public virtual void TestContains_IAtomContainer()
{
IRingSet ringset = (IRingSet)NewChemObject();
IAtom ring1Atom1 = ringset.Builder.NewAtom("C"); // rather artificial molecule
IAtom ring1Atom2 = ringset.Builder.NewAtom("C");
IAtom sharedAtom1 = ringset.Builder.NewAtom("C");
IAtom sharedAtom2 = ringset.Builder.NewAtom("C");
IAtom ring2Atom1 = ringset.Builder.NewAtom("C");
IAtom ring2Atom2 = ringset.Builder.NewAtom("C");
IBond ring1Bond1 = ringset.Builder.NewBond(ring1Atom1, ring1Atom2);
IBond ring1Bond2 = ringset.Builder.NewBond(sharedAtom1, ring1Atom1);
IBond ring1Bond3 = ringset.Builder.NewBond(sharedAtom2, ring1Atom2);
IBond sharedBond = ringset.Builder.NewBond(sharedAtom1, sharedAtom2);
IBond ring2Bond1 = ringset.Builder.NewBond(ring2Atom1, ring2Atom2);
IBond ring2Bond2 = ringset.Builder.NewBond(sharedAtom1, ring2Atom1);
IBond ring2Bond3 = ringset.Builder.NewBond(sharedAtom2, ring2Atom2);
IRing ring1 = ringset.Builder.NewRing();
ring1.Atoms.Add(ring1Atom1);
ring1.Atoms.Add(ring1Atom2);
ring1.Atoms.Add(sharedAtom1);
ring1.Atoms.Add(sharedAtom2);
ring1.Bonds.Add(ring1Bond1);
ring1.Bonds.Add(ring1Bond2);
ring1.Bonds.Add(ring1Bond3);
ring1.Bonds.Add(sharedBond);
IRing ring2 = ringset.Builder.NewRing();
ring2.Atoms.Add(ring2Atom1);
ring2.Atoms.Add(ring2Atom2);
ring2.Atoms.Add(sharedAtom1);
ring2.Atoms.Add(sharedAtom2);
ring2.Bonds.Add(ring2Bond1);
ring2.Bonds.Add(ring2Bond2);
ring2.Bonds.Add(ring2Bond3);
ring2.Bonds.Add(sharedBond);
ringset.Add(ring1);
ringset.Add(ring2);
Assert.IsTrue(ringset.Contains(ring1));
Assert.IsTrue(ringset.Contains(ring2));
}
/// <summary>
/// Perform a walk in the given RingSet, starting at a given Ring and
/// recursively searching for other Rings connected to this ring. By doing
/// this it finds all rings in the RingSet connected to the start ring,
/// putting them in newRs, and removing them from rs.
/// </summary>
/// <param name="rs">The RingSet to be searched</param>
/// <param name="ring">The ring to start with</param>
/// <param name="newRs">The RingSet containing all Rings connected to ring</param>
/// <returns>newRs The RingSet containing all Rings connected to ring</returns>
private static IRingSet WalkRingSystem(IRingSet rs, IRing ring, IRingSet newRs)
{
IRing tempRing;
var tempRings = rs.GetConnectedRings(ring);
rs.Remove(ring);
foreach (var container in tempRings)
{
tempRing = (IRing)container;
if (!newRs.Contains(tempRing))
{
newRs.Add(tempRing);
newRs.Add(WalkRingSystem(rs, tempRing, newRs));
}
}
return(newRs);
}
/// <summary>
/// Returns all the rings in the RingSet that share one or more atoms with a given ring.
/// </summary>
/// <param name="ring">A ring with which all return rings must share one or more atoms</param>
/// <returns>All the rings that share one or more atoms with a given ring.</returns>
public IEnumerable <IRing> GetConnectedRings(IRing ring)
{
IRingSet connectedRings = ring.Builder.NewRingSet();
foreach (var atom in ring.Atoms)
{
foreach (var tempRing in this)
{
if (tempRing != ring &&
!connectedRings.Contains(tempRing) &&
tempRing.Contains(atom))
{
connectedRings.Add(tempRing);
}
}
}
return(connectedRings);
}
/// <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);
}
