IBond newBond = container.Builder.newBond((IAtom)atom, hydrogen, 1.0);
totalContainer.addBond(newBond);
changedAtomsAndBonds.addAtom(hydrogen);
changedAtomsAndBonds.addBond(newBond);
}
return(changedAtomsAndBonds);
}
/// <summary> Method that saturates an atom in a molecule by adding implicit hydrogens.
///
/// </summary>
/// <param name="container"> Molecule to saturate
/// </param>
/// <param name="atom"> Atom to satureate.
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> implicit hydrogen </cdk.keyword>
public virtual int[] addImplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom)
{
int formerHydrogens = atom.getHydrogenCount();
int missingHydrogens = valencyChecker.calculateNumberOfImplicitHydrogens(atom, container);
atom.setHydrogenCount(missingHydrogens);
int[] hydrogens = new int[2];
hydrogens[0] = formerHydrogens;
hydrogens[1] = missingHydrogens;
return hydrogens;
}
/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="count"> Number of hydrogens to add
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer)
{
//boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
IIsotope isotope = IsotopeFactory.getInstance(container.Builder).getMajorIsotope("H");
atom.setHydrogenCount(0);
IAtomContainer changedAtomsAndBonds = container.Builder.newAtomContainer();
for (int i = 1; i <= count; i++)
{
IAtom hydrogen = container.Builder.newAtom("H");
IsotopeFactory.getInstance(container.Builder).configure(hydrogen, isotope);
totalContainer.addAtom(hydrogen);
IBond newBond = container.Builder.newBond((IAtom) atom, hydrogen, 1.0);
totalContainer.addBond(newBond);
changedAtomsAndBonds.addAtom(hydrogen);
changedAtomsAndBonds.addBond(newBond);
}
return changedAtomsAndBonds;
}
/// <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...");
}
/// <summary> Produces an AtomContainer without explicit Hs but with H count from one with Hs.
/// The new molecule is a deep copy.
///
/// </summary>
/// <param name="atomContainer">The AtomContainer from which to remove the hydrogens
/// </param>
/// <returns> The molecule without Hs.
/// </returns>
/// <cdk.keyword> hydrogen, removal </cdk.keyword>
public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones.
System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs.
// Clone atoms except those to be removed.
IMolecule mol = atomContainer.Builder.newMolecule();
int count = atomContainer.AtomCount;
for (int i = 0; i < count; i++)
{
// Clone/remove this atom?
IAtom atom = atomContainer.getAtomAt(i);
if (!atom.Symbol.Equals("H"))
{
IAtom clonedAtom = null;
try
{
clonedAtom = (IAtom)atom.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clonedAtom.setHydrogenCount(0);
mol.addAtom(clonedAtom);
map[atom] = clonedAtom;
}
else
{
remove.Add(atom); // maintain list of removed H.
}
}
// Clone bonds except those involving removed atoms.
count = atomContainer.getBondCount();
for (int i = 0; i < count; i++)
{
// Check bond.
//UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
IBond bond = atomContainer.getBondAt(i);
IAtom[] atoms = bond.getAtoms();
bool removedBond = false;
//UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
int length = atoms.Length;
for (int k = 0; k < length; k++)
{
if (remove.Contains(atoms[k]))
{
removedBond = true;
break;
}
}
// Clone/remove this bond?
if (!removedBond)
// if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
{
IBond clone = null;
try
{
clone = (IBond)atomContainer.getBondAt(i).Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] });
mol.addBond(clone);
}
}
// Recompute hydrogen counts of neighbours of removed Hydrogens.
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator i = remove.GetEnumerator(); i.MoveNext();)
{
// Process neighbours.
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
for (System.Collections.IEnumerator n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext();)
{
//UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
IAtom neighb = (IAtom)map[n.Current];
neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
}
}
mol.Properties = atomContainer.Properties;
mol.Flags = atomContainer.Flags;
return(mol);
}
