public void TestMakeAtomContainer()
{
var builder = CDK.Builder;
IAtom atom = builder.NewAtom("C");
IAtom exclude = builder.NewAtom("C");
IAtom a1 = builder.NewAtom("C");
IAtom a2 = builder.NewAtom("C");
IBond[] bonds = new IBond[] { builder.NewBond(atom, exclude),
builder.NewBond(a1, a2), builder.NewBond(a1, atom),
builder.NewBond(a2, exclude) };
IAtomContainer part = FragmentUtils.MakeAtomContainer(atom, bonds, exclude);
Assert.AreEqual(3, part.Atoms.Count);
Assert.AreEqual(2, part.Bonds.Count);
Assert.IsTrue(part.Contains(atom));
Assert.IsTrue(part.Contains(a1));
Assert.IsTrue(part.Contains(a2));
Assert.IsFalse(part.Contains(exclude));
Assert.IsTrue(part.Contains(bonds[1]));
Assert.IsTrue(part.Contains(bonds[2]));
}
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" }));
}
public void TestTraversal_Chain()
{
var builder = CDK.Builder;
IAtom[] atoms = new IAtom[] { builder.NewAtom("C"), builder.NewAtom("C"),
builder.NewAtom("C"), builder.NewAtom("C"),
builder.NewAtom("C"), builder.NewAtom("C") };
IBond[] bonds = new IBond[] { builder.NewBond(atoms[0], atoms[1]),
builder.NewBond(atoms[1], atoms[2]),
builder.NewBond(atoms[2], atoms[3]),
builder.NewBond(atoms[3], atoms[4]),
builder.NewBond(atoms[4], atoms[5]) };
IAtomContainer m = builder.NewAtomContainer();
m.SetAtoms(atoms);
m.SetBonds(bonds);
List <IBond> accumulator = new List <IBond>();
// traverse from one end
FragmentUtils.Traverse(m, atoms[0], accumulator);
Assert.AreEqual(5, accumulator.Count);
Assert.AreEqual(bonds[0], accumulator[0]);
Assert.AreEqual(bonds[1], accumulator[1]);
Assert.AreEqual(bonds[2], accumulator[2]);
Assert.AreEqual(bonds[3], accumulator[3]);
Assert.AreEqual(bonds[4], accumulator[4]);
// traverse from the middle
accumulator.Clear();
FragmentUtils.Traverse(m, atoms[3], accumulator);
Assert.AreEqual(5, accumulator.Count);
Assert.AreEqual(bonds[2], accumulator[0]);
Assert.AreEqual(bonds[1], accumulator[1]);
Assert.AreEqual(bonds[0], accumulator[2]);
Assert.AreEqual(bonds[3], accumulator[3]);
Assert.AreEqