private void SetCompareTable(IAtomContainer mol)
{
this.compare = mol;
this.compareTable = MorganNumbersTools.GetMorganNumbers(compare);
sortedCompareTable = new long[compareTable.Length];
Array.Copy(compareTable, 0, sortedCompareTable, 0, compareTable.Length);
Array.Sort(sortedCompareTable);
}
private void SetBaseTable(IAtomContainer mol)
{
this.base_ = mol;
this.baseTable = MorganNumbersTools.GetMorganNumbers(base_);
sortedBaseTable = new long[baseTable.Length];
Array.Copy(baseTable, 0, sortedBaseTable, 0, baseTable.Length);
Array.Sort(sortedBaseTable);
}
/// <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)
{
var bondNumber = container.Bonds.IndexOf(container.GetBond(atom, parent));
if (bondNumber == -1 ||
doubleBondConfiguration.Length <= bondNumber ||
!doubleBondConfiguration[bondNumber])
{
return(false);
}
int hcount = atom.ImplicitHydrogenCount ?? 0;
int lengthAtom = container.GetConnectedAtoms(atom).Count() + hcount;
hcount = parent.ImplicitHydrogenCount ?? 0;
int lengthParent = container.GetConnectedAtoms(parent).Count() + hcount;
if (container.GetBond(atom, parent) != null)
{
if (container.GetBond(atom, parent).Order == BondOrder.Double &&
(lengthAtom == 3 || (lengthAtom == 2 && atom.AtomicNumber.Equals(AtomicNumbers.N))) &&
(lengthParent == 3 || (lengthParent == 2 && parent.AtomicNumber.Equals(AtomicNumbers.N))))
{
var atoms = container.GetConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
foreach (var conAtom in atoms)
{
if (conAtom != parent && one == null)
{
one = conAtom;
}
else if (conAtom != parent && one != null)
{
two = conAtom;
}
}
string[] morgannumbers = MorganNumbersTools.GetMorganNumbersWithElementSymbol(container);
if ((one != null && two == null &&
atom.AtomicNumber.Equals(AtomicNumbers.N) &&
Math.Abs(GiveAngleBothMethods(parent, atom, one, true)) > Math.PI / 10) ||
(!atom.AtomicNumber.Equals(AtomicNumbers.N) &&
one != null && two != null &&
!morgannumbers[container.Atoms.IndexOf(one)].Equals(morgannumbers[container.Atoms.IndexOf(two)], StringComparison.Ordinal)))
{
return(true);
}
else
{
return(false);
}
}
}
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 hcount;
hcount = a.ImplicitHydrogenCount ?? 0;
int lengthAtom = container.GetConnectedAtoms(a).Count() + hcount;
if (lengthAtom != 3 && (lengthAtom != 2 && !(a.AtomicNumber.Equals(AtomicNumbers.N))))
{
return(false);
}
var atoms = container.GetConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
foreach (var atom in atoms)
{
if (atom != parent && container.GetBond(atom, a).Order == BondOrder.Double &&
IsEndOfDoubleBond(container, atom, a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atom;
}
if (atom != nextAtom && one == null)
{
one = atom;
}
else if (atom != nextAtom && one != null)
{
two = atom;
}
}
string[] morgannumbers = MorganNumbersTools.GetMorganNumbersWithElementSymbol(container);
if (one != null &&
((!a.AtomicNumber.Equals(AtomicNumbers.N) &&
two != null &&
!morgannumbers[container.Atoms.IndexOf(one)].Equals(morgannumbers[container.Atoms.IndexOf(two)], StringComparison.Ordinal) &&
doubleBond &&
doubleBondConfiguration[container.Bonds.IndexOf(container.GetBond(a, nextAtom))]) ||
(doubleBond && a.AtomicNumber.Equals(AtomicNumbers.N) &&
Math.Abs(GiveAngleBothMethods(nextAtom, a, parent, true)) > Math.PI / 10)))
{
return(true);
}
else
{
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>
/// Says if an atom as a center of any valid stereo configuration or not.
/// This method uses wedge bonds. 3D coordinates are not taken into account. If there
/// are no wedge bonds around a potential stereo center, it will not be found.
