private static void FixPyridineNOxides(IAtomContainer atomContainer, IRingSet ringSet)
{
//convert n(=O) to [n+][O-]
for (int i = 0; i < atomContainer.Atoms.Count; i++)
{
var ai = atomContainer.Atoms[i];
if (ai.AtomicNumber.Equals(AtomicNumbers.N) &&
(ai.FormalCharge == null || ai.FormalCharge == 0))
{
if (InRingSet(ai, ringSet))
{
var ca = atomContainer.GetConnectedAtoms(ai);
foreach (var caj in ca)
{
if (caj.AtomicNumber.Equals(AtomicNumbers.O) &&
atomContainer.GetBond(ai, caj).Order == BondOrder.Double)
{
ai.FormalCharge = 1;
caj.FormalCharge = -1;
atomContainer.GetBond(ai, caj).Order = BondOrder.Single;
}
} // end for (int j=0;j<ca.Count;j++)
} // end if (InRingSet(ai,ringSet)) {
} // end if (ai.Symbol.Equals("N") && ai.FormalCharge==0)
} // end for (int i=0;i<atomContainer.Atoms.Count;i++)
}
/// <summary>
/// Checks whether the P atom is in a PO environment.
/// </summary>
/// <remarks>
/// This environment is noted in Kier & Hall (1986), page 20
/// </remarks>
/// <param name="atom">The P atom in question</param>
/// <param name="atomContainer">The molecule containing the P atom</param>
/// <returns>The empirical delta V if present in the above environment, -1 otherwise</returns>
private static double DeltavPhosphorous(IAtom atom, IAtomContainer atomContainer)
{
if (!atom.AtomicNumber.Equals(AtomicNumbers.P))
{
return(-1);
}
var connected = atomContainer.GetConnectedAtoms(atom);
int conditions = 0;
if (connected.Count() == 4)
{
conditions++;
}
foreach (var connectedAtom in connected)
{
if (connectedAtom.AtomicNumber.Equals(AtomicNumbers.O) &&
atomContainer.GetBond(atom, connectedAtom).Order == BondOrder.Double)
{
conditions++;
}
if (atomContainer.GetBond(atom, connectedAtom).Order == BondOrder.Single)
{
conditions++;
}
}
if (conditions == 5)
{
return(2.22);
}
return(-1);
}
/// <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>
/// Prepares for a breadth first search within the <see cref="IAtomContainer"/>. The actual
/// recursion is done in <see cref="NextSphere"/>.
/// </summary>
/// <param name="root">The atom at which we start the search</param>
/// <param name="addTreeNode"></param>
/// <exception cref="CDKException"> If something goes wrong.</exception>
private void BreadthFirstSearch(IAtom root, bool addTreeNode)
{
sphere = 0;
TreeNode tempNode = null;
var conAtoms = atomContainer.GetConnectedAtoms(root);
IBond bond = null;
sphereNodes.Clear();
sphereNodesWithAtoms.Clear();
foreach (var atom in conAtoms)
{
try
{
if (atom.AtomicNumber.Equals(AtomicNumbers.H))
{
continue;
}
bond = atomContainer.GetBond(root, atom);
// In the first sphere the atoms are labeled with their own atom
// atom as source
if (bond.IsAromatic)
{
tempNode = new TreeNode(this, atom.Symbol, new TreeNode(this, root.Symbol, null, root, (double)0, 0,
(long)0), atom, 4, atomContainer.GetConnectedBonds(atom).Count(), 0);
}
else
{
tempNode = new TreeNode(
this, atom.Symbol,
new TreeNode(this, root.Symbol, null, root, (double)0, 0, (long)0), atom,
bond.Order.Numeric(), atomContainer.GetConnectedBonds(atom).Count(), 0);
}
sphereNodes.Add(tempNode);
if (!addTreeNode)
{
sphereNodesWithAtoms.Add(atom);
}
// rootNode.childs.AddElement(tempNode);
atom.IsVisited = true;
}
catch (Exception exc)
{
throw new CDKException("Error in HOSECodeGenerator->breadthFirstSearch.", exc);
}
}
sphereNodes.Sort(new TreeNodeComparator());
NextSphere(sphereNodes);
}
public void Z_1_2_difluroethene()
{
IAtomContainer ac = Convert("F/C=C\\F");
var se = ac.StereoElements.First();
Assert.IsInstanceOfType(se, typeof(IDoubleBondStereochemistry));
IDoubleBondStereochemistry dbs = (IDoubleBondStereochemistry)se;
Assert.AreEqual(ac.GetBond(ac.Atoms[1], ac.Atoms[2]), dbs.StereoBond);
Assert.IsTrue(Compares.AreDeepEqual(new IBond[] { ac.GetBond(ac.Atoms[0], ac.Atoms[1]), ac.GetBond(ac.Atoms[2], ac.Atoms[3]) }, dbs.Bonds));
Assert.AreEqual(DoubleBondConformation.Together, dbs.Stereo);
}
/// <summary>
/// Helper method to locate two terminal atoms in a container for this
/// extended tetrahedral element. The atoms are ordered such that the first
/// index is attached to the first two peripheral atoms and the second index
/// is attached to the second two peripheral atoms.
