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> Determines if the atom can be of type AtomType. That is, it sees if this
/// AtomType only differs in bond orders, or implicit hydrogen count.
/// </summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
//logger.debug("couldMatchAtomType: formal charge matches...");
if (atom.Hybridization == type.Hybridization)
{
//logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.BondOrderSum)
{
//logger.debug("couldMatchAtomType: bond order sum is OK...");
if (maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return(true);
}
}
else
{
//logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ", "" + type.BondOrderSum);
}
}
}
else
{
//logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
//logger.debug("couldMatchAtomType: No Match");
return(false);
}
/// <summary> Checks if the current atom has exceeded its bond order sum value.
///
/// </summary>
/// <param name="atom">The Atom to check
/// </param>
/// <param name="ac"> The atomcontainer context
/// </param>
/// <returns> oversaturated or not
/// </returns>
public virtual bool isOverSaturated(IAtom atom, IAtomContainer ac)
{
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
return(false);
}
double bondOrderSum = ac.getBondOrderSum(atom);
double maxBondOrder = ac.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
try
{
//logger.debug("*** Checking saturation of atom " + ac.getAtomNumber(atom) + " ***");
//logger.debug("bondOrderSum: " + bondOrderSum);
//logger.debug("maxBondOrder: " + maxBondOrder);
//logger.debug("hcount: " + hcount);
}
catch (System.Exception exc)
{
}
for (int f = 0; f < atomTypes.Length; f++)
{
if (bondOrderSum - charge + hcount > atomTypes[f].BondOrderSum)
{
//logger.debug("*** Good ! ***");
return(true);
}
}
//logger.debug("*** Bad ! ***");
return(false);
}
/// <summary> Checks wether an Atom is saturated by comparing it with known AtomTypes.
/// It returns true if the atom is an PseudoAtom and when the element is not in the list.
/// </summary>
public virtual bool isSaturated(IAtom atom, IAtomContainer container)
{
if (atom is IPseudoAtom)
{
//logger.debug("don't figure it out... it simply does not lack H's");
return(true);
}
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
//logger.warn("Missing entry in atom type list for ", atom.Symbol);
return(true);
}
double bondOrderSum = container.getBondOrderSum(atom);
double maxBondOrder = container.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
//logger.debug("Checking saturation of atom ", atom.Symbol);
//logger.debug("bondOrderSum: ", bondOrderSum);
//logger.debug("maxBondOrder: ", maxBondOrder);
//logger.debug("hcount: ", hcount);
//logger.debug("charge: ", charge);
bool elementPlusChargeMatches = false;
for (int f = 0; f < atomTypes.Length; f++)
{
IAtomType type = atomTypes[f];
if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type))
{
if (bondOrderSum + hcount == type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("We have a match: ", type);
//logger.debug("Atom is saturated: ", atom.Symbol);
return(true);
}
else
{
// ok, the element and charge matche, but unfulfilled
elementPlusChargeMatches = true;
}
} // else: formal charges don't match
}
if (elementPlusChargeMatches)
{
//logger.debug("No, atom is not saturated.");
return(false);
}
// ok, the found atom was not in the list
throw new CDKException("The atom with element " + atom.Symbol + " and charge " + charge + " is not found.");
}
/// <summary> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", atomType);
if (atomContainer.getBondOrderSum(atom) + atom.getHydrogenCount() < atomType.BondOrderSum)
{
//logger.debug(" Match!");
return(true);
}
//logger.debug(" No Match");
return(false);
}
/// <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> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
if (bondOrderSum + hcount <= type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug(" We have a match!");
return(true);
}
}
//logger.debug(" No Match");
return(false);
}
/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private static bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return(false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return(true);
}
else
{
return(false);
}
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private static bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return(false);
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return(true);
}
else
{
return(false);
}
}
}
return(false);
}
/// <summary> Returns the currently maximum formable bond order for this atom.
///
/// </summary>
/// <param name="atom"> The atom to be checked
/// </param>
/// <param name="ac"> The AtomContainer that provides the context
/// </param>
/// <returns> the currently maximum formable bond order for this atom
/// </returns>
public virtual double getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)
{
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
return(0);
}
double bondOrderSum = ac.getBondOrderSum(atom);
int hcount = atom.getHydrogenCount();
double max = 0;
double current = 0;
for (int f = 0; f < atomTypes.Length; f++)
{
current = hcount + bondOrderSum;
if (atomTypes[f].BondOrderSum - current > max)
{
max = atomTypes[f].BondOrderSum - current;
}
}
return(max);
}
/// <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> The method is known to fail for certain compounds. For more information, see
/// cdk.test.limitations package.
