public void TestAssignAtomTyps_bug_amideRingAtomType()
{
var smiles = "O=C1N(C(=O)C(C(=O)N1)(CC)CC)C";
var parser = CDK.SmilesParser;
var bugmol = parser.ParseSmiles(smiles);
forceFieldConfigurator.SetForceFieldConfigurator("mmff94");
IAtom nitrogen1 = bugmol.Atoms[2];
HOSECodeGenerator hscodegen = new HOSECodeGenerator();
forceFieldConfigurator.ConfigureAtom(nitrogen1, hscodegen.GetHOSECode(bugmol, nitrogen1, 3), false);
Assert.AreEqual("NC=O", nitrogen1.AtomTypeName);
}
public void TestAssignAtomTyps_bug_so2()
{
var smiles = "CS(=O)(=O)NC(=O)NN1CC2CCCC2C1";
var parser = CDK.SmilesParser;
var bugmol = parser.ParseSmiles(smiles);
forceFieldConfigurator.SetForceFieldConfigurator("mmff94");
IAtom sulphur = bugmol.Atoms[1];
HOSECodeGenerator hscodegen = new HOSECodeGenerator();
forceFieldConfigurator.ConfigureAtom(sulphur, hscodegen.GetHOSECode(bugmol, sulphur, 3), false);
Assert.AreEqual("SO2", sulphur.AtomTypeName);
}
[TestMethod(), Ignore()] // Old atom typing method - see new Mmff class
public void TestAssignAtomTyps_bug_nitrogenatomType()
{
var smiles = "CNC(=O)N(C)N=O";
var parser = CDK.SmilesParser;
var bugmol = parser.ParseSmiles(smiles);
forceFieldConfigurator.SetForceFieldConfigurator("mmff94");
IAtom nitrogen1 = bugmol.Atoms[1];
IAtom nitrogen2 = bugmol.Atoms[4];
IAtom nitrogen3 = bugmol.Atoms[6];
HOSECodeGenerator hscodegen = new HOSECodeGenerator();
forceFieldConfigurator.ConfigureAtom(nitrogen1, hscodegen.GetHOSECode(bugmol, nitrogen1, 3), false);
forceFieldConfigurator.ConfigureAtom(nitrogen2, hscodegen.GetHOSECode(bugmol, nitrogen2, 3), false);
forceFieldConfigurator.ConfigureAtom(nitrogen3, hscodegen.GetHOSECode(bugmol, nitrogen3, 3), false);
Assert.AreEqual("NC=O", nitrogen1.AtomTypeName);
Assert.AreEqual("NC=O", nitrogen2.AtomTypeName);
}
private static void SetActiveCenters(IAtomContainer reactant, int length, bool checkPrev, AtomCheck atomCheck)
{
var hcg = new HOSECodeGenerator();
foreach (var atomi in reactant.Atoms)
{
if (reactant.GetConnectedSingleElectrons(atomi).Count() == 1)
{
IEnumerable <IAtom> atom1s = null;
if (checkPrev)
{
hcg.GetSpheres(reactant, atomi, length - 1, true);
atom1s = hcg.GetNodesInSphere(length - 1);
}
hcg.GetSpheres(reactant, atomi, length, true);
foreach (var atoml in hcg.GetNodesInSphere(length))
{
if (atoml != null &&
!atoml.IsInRing &&
(atoml.FormalCharge ?? 0) == 0 &&
!atoml.AtomicNumber.Equals(AtomicNumbers.H) &&
reactant.GetMaximumBondOrder(atoml) == BondOrder.Single)
{
foreach (var atomR in reactant.GetConnectedAtoms(atoml))
{
if (atom1s != null && atom1s.Contains(atomR))
{
continue;
}
if (atomCheck(atomR))
{
atomi.IsReactiveCenter = true;
atoml.IsReactiveCenter = true;
atomR.IsReactiveCenter = true;
reactant.GetBond(atomR, atoml).IsReactiveCenter = true;;
}
}
}
}
}
}
}
internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, int length, bool checkPrev, AtomCheck atomCheck)
{
CheckInitiateParams(reactants, agents);
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
Aromaticity.CDKLegacy.Apply(reactant);
AllRingsFinder arf = new AllRingsFinder();
IRingSet ringSet = arf.FindAllRings(reactant);
for (int ir = 0; ir < ringSet.Count; ir++)
{
IRing ring = (IRing)ringSet[ir];
for (int jr = 0; jr < ring.Atoms.Count; jr++)