/// </summary>
/// <param name="container">structure representation</param>
/// <returns>the terminal atoms (ordered)</returns>
public IAtom[] FindTerminalAtoms(IAtomContainer container)
{
var atoms = FindTerminalAtoms(container, Focus);
var carriers = Carriers;
if (container.GetBond(atoms[0], carriers[2]) != null ||
container.GetBond(atoms[0], carriers[3]) != null)
{
var tmp = atoms[0];
atoms[0] = atoms[1];
atoms[1] = tmp;
}
return(atoms);
}
/// <summary>
/// Says if of four atoms connected two one atom the up and down bonds are
/// opposite or not, i. e.if it's tetrahedral or square planar. The method
/// does not check if there are four atoms and if two or up and two are down
/// </summary>
/// <param name="atom">The atom which is the center</param>
/// <param name="container">The atomContainer the atom is in</param>
/// <returns>true=are opposite, false=are not</returns>
public static bool StereosAreOpposite(IAtomContainer container, IAtom atom)
{
var atoms = container.GetConnectedAtoms(atom).ToReadOnlyList();
var hm = new SortedDictionary <double, int>();
for (int i = 1; i < atoms.Count; i++)
{
hm.Add(GiveAngle(atom, atoms[0], atoms[i]), i);
}
var ohere = hm.Values.ToArray();
var stereoOne = container.GetBond(atom, atoms[0]).Stereo;
var stereoOpposite = container.GetBond(atom, atoms[ohere[1]]).Stereo;
return(stereoOpposite == stereoOne);
}
public void Z_1_2_difluroethene_explicit()
{
IAtomContainer ac = Convert("FC(\\[H])=C([H])/F");
var se = ac.StereoElements.First();
Assert.IsInstanceOfType(se, typeof(IDoubleBondStereochemistry));
IDoubleBondStereochemistry dbs = (IDoubleBondStereochemistry)se;
Assert.AreEqual(ac.GetBond(ac.Atoms[1], ac.Atoms[3]), dbs.StereoBond);
Assert.IsTrue(Compares.AreDeepEqual(new IBond[] { ac.GetBond(ac.Atoms[1], ac.Atoms[2]), ac.GetBond(ac.Atoms[3], ac.Atoms[5]) }, dbs.Bonds));
// the two 'F' are together but we use a H so they are 'opposite'
Assert.AreEqual(DoubleBondConformation.Opposite, dbs.Stereo);
}
/// <summary>
/// Returns Ring set based on Hanser Ring Finding method
/// <param name="molecule"></param>
/// </summary>
/// <returns>report collected the rings</returns>
/// <seealso cref="IRingFinder.GetRingSet(IAtomContainer)"/>
public IRingSet GetRingSet(IAtomContainer molecule)
{
var cycles = FindRings(molecule);
IRingSet ringSet = molecule.Builder.NewRingSet();
foreach (var ringAtoms in cycles)
{
IRing ring = molecule.Builder.NewRing();
foreach (var atom in ringAtoms)
{
atom.IsInRing = true;
ring.Atoms.Add(atom);
foreach (var atomNext in ringAtoms)
{
if (!atom.Equals(atomNext))
{
IBond bond = molecule.GetBond(atom, atomNext);
if (bond != null)
{
bond.IsInRing = true;
ring.Bonds.Add(bond);
}
}
}
}
ringSet.Add(ring);
}
return(ringSet);
}
/// <summary>
/// Encode the provided path of atoms to a string.