///
/// </summary>
public virtual void saturate(IAtomContainer atomContainer)
{
/* newSaturate(atomContainer);
* }
* public void oldSaturate(AtomContainer atomContainer) throws CDKException { */
IAtom partner = null;
IAtom atom = null;
IAtom[] partners = null;
IAtomType[] atomTypes1 = null;
IAtomType[] atomTypes2 = null;
IBond bond = null;
for (int i = 1; i < 4; i++)
{
// handle atoms with degree 1 first and then proceed to higher order
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
//logger.debug("symbol: ", atom.Symbol);
atomTypes1 = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes1.Length > 0)
{
//logger.debug("first atom type: ", atomTypes1[0]);
if (atomContainer.getBondCount(atom) == i)
{
if (atom.getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
{
return;
}
if (atomContainer.getBond(partner, atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
if (atomContainer.getBondOrderSum(atom) < atomTypes1[0].BondOrderSum - atom.getHydrogenCount())
{
//logger.debug("Atom has " + atomContainer.getBondOrderSum(atom) + ", may have: " + atomTypes1[0].BondOrderSum);
partners = atomContainer.getConnectedAtoms(atom);
for (int g = 0; g < partners.Length; g++)
{
partner = partners[g];
//logger.debug("Atom has " + partners.Length + " partners");
atomTypes2 = getAtomTypeFactory(atom.Builder).getAtomTypes(partner.Symbol);
if (atomTypes2.Length == 0)
{
return;
}
if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].BondOrderSum - partner.getHydrogenCount())
{
//logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].BondOrderSum);
bond = atomContainer.getBond(atom, partner);
//logger.debug("Bond order was " + bond.Order);
bond.Order = bond.Order + 1;
//logger.debug("Bond order now " + bond.Order);
break;
}
}
}
}
}
}
}
}
/// <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);
}
/// <summary> Checks wether an Atom is saturated by comparing it with known AtomTypes.
/// It returns true if the atom is an PseudoAtom and when the element is not in the list.
/// </summary>
public virtual bool isSaturated(IAtom atom, IAtomContainer container)
{
if (atom is IPseudoAtom)
{
//logger.debug("don't figure it out... it simply does not lack H's");
return true;
}
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
{
//logger.warn("Missing entry in atom type list for ", atom.Symbol);
return true;
}
double bondOrderSum = container.getBondOrderSum(atom);
double maxBondOrder = container.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
//logger.debug("Checking saturation of atom ", atom.Symbol);
//logger.debug("bondOrderSum: ", bondOrderSum);
//logger.debug("maxBondOrder: ", maxBondOrder);
//logger.debug("hcount: ", hcount);
//logger.debug("charge: ", charge);
bool elementPlusChargeMatches = false;
for (int f = 0; f < atomTypes.Length; f++)
{
IAtomType type = atomTypes[f];
if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type))
{
if (bondOrderSum + hcount == type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("We have a match: ", type);
//logger.debug("Atom is saturated: ", atom.Symbol);
return true;
}
else
{
// ok, the element and charge matche, but unfulfilled
elementPlusChargeMatches = true;
}
} // else: formal charges don't match
}
if (elementPlusChargeMatches)
{
//logger.debug("No, atom is not saturated.");
return false;
}
// ok, the found atom was not in the list
throw new CDKException("The atom with element " + atom.Symbol + " and charge " + charge + " is not found.");
}
/// <summary> Determines if the atom can be of type AtomType. That is, it sees if this
/// AtomType only differs in bond orders, or implicit hydrogen count.
/// </summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
//logger.debug("couldMatchAtomType: formal charge matches...");
if (atom.Hybridization == type.Hybridization)
{
//logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.BondOrderSum)
{
//logger.debug("couldMatchAtomType: bond order sum is OK...");
if (maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return true;
}
}
else
{
//logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ", "" + type.BondOrderSum);
}
}
}
else
{
//logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
//logger.debug("couldMatchAtomType: No Match");
return false;
}
/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return (false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(BondTools.giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return (true);
}
else
{
return (false);
}
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return false;
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(BondTools.giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return (true);
}
else
{
return (false);
}
}
}
return (false);
}
/// <summary> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", atomType);
if (atomContainer.getBondOrderSum(atom) + atom.getHydrogenCount() < atomType.BondOrderSum)
{
//logger.debug(" Match!");
return true;
}
//logger.debug(" No Match");
return false;
}
/// <summary> Returns the currently maximum formable bond order for this atom.
///
/// </summary>
/// <param name="atom"> The atom to be checked
/// </param>
/// <param name="ac"> The AtomContainer that provides the context
/// </param>
/// <returns> the currently maximum formable bond order for this atom
/// </returns>
public virtual double getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)
{
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
return 0;
double bondOrderSum = ac.getBondOrderSum(atom);
int hcount = atom.getHydrogenCount();
double max = 0;
double current = 0;
for (int f = 0; f < atomTypes.Length; f++)
{
current = hcount + bondOrderSum;
if (atomTypes[f].BondOrderSum - current > max)
{
max = atomTypes[f].BondOrderSum - current;
}
}
return max;
}
/// <summary> Checks if the current atom has exceeded its bond order sum value.
///
/// </summary>
/// <param name="atom">The Atom to check
/// </param>
/// <param name="ac"> The atomcontainer context
/// </param>
/// <returns> oversaturated or not
/// </returns>
public virtual bool isOverSaturated(IAtom atom, IAtomContainer ac)
{
IAtomType[] atomTypes = getAtomTypeFactory(atom.Builder).getAtomTypes(atom.Symbol);
if (atomTypes.Length == 0)
return false;
double bondOrderSum = ac.getBondOrderSum(atom);
double maxBondOrder = ac.getMaximumBondOrder(atom);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
try
{
//logger.debug("*** Checking saturation of atom " + ac.getAtomNumber(atom) + " ***");
//logger.debug("bondOrderSum: " + bondOrderSum);
//logger.debug("maxBondOrder: " + maxBondOrder);
//logger.debug("hcount: " + hcount);
}
catch (System.Exception exc)
{
}
for (int f = 0; f < atomTypes.Length; f++)
{
if (bondOrderSum - charge + hcount > atomTypes[f].BondOrderSum)
{
//logger.debug("*** Good ! ***");
return true;
}
}
//logger.debug("*** Bad ! ***");
return false;
}
/// <summary> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
if (bondOrderSum + hcount <= type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug(" We have a match!");
return true;
}
}
//logger.debug(" No Match");
return false;
}