{
IAtom aring = ring.Atoms[jr];
aring.IsInRing = true;
}
}
// if the parameter hasActiveCenter is not fixed yet, set the active centers
IParameterReaction ipr = base.GetParameterClass(typeof(SetReactionCenter));
if (ipr != null && !ipr.IsSetParameter)
{
SetActiveCenters(reactant, length, checkPrev, atomCheck);
}
HOSECodeGenerator hcg = new HOSECodeGenerator();
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter && reactant.GetConnectedSingleElectrons(atomi).Count() == 1)
{
IEnumerable <IAtom> atom1s = null;
if (checkPrev)
{
hcg.GetSpheres(reactant, atomi, length - 1, true);
atom1s = hcg.GetNodesInSphere(length - 1);
}
hcg.GetSpheres(reactant, atomi, length, true);
foreach (var atoml in hcg.GetNodesInSphere(length))
{
if (atoml != null &&
atoml.IsReactiveCenter &&
!atoml.IsInRing &&
(atoml.FormalCharge ?? 0) == 0 &&
!atoml.AtomicNumber.Equals(AtomicNumbers.H) &&
reactant.GetMaximumBondOrder(atoml) == BondOrder.Single)
{
foreach (var atomR in reactant.GetConnectedAtoms(atoml))
{
if (atom1s != null && atom1s.Contains(atomR))
{
continue;
}
if (reactant.GetBond(atomR, atoml).IsReactiveCenter &&
atomR.IsReactiveCenter &&
atomCheck(atomR))
{
var atomList = new List <IAtom>
{
atomR,
atomi,
atoml
};
var bondList = new List <IBond>
{
reactant.GetBond(atomR, atoml)
};
var moleculeSet = reactant.Builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Add(reactant);
var reaction = Mechanism.Initiate(moleculeSet, atomList, bondList);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
}
}
}
}
return(setOfReactions);
}
/// <summary>
/// Method assigns atom types to atoms (calculates sssr and aromaticity)
/// </summary>
/// <returns>sssrf set</returns>
/// <exception cref="CDKException"> Problems detecting aromaticity or making hose codes.</exception>
public IRingSet AssignAtomTyps(IAtomContainer molecule)
{
IAtom atom = null;
string hoseCode = "";
HOSECodeGenerator hcg = new HOSECodeGenerator();
int NumberOfRingAtoms = 0;
IRingSet ringSetMolecule = Cycles.FindSSSR(molecule).ToRingSet();
bool isInHeteroRing = false;
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.CDKLegacy.Apply(molecule);
}
catch (Exception cdk1)
{
throw new CDKException("AROMATICITYError: Cannot determine aromaticity due to: " + cdk1.Message, cdk1);
}
for (int i = 0; i < molecule.Atoms.Count; i++)
{
atom = molecule.Atoms[i];
if (ringSetMolecule.Contains(atom))
{
NumberOfRingAtoms = NumberOfRingAtoms + 1;
atom.IsInRing = true;
atom.IsAliphatic = false;
var ringSetA = ringSetMolecule.GetRings(atom).ToList();
RingSetManipulator.Sort(ringSetA);
IRing sring = (IRing)ringSetA[ringSetA.Count - 1];
atom.SetProperty("RING_SIZE", sring.RingSize);
foreach (var ring in ringSetA)
{
if (IsHeteroRingSystem(ring))
{
break;
}
}
}
else
{
atom.IsAliphatic = true;
atom.IsInRing = false;
isInHeteroRing = false;
}
atom.SetProperty("MAX_BOND_ORDER", molecule.GetMaximumBondOrder(atom).Numeric());
try
{
hoseCode = hcg.GetHOSECode(molecule, atom, 3);
//Debug.WriteLine("HOSECODE GENERATION: ATOM "+i+" HoseCode: "+hoseCode+" ");
}
catch (CDKException ex1)
{
Console.Out.WriteLine("Could not build HOSECode from atom " + i + " due to " + ex1.ToString());
throw new CDKException("Could not build HOSECode from atom " + i + " due to " + ex1.ToString(), ex1);