/// </summary>
/// <param name="stereoAtom">The atom which is the center</param>
/// <param name="container">The atomContainer the atom is in</param>
/// <returns>true=is a stereo atom, false=is not</returns>
public static bool IsStereo(IAtomContainer container, IAtom stereoAtom)
{
var atoms = container.GetConnectedAtoms(stereoAtom).ToReadOnlyList();
if (atoms.Count < 4 || atoms.Count > 6)
{
return(false);
}
var bonds = container.GetConnectedBonds(stereoAtom);
int stereo = 0;
foreach (var bond in bonds)
{
if (bond.Stereo != BondStereo.None)
{
stereo++;
}
}
if (stereo == 0)
{
return(false);
}
int differentAtoms = 0;
for (int i = 0; i < atoms.Count; i++)
{
bool isDifferent = true;
for (int k = 0; k < i; k++)
{
if (atoms[i].Symbol.Equals(atoms[k].Symbol, StringComparison.Ordinal))
{
isDifferent = false;
break;
}
}
if (isDifferent)
{
differentAtoms++;
}
}
if (differentAtoms != atoms.Count)
{
long[] morgannumbers = MorganNumbersTools.GetMorganNumbers(container);
var differentSymbols = new List <string>();
foreach (var atom in atoms)
{
if (!differentSymbols.Contains(atom.Symbol))
{
differentSymbols.Add(atom.Symbol);
}
}
int[] onlyRelevantIfTwo = new int[2];
if (differentSymbols.Count == 2)
{
foreach (var atom in atoms)
{
if (differentSymbols.IndexOf(atom.Symbol) == 0)
{
onlyRelevantIfTwo[0]++;
}
else
{
onlyRelevantIfTwo[1]++;
}
}
}
bool[] symbolsWithDifferentMorganNumbers = new bool[differentSymbols.Count];
var symbolsMorganNumbers = new List <long> [symbolsWithDifferentMorganNumbers.Length];
for (int i = 0; i < symbolsWithDifferentMorganNumbers.Length; i++)
{
symbolsWithDifferentMorganNumbers[i] = true;
symbolsMorganNumbers[i] = new List <long>();
}
foreach (var atom in atoms)
{
int elementNumber = differentSymbols.IndexOf(atom.Symbol);
if (symbolsMorganNumbers[elementNumber].Contains(morgannumbers[container.Atoms.IndexOf(atom)]))
{
symbolsWithDifferentMorganNumbers[elementNumber] = false;
}
else
{
symbolsMorganNumbers[elementNumber].Add(morgannumbers[container.Atoms.IndexOf(atom)]);
}
}
int numberOfSymbolsWithDifferentMorganNumbers = 0;
foreach (var symbolWithDifferentMorganNumber in symbolsWithDifferentMorganNumbers)
{
if (symbolWithDifferentMorganNumber)
{
numberOfSymbolsWithDifferentMorganNumbers++;
}
}
if (numberOfSymbolsWithDifferentMorganNumbers != differentSymbols.Count)
{
if ((atoms.Count == 5 || atoms.Count == 6) &&
(numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 &&
onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)))
{
return(true);
}
return(IsSquarePlanar(container, stereoAtom) &&
(numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 &&
onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)));
}
}
return(true);
}
/// <summary> Says if an atom as a center of any valid stereo configuration or not
///
/// </summary>
/// <param name="a"> The atom which is the center
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <returns> true=is a stereo atom, false=is not
/// </returns>
public static bool isStereo(IAtomContainer container, IAtom a)
{
IAtom[] atoms = container.getConnectedAtoms(a);
if (atoms.Length < 4 || atoms.Length > 6)
{
return(false);
}
IBond[] bonds = container.getConnectedBonds(a);
int stereo = 0;
for (int i = 0; i < bonds.Length; i++)
{
if (bonds[i].Stereo != 0)
{
stereo++;
}
}
if (stereo == 0)
{
return(false);
}
int differentAtoms = 0;
for (int i = 0; i < atoms.Length; i++)
{
bool isDifferent = true;
for (int k = 0; k < i; k++)
{
if (atoms[i].Symbol.Equals(atoms[k].Symbol))
{
isDifferent = false;
break;
}
}
if (isDifferent)
{
differentAtoms++;
}
}
if (differentAtoms != atoms.Length)
{
int[] morgannumbers = MorganNumbersTools.getMorganNumbers(container);
System.Collections.ArrayList differentSymbols = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < atoms.Length; i++)
{
if (!differentSymbols.Contains(atoms[i].Symbol))
{
differentSymbols.Add(atoms[i].Symbol);
}
}
int[] onlyRelevantIfTwo = new int[2];
if (differentSymbols.Count == 2)
{
for (int i = 0; i < atoms.Length; i++)
{
if (differentSymbols.IndexOf(atoms[i].Symbol) == 0)
{
onlyRelevantIfTwo[0]++;
}
else
{
onlyRelevantIfTwo[1]++;
}
}
}
bool[] symbolsWithDifferentMorganNumbers = new bool[differentSymbols.Count];
System.Collections.ArrayList[] symbolsMorganNumbers = new System.Collections.ArrayList[differentSymbols.Count];
for (int i = 0; i < symbolsWithDifferentMorganNumbers.Length; i++)
{
symbolsWithDifferentMorganNumbers[i] = true;
symbolsMorganNumbers[i] = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
}
for (int k = 0; k < atoms.Length; k++)
{
int elementNumber = differentSymbols.IndexOf(atoms[k].Symbol);
if (symbolsMorganNumbers[elementNumber].Contains((System.Int32)morgannumbers[container.getAtomNumber(atoms[k])]))
{
symbolsWithDifferentMorganNumbers[elementNumber] = false;
}
else
{
symbolsMorganNumbers[elementNumber].Add((System.Int32)morgannumbers[container.getAtomNumber(atoms[k])]);
}
}
int numberOfSymbolsWithDifferentMorganNumbers = 0;
for (int i = 0; i < symbolsWithDifferentMorganNumbers.Length; i++)
{
if (symbolsWithDifferentMorganNumbers[i] == true)
{
numberOfSymbolsWithDifferentMorganNumbers++;
}
}
if (numberOfSymbolsWithDifferentMorganNumbers != differentSymbols.Count)
{
if ((atoms.Length == 5 || atoms.Length == 6) && (numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 && onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)))
{
return(true);
}
if (isSquarePlanar(container, a) && (numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 && onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)))
{
return(true);
}
return(false);
}
}
return(true);
}