/// </summary>
/// <param name="path">inclusive array of vertex indices</param>
/// <returns>encoded path</returns>
private string Encode(int[] path)
{
var sb = new StringBuilder(path.Length * 3);
for (int i = 0, n = path.Length - 1; i <= n; i++)
{
var atom = container.Atoms[path[i]];
sb.Append(ToAtomPattern(atom));
if (atom is IPseudoAtom)
{
pseudoAtoms.Add(atom.Symbol);
// potential bug, although the atoms are canonical we cannot guarantee the order we will visit them.
// sb.Append(PeriodicTable.GetElementCount() + pseudoAtoms.Count());
}
// if we are not at the last index, add the connecting bond
if (i < n)
{
IBond bond = container.GetBond(container.Atoms[path[i]], container.Atoms[path[i + 1]]);
sb.Append(GetBondSymbol(bond));
}
}
return(sb.ToString());
}
/// <summary>
/// Constructor for the TopologicalEquivalentClass object.
/// </summary>
public EquivalentClassPartitioner(IAtomContainer atomContainer)
{
adjaMatrix = ConnectionMatrix.GetMatrix(atomContainer);
apspMatrix = PathTools.ComputeFloydAPSP(adjaMatrix);
layerNumber = 1;
nodeNumber = atomContainer.Atoms.Count;
for (int i = 1; i < atomContainer.Atoms.Count; i++)
{
for (int j = 0; j < i; j++)
{
// define the number of layer equal to the longest path obtained
// by calculating the all-pair-shortest path
if (apspMatrix[i][j] > layerNumber)
{
layerNumber = apspMatrix[i][j];
}
// correct adjacency matrix to consider aromatic bonds as such
if (adjaMatrix[i][j] > 0)
{
IBond bond = atomContainer.GetBond(atomContainer.Atoms[i], atomContainer.Atoms[j]);
bool isArom = bond.IsAromatic;
adjaMatrix[i][j] = (isArom) ? 1.5 : adjaMatrix[i][j];
adjaMatrix[j][i] = adjaMatrix[i][j];
}
}
}
nodeMatrix = Arrays.CreateJagged <double>(nodeNumber, layerNumber + 1);
bondMatrix = Arrays.CreateJagged <double>(nodeNumber, layerNumber);
weight = new double[nodeNumber + 1];
}
/// <inheritdoc/>
public override bool IsConnected(int index1, int index2)
{
IAtom atom1 = atomContainer.Atoms[index1];
IAtom atom2 = atomContainer.Atoms[index2];
return(atomContainer.GetBond(atom1, atom2) != null);
}
/// <summary>
///
/// Returns bond map between source and target molecules based on the atoms
/// <param name="ac1">source molecule</param>
/// <param name="ac2">target molecule</param>
/// <param name="mapping">mappings between source and target molecule atoms</param>
/// <returns>bond map between source and target molecules based on the atoms</returns>
/// </summary>
public static IReadOnlyDictionary <IBond, IBond> MakeBondMapOfAtomMap(
IAtomContainer ac1, IAtomContainer ac2,
IReadOnlyDictionary <IAtom, IAtom> mapping)
{
var maps = new Dictionary <IBond, IBond>();
foreach (var mapS in mapping)
{
IAtom indexI = mapS.Key;
IAtom indexJ = mapS.Value;
foreach (var mapD in mapping)
{
IAtom indexIPlus = mapD.Key;
IAtom indexJPlus = mapD.Value;
if (!indexI.Equals(indexIPlus) && !indexJ.Equals(indexJPlus))
{
IBond ac1Bond = ac1.GetBond(indexI, indexIPlus);
if (ac1Bond != null)
{
IBond ac2Bond = ac2.GetBond(indexJ, indexJPlus);
if (ac2Bond != null)
{
maps[ac1Bond] = ac2Bond;
}
}
}
}
}
return(maps);
}
/// <summary>
/// Obtain the bond between the atoms at index <paramref name="u"/> and 'v'. If the 'bondMap'
/// is non-null it is used for direct lookup otherwise the slower linear
/// lookup in 'container' is used.