}
try
{
ConfigureAtom(atom, hoseCode, isInHeteroRing);
}
catch (CDKException ex2)
{
Console.Out.WriteLine("Could not final configure atom " + i + " due to " + ex2.ToString());
throw new CDKException("Could not final configure atom due to problems with force field", ex2);
}
}
// IBond[] bond = molecule.Bonds;
string bondType;
foreach (var bond in molecule.Bonds)
{
//Debug.WriteLine("bond[" + i + "] properties : " + molecule.Bonds[i].GetProperties());
bondType = "0";
if (bond.Order == BondOrder.Single)
{
if ((bond.Begin.AtomTypeName.Equals("Csp2", StringComparison.Ordinal)) &&
((bond.End.AtomTypeName.Equals("Csp2", StringComparison.Ordinal)) ||
(bond.End.AtomTypeName.Equals("C=", StringComparison.Ordinal))))
{
bondType = "1";
}
if ((bond.Begin.AtomTypeName.Equals("C=", StringComparison.Ordinal)) &&
((bond.End.AtomTypeName.Equals("Csp2", StringComparison.Ordinal)) ||
(bond.End.AtomTypeName.Equals("C=", StringComparison.Ordinal))))
{
bondType = "1";
}
if ((bond.Begin.AtomTypeName.Equals("Csp", StringComparison.Ordinal)) &&
(bond.End.AtomTypeName.Equals("Csp", StringComparison.Ordinal)))
{
bondType = "1";
}
}
// molecule.Bonds[i].SetProperty("MMFF94 bond type", bondType);
bond.SetProperty("MMFF94 bond type", bondType);
//Debug.WriteLine("bond[" + i + "] properties : " + molecule.Bonds[i].GetProperties());
}
return(ringSetMolecule);
}
/// <summary>
/// extract from the db the ionization energy.
/// </summary>
/// <param name="container">The IAtomContainer</param>
/// <param name="atom">The IAtom</param>
/// <returns>The energy value</returns>
public static double ExtractIP(IAtom atom, IAtomContainer container,
IReadOnlyDictionary <string, double> hoseVSenergy,
IReadOnlyDictionary <string, double> hoseVSenergyS)
{
if (!FamilyHalogen(atom))
{
return(0);
}
var hcg = new HOSECodeGenerator();
//Check starting from the exact sphere hose code and maximal a value of 10
int exactSphere = 0;
string hoseCode = "";
for (int spheres = maxSpheresToUse; spheres > 0; spheres--)
{
hcg.GetSpheres(container, atom, spheres, true);
var atoms = hcg.GetNodesInSphere(spheres);
if (atoms.Any())
{
exactSphere = spheres;
hoseCode = hcg.GetHOSECode(container, atom, spheres, true);
if (hoseVSenergy.ContainsKey(hoseCode))
{
return(hoseVSenergy[hoseCode]);
}
if (hoseVSenergyS.ContainsKey(hoseCode))
{
return(hoseVSenergyS[hoseCode]);
}
break;
}
}
//Check starting from the rings bigger and smaller
//TODO:IP: Better application
for (int i = 0; i < 3; i++)
{ // two rings
for (int plusMinus = 0; plusMinus < 2; plusMinus++)
{ // plus==bigger, minus==smaller
int sign = -1;
if (plusMinus == 1)
{
sign = 1;
}
var st = Strings.Tokenize(hoseCode, '(', ')', '/').GetEnumerator();
var hoseCodeBuffer = new StringBuilder();
int sum = exactSphere + sign * (i + 1);
for (int k = 0; k < sum; k++)
{
if (st.MoveNext())
{
string partcode = st.Current;
hoseCodeBuffer.Append(partcode);
}
switch (k)
{
case 0:
hoseCodeBuffer.Append('(');
break;
case 3:
hoseCodeBuffer.Append(')');
break;
default:
hoseCodeBuffer.Append('/');
break;
}
}
string hoseCodeBU = hoseCodeBuffer.ToString();
if (hoseVSenergyS.ContainsKey(hoseCodeBU))
{
return(hoseVSenergyS[hoseCodeBU]);
}
}
}
return(0);
}
