public void TestSplit()
{
var mol = smilesParser.ParseSmiles("C1CC1C2CCC2");
SpanningTree st = new SpanningTree(mol);
IRingSet rings = st.GetAllRings();
IBond splitBond = null;
for (int i = 0; i < mol.Bonds.Count; i++)
{
if (rings.GetRings(mol.Bonds[i]).Count() == 0)
{
splitBond = mol.Bonds[i];
break;
}
}
var frags = FragmentUtils.SplitMolecule(mol, splitBond);
SmilesGenerator sg = new SmilesGenerator();
var uniqueFrags = new HashSet <string>();
foreach (var frag in frags)
{
uniqueFrags.Add(sg.Create(frag));
}
Assert.AreEqual(2, uniqueFrags.Count);
// You can put the fragments back together with a ring closure and dot
// [CH]12CC1.[CH]12CCC1
Assert.IsTrue(uniqueFrags.IsSupersetOf(new[] { "[CH]1CC1", "[CH]1CCC1" }));
}
private string GetRingcode(IAtom root, IAtomContainer ac)
{
if (ac != acold)
{
soar = Cycles.FindSSSR(ac).ToRingSet();
}
bool[] bool_ = new bool[1000];
var sb = new StringBuilder();
foreach (var soar_ring in soar.GetRings(root))
{
if (soar_ring.Atoms.Count < bool_.Length)
{
bool_[soar_ring.Atoms.Count] = true;
}
}
for (int i = 0; i < bool_.Length; i++)
{
if (bool_[i])
{
sb.Append(i + "");
}
}
if (sb.Length == 0)
{
return("");
}
else
{
return("-" + sb.ToString());
}
}
/// <summary>
/// We define the heaviest ring as the one with the highest number of double bonds.
/// Needed for example for the placement of in-ring double bonds.
/// </summary>
/// <param name="ringSet">The collection of rings</param>
/// <param name="bond">A bond which must be contained by the heaviest ring</param>
/// <returns>The ring with the highest number of double bonds connected to a given bond</returns>
public static IRing GetHeaviestRing(IRingSet ringSet, IBond bond)
{
var rings = ringSet.GetRings(bond);
IRing ring = null;
int maxOrderSum = 0;
foreach (var ring1 in rings)
{
if (maxOrderSum < ((IRing)ring1).GetBondOrderSum())
{
ring = (IRing)ring1;
maxOrderSum = ring.GetBondOrderSum();
}
}
return(ring);
}
public virtual void TestGetRings_IBond()
{
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.AreEqual(1, ringset.GetRings(ring1Bond1).Count());
Assert.AreEqual(1, ringset.GetRings(ring1Bond2).Count());
Assert.AreEqual(1, ringset.GetRings(ring1Bond3).Count());
Assert.AreEqual(2, ringset.GetRings(sharedBond).Count());
Assert.AreEqual(1, ringset.GetRings(ring2Bond1).Count());
Assert.AreEqual(1, ringset.GetRings(ring2Bond2).Count());
Assert.AreEqual(1, ringset.GetRings(ring2Bond3).Count());
}
/// <summary>
/// Positions the aliphatic substituents of a ring system
/// </summary>
/// <param name="rs">The RingSystem for which the substituents are to be laid out</param>
/// <returns>A list of atoms that where laid out</returns>
public IAtomContainer PlaceRingSubstituents(IRingSet rs, double bondLength)
{
Debug.WriteLine("RingPlacer.PlaceRingSubstituents() start");
IRing ring = null;
IAtom atom = null;
IAtomContainer unplacedPartners = rs.Builder.NewAtomContainer();
IAtomContainer sharedAtoms = rs.Builder.NewAtomContainer();
IAtomContainer primaryAtoms = rs.Builder.NewAtomContainer();
IAtomContainer treatedAtoms = rs.Builder.NewAtomContainer();
for (int j = 0; j < rs.Count; j++)
{
ring = (IRing)rs[j]; // Get the j-th Ring in RingSet rs
for (int k = 0; k < ring.Atoms.Count; k++)
{
unplacedPartners.RemoveAllElements();
sharedAtoms.RemoveAllElements();
primaryAtoms.RemoveAllElements();
atom = ring.Atoms[k];
var rings = rs.GetRings(atom);
var centerOfRingGravity = GeometryUtil.Get2DCenter(rings);
AtomPlacer.PartitionPartners(atom, unplacedPartners, sharedAtoms);
AtomPlacer.MarkNotPlaced(unplacedPartners);
try
{
for (int f = 0; f < unplacedPartners.Atoms.Count; f++)
{
Debug.WriteLine("placeRingSubstituents->unplacedPartners: "
+ (Molecule.Atoms.IndexOf(unplacedPartners.Atoms[f]) + 1));
}
}
catch (Exception)
{
}
treatedAtoms.Add(unplacedPartners);
if (unplacedPartners.Atoms.Count > 0)
{
AtomPlacer.DistributePartners(atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
}
}
}
Debug.WriteLine("RingPlacer.PlaceRingSubstituents() end");
return(treatedAtoms);
}
/// <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);
}