/// </summary>
/// <param name="container">a structure</param>
/// <param name="bondMap">optimised map of atom indices to bond instances</param>
/// <param name="u">an atom index</param>
/// <param name="v">an atom index (connected to u)</param>
/// <returns>the bond between u and v</returns>
private static IBond GetBond(IAtomContainer container, EdgeToBondMap bondMap, int u, int v)
{
if (bondMap != null)
{
return(bondMap[u, v]);
}
return(container.GetBond(container.Atoms[u], container.Atoms[v]));
}
public static void MakeUpDownBonds(IAtomContainer container)
{
for (int i = 0; i < container.Atoms.Count; i++)
{
var a = container.Atoms[i];
var connectedAtoms = container.GetConnectedAtoms(a).ToReadOnlyList();
if (connectedAtoms.Count == 4)
{
int up = 0;
int down = 0;
int hs = 0;
IAtom h = null;
for (int k = 0; k < 4; k++)
{
IAtom conAtom = connectedAtoms[k];
BondStereo stereo = container.GetBond(a, conAtom).Stereo;
if (stereo == BondStereo.Up)
{
up++;
}
else if (stereo == BondStereo.Down)
{
down++;
}
else if (stereo == BondStereo.None && conAtom.AtomicNumber.Equals(AtomicNumbers.H))
{
h = conAtom;
hs++;
}
else
{
h = null;
}
}
if (up == 0 && down == 1 && h != null && hs == 1)
{
container.GetBond(a, h).Stereo = BondStereo.Up;
}
if (up == 1 && down == 0 && h != null && hs == 1)
{
container.GetBond(a, h).Stereo = BondStereo.Down;
}
}
}
}
private static IReadOnlyDictionary <IBond, IBond> MakeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2, IReadOnlyDictionary <int, int> mappings)
{
var maps = new Dictionary <IBond, IBond>();
foreach (var atoms in ac1.Atoms)
{
int ac1AtomNumber = ac1.Atoms.IndexOf(atoms);
if (mappings.ContainsKey(ac1AtomNumber))
{
int ac2AtomNumber = mappings[ac1AtomNumber];
var connectedAtoms = ac1.GetConnectedAtoms(atoms);
foreach (var cAtoms in connectedAtoms)
{
int ac1ConnectedAtomNumber = ac1.Atoms.IndexOf(cAtoms);
if (mappings.ContainsKey(ac1ConnectedAtomNumber))
{
{
int ac2ConnectedAtomNumber = mappings[ac1ConnectedAtomNumber];
IBond ac1Bond = ac1.GetBond(atoms, cAtoms);
IBond ac2Bond = ac2.GetBond(ac2.Atoms[ac2AtomNumber], ac2.Atoms[ac2ConnectedAtomNumber]);
if (ac2Bond == null)
{
ac2Bond = ac2.GetBond(ac2.Atoms[ac2ConnectedAtomNumber], ac2.Atoms[ac2AtomNumber]);
}
if (ac1Bond != null && ac2Bond != null)
{
maps[ac1Bond] = ac2Bond;
}
}
}
}
}
}
return(maps);
}
internal static bool IsFurtherMappingPossible(IAtomContainer source, IAtomContainer target,
McgregorHelper mcGregorHelper, bool shouldMatchBonds)
{
int neighborBondNumA = mcGregorHelper.NeighborBondNumA;
int neighborBondNumB = mcGregorHelper.NeighborBondNumB;
var iBondNeighborAtomsA = mcGregorHelper.GetIBondNeighborAtomsA();
var iBondNeighborAtomsB = mcGregorHelper.GetIBondNeighborAtomsB();
var cBondNeighborsA = mcGregorHelper.GetCBondNeighborsA();
var cBondNeighborsB = mcGregorHelper.GetCBondNeighborsB();
for (int row = 0; row < neighborBondNumA; row++)
{
// Console.Out.WriteLine("i " + row);
string g1A = cBondNeighborsA[row * 4 + 0];
string g2A = cBondNeighborsA[row * 4 + 1];
for (int column = 0; column < neighborBondNumB; column++)
{
string g1B = cBondNeighborsB[column * 4 + 0];
string g2B = cBondNeighborsB[column * 4 + 1];
if (IsAtomMatch(g1A, g2A, g1B, g2B))
{
try
{
int indexI = iBondNeighborAtomsA[row * 3 + 0];
int indexIPlus1 = iBondNeighborAtomsA[row * 3 + 1];
int indexJ = iBondNeighborAtomsB[column * 3 + 0];
int indexJPlus1 = iBondNeighborAtomsB[column * 3 + 1];
IAtom r1A = source.Atoms[indexI];
IAtom r2A = source.Atoms[indexIPlus1];
IBond reactantBond = source.GetBond(r1A, r2A);
IAtom p1B = target.Atoms[indexJ];
IAtom p2B = target.Atoms[indexJPlus1];
IBond productBond = target.GetBond(p1B, p2B);
if (IsMatchFeasible(source, reactantBond, target, productBond, shouldMatchBonds))
{
return(true);
}
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
}
}
}
return(false);
}
private void SetModifedArcs(McgregorHelper mcGregorHelper)
{
int neighborBondNumA = mcGregorHelper.NeighborBondNumA;
int neighborBondNumB = mcGregorHelper.NeighborBondNumB;
var iBondNeighborAtomsA = mcGregorHelper.GetIBondNeighborAtomsA();
var iBondNeighborAtomsB = mcGregorHelper.GetIBondNeighborAtomsB();
var cBondNeighborsA = mcGregorHelper.GetCBondNeighborsA();
var cBondNeighborsB = mcGregorHelper.GetCBondNeighborsB();
for (int row = 0; row < neighborBondNumA; row++)
{
for (int column = 0; column < neighborBondNumB; column++)
{
string g1A = cBondNeighborsA[row * 4 + 0];
string g2A = cBondNeighborsA[row * 4 + 1];
string g1B = cBondNeighborsB[column * 4 + 0];
string g2B = cBondNeighborsB[column * 4 + 1];
if (MatchGAtoms(g1A, g2A, g1B, g2B))
{
int indexI = iBondNeighborAtomsA[row * 3 + 0];
int indexIPlus1 = iBondNeighborAtomsA[row * 3 + 1];
IAtom r1A = source.Atoms[indexI];
IAtom r2A = source.Atoms[indexIPlus1];
IBond reactantBond = source.GetBond(r1A, r2A);
int indexJ = iBondNeighborAtomsB[column * 3 + 0];
int indexJPlus1 = iBondNeighborAtomsB[column * 3 + 1];
IAtom p1B = target.Atoms[indexJ];
IAtom p2B = target.Atoms[indexJPlus1];
IBond productBond = target.GetBond(p1B, p2B);
if (McGregorChecks.IsMatchFeasible(source, reactantBond, target, productBond, IsBondMatch))
{
modifiedARCS[row * neighborBondNumB + column] = 1;
}
}
}
}
}
/// <summary>
/// Says if two atoms are in cis or trans position around a double bond.
/// The atoms have to be given to the method like this: firstOuterAtom - firstInnerAtom = secondInnterAtom - secondOuterAtom
/// </summary>
/// <param name="firstOuterAtom">See above.</param>
/// <param name="firstInnerAtom">See above.</param>
/// <param name="secondInnerAtom">See above.</param>
/// <param name="secondOuterAtom">See above.</param>
/// <param name="ac">The atom container the atoms are in.</param>
/// <returns>true=trans, false=cis.</returns>
/// <exception cref="CDKException"> The atoms are not in a double bond configuration (no double bond in the middle, same atoms on one side)</exception>
public static bool IsCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom,
IAtom secondOuterAtom, IAtomContainer ac)
{
if (!IsValidDoubleBondConfiguration(ac, ac.GetBond(firstInnerAtom, secondInnerAtom)))
{
throw new CDKException("There is no valid double bond configuration between your inner atoms!");
}
bool firstDirection = IsLeft(firstOuterAtom, firstInnerAtom, secondInnerAtom);
bool secondDirection = IsLeft(secondOuterAtom, secondInnerAtom, firstInnerAtom);
return(firstDirection == secondDirection);
}
public void GetConnectivityTest()
{
string acpString = "C0C1C2C3 0:1(1),0:3(1),1:2(2),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(ac);
IBond bond = ac.GetBond(ac.Atoms[1], ac.Atoms[2]);
int orderN = bond.Order.Numeric();
Assert.AreEqual(orderN, refiner.GetConnectivity(1, 2));
}
public void Benzene_kekule()
{
IAtomContainer ac = Convert("C=1C=CC=CC1");
Assert.AreEqual(6, ac.Atoms.Count);
Assert.AreEqual(6, ac.Bonds.Count);
foreach (var a in ac.Atoms)
{
Assert.AreEqual("C", a.Symbol);
Assert.AreEqual(1, a.ImplicitHydrogenCount);
}
Assert.AreEqual(BondOrder.Single, ac.GetBond(ac.Atoms[0], ac.Atoms[1]).Order);
Assert.AreEqual(BondOrder.Double, ac.GetBond(ac.Atoms[1], ac.Atoms[2]).Order);
Assert.AreEqual(BondOrder.Single, ac.GetBond(ac.Atoms[2], ac.Atoms[3]).Order);
Assert.AreEqual(BondOrder.Double, ac.GetBond(ac.Atoms[3], ac.Atoms[4]).Order);
Assert.AreEqual(BondOrder.Single, ac.GetBond(ac.Atoms[4], ac.Atoms[5]).Order);
Assert.AreEqual(BondOrder.Double, ac.GetBond(ac.Atoms[5], ac.Atoms[0]).Order);
Assert.IsFalse(ac.Bonds[0].IsAromatic);
Assert.IsFalse(ac.Bonds[1].IsAromatic);
Assert.IsFalse(ac.Bonds[2].IsAromatic);
Assert.IsFalse(ac.Bonds[3].IsAromatic);
Assert.IsFalse(ac.Bonds[4].IsAromatic);
Assert.IsFalse(ac.Bonds[5].IsAromatic);
}
public void Imidazole_kekule()
{
IAtomContainer ac = Convert("N1C=CN=C1");
Assert.AreEqual(5, ac.Atoms.Count);
Assert.AreEqual(5, ac.Bonds.Count);
foreach (var a in ac.Atoms)
{
Assert.IsFalse(a.IsAromatic);
}
Assert.AreEqual("N", ac.Atoms[0].Symbol);
Assert.AreEqual("C", ac.Atoms[1].Symbol);
Assert.AreEqual("C", ac.Atoms[2].Symbol);
Assert.AreEqual("N", ac.Atoms[3].Symbol);
Assert.AreEqual("C", ac.Atoms[4].Symbol);
Assert.AreEqual(1, ac.Atoms[0].ImplicitHydrogenCount);
Assert.AreEqual(1, ac.Atoms[1].ImplicitHydrogenCount);
Assert.AreEqual(1, ac.Atoms[2].ImplicitHydrogenCount);
Assert.AreEqual(0, ac.Atoms[3].ImplicitHydrogenCount);
Assert.AreEqual(1, ac.Atoms[4].ImplicitHydrogenCount);
foreach (var a in ac.Atoms)
{
Assert.IsFalse(a.IsAromatic);
}
Assert.AreEqual(BondOrder.Single, ac.GetBond(ac.Atoms[0], ac.Atoms[1]).Order);
Assert.AreEqual(BondOrder.Double, ac.GetBond(ac.Atoms[1], ac.Atoms[2]).Order);
Assert.AreEqual(BondOrder.Single, ac.GetBond(ac.Atoms[2], ac.Atoms[3]).Order);
Assert.AreEqual(BondOrder.Double, ac.GetBond(ac.Atoms[3], ac.Atoms[4]).Order);
Assert.AreEqual(BondOrder.Single, ac.GetBond(ac.Atoms[4], ac.Atoms[0]).Order);
foreach (var b in ac.Bonds)
{
Assert.IsFalse(b.IsAromatic);
}
}
/// <summary>
/// Evaluates the empirical delt V for some S environments.
/// </summary>
/// <remarks>
/// The method checks to see whether a S atom is in a -S-S-,
/// -SO-, -SO2- group and returns the empirical values noted
/// in Kier & Hall (1986), page 20.
/// </remarks>
/// <param name="atom">The S atom in question</param>
/// <param name="atomContainer">The molecule containing the S</param>
/// <returns>The empirical delta V if it is present in one of the above environments, -1 otherwise</returns>
protected internal static double DeltavSulphur(IAtom atom, IAtomContainer atomContainer)
{
if (!atom.AtomicNumber.Equals(AtomicNumbers.S))
{
return(-1);
}
// check whether it's a S in S-S
var connected = atomContainer.GetConnectedAtoms(atom);
foreach (var connectedAtom in connected)
{
if (connectedAtom.AtomicNumber.Equals(AtomicNumbers.S) &&
atomContainer.GetBond(atom, connectedAtom).Order == BondOrder.Single)
{
return(0.89);
}
}
int count = 0;
foreach (var connectedAtom in connected)
{
if (connectedAtom.AtomicNumber.Equals(AtomicNumbers.O) &&
atomContainer.GetBond(atom, connectedAtom).Order == BondOrder.Double)
{
count++;
}
}
if (count == 1)
{
return(1.33); // check whether it's a S in -SO-
}
else if (count == 2)
{
return(2.67); // check whether it's a S in -SO2-
}
return(-1);
}
public static void FixSulphurH(IAtomContainer m)
{
// removes extra H's attached to sulphurs
for (int i = 0; i <= m.Atoms.Count - 1; i++)
{
var a = m.Atoms[i];
if (a.AtomicNumber.Equals(AtomicNumbers.S))
{
var connectedAtoms = m.GetConnectedAtoms(a);
int bondOrderSum = 0;
foreach (var conAtom in connectedAtoms)
{
if (!conAtom.AtomicNumber.Equals(AtomicNumbers.H))
{
IBond bond = m.GetBond(a, conAtom);
if (bond.Order == BondOrder.Single)
{
bondOrderSum += 1;
}
else if (bond.Order == BondOrder.Double)
{
bondOrderSum += 2;
}
else if (bond.Order == BondOrder.Triple)
{
bondOrderSum += 3;
}
else if (bond.Order == BondOrder.Quadruple)
{
bondOrderSum += 4;
}
}
}
if (bondOrderSum > 1)
{
foreach (var conAtom in connectedAtoms)
{
if (conAtom.AtomicNumber.Equals(AtomicNumbers.H))
{
m.RemoveAtom(conAtom);
}
}
}
}
}
}
/// <summary>
/// Checks whether both atoms are involved in an amide C-N bond: *N(*)C(*)=O.
///
/// Only the most common constitution is considered. Tautomeric, O\C(*)=N\*,
/// and charged forms, [O-]\C(*)=N\*, are ignored.
/// </summary>
/// <param name="atom0">the first bonding partner</param>
/// <param name="atom1">the second bonding partner</param>
/// <param name="container">the parent container</param>
/// <returns>if both partners are involved in an amide C-N bond</returns>
private static bool IsAmide(IAtom atom0, IAtom atom1, IAtomContainer container)
{
if (atom0.AtomicNumber.Equals(AtomicNumbers.C) && atom1.AtomicNumber.Equals(AtomicNumbers.N))
{
foreach (var neighbor in container.GetConnectedAtoms(atom0))
{
if (neighbor.AtomicNumber.Equals(AtomicNumbers.O) &&
container.GetBond(atom0, neighbor).Order == BondOrder.Double)
{
return(true);
}
}
}
return(false);
}
private static void ApplyBonds(IAtomContainer m, IList <string> al)
{
for (int i = 0; i <= al.Count - 1; i++)
{
var s = al[i];
var s1 = s.Substring(0, s.IndexOf('-'));
var s2 = s.Substring(s.IndexOf('-') + 1);
var i1 = int.Parse(s1, NumberFormatInfo.InvariantInfo);
var i2 = int.Parse(s2, NumberFormatInfo.InvariantInfo);
var b = m.GetBond(m.Atoms[i1], m.Atoms[i2]);
b.Order = BondOrder.Double;
}
}
/// <summary>
/// Generate Compatibility Graph Nodes Bond Insensitive
/// </summary>
/// <exception cref="System.IO.IOException"></exception>
internal int CompatibilityGraph()
{
int compGraphNodesListSize = compGraphNodes.Count;
cEdges = new List <int>(); //Initialize the cEdges List
dEdges = new List <int>(); //Initialize the dEdges List
for (int a = 0; a < compGraphNodesListSize; a += 3)
{
int indexA = compGraphNodes[a];
int indexAPlus1 = compGraphNodes[a + 1];
for (int b = a + 3; b < compGraphNodesListSize; b += 3)
{
int indexB = compGraphNodes[b];
int indexBPlus1 = compGraphNodes[b + 1];
// if element atomCont !=jIndex and atoms on the adjacent sides of the bonds are not equal
if (a != b && indexA != indexB && indexAPlus1 != indexBPlus1)
{
IBond reactantBond = null;
IBond productBond = null;
reactantBond = source.GetBond(source.Atoms[indexA], source.Atoms[indexB]);
productBond = target.GetBond(target.Atoms[indexAPlus1], target.Atoms[indexBPlus1]);
if (reactantBond != null && productBond != null)
{
AddEdges(reactantBond, productBond, a, b);
}
}
}
}
cEdgesSize = cEdges.Count;
dEdgesSize = dEdges.Count;
return(0);
}
private void ProcessBondsBlock(int lineCount, IAtomContainer container)
{
for (int i = 0; i < lineCount; i++)
{
string line = input.ReadLine();
int atom1 = int.Parse(line.Substring(10, 3).Trim(), NumberFormatInfo.InvariantInfo) - 1;
int atom2 = int.Parse(line.Substring(16, 3).Trim(), NumberFormatInfo.InvariantInfo) - 1;
if (container.GetBond(container.Atoms[atom1], container.Atoms[atom2]) == null)
{
IBond bond = container.Builder.NewBond(container.Atoms[atom1],
container.Atoms[atom2]);
int order = int.Parse(line.Substring(23).Trim(), NumberFormatInfo.InvariantInfo);
bond.Order = BondManipulator.CreateBondOrder((double)order);
container.Bonds.Add(bond);
} // else: bond already present; CTX store the bonds twice
}
}
/// <summary>
/// Encode the provided path of atoms to a string.
/// </summary>
/// <param name="path">inclusive array of vertex indices</param>
/// <returns>encoded path</returns>
private string Encode(int[] path)
{
var sb = new StringBuilder(path.Length * 3);
for (int i = 0, n = path.Length - 1; i <= n; i++)
{
var atom = container.Atoms[path[i]];
sb.Append(ToAtomPattern(atom));
// if we are not at the last index, add the connecting bond
if (i < n)
{
var bond = container.GetBond(container.Atoms[path[i]], container.Atoms[path[i + 1]]);
sb.Append(GetBondSymbol(bond));
}
}
return(sb.ToString());
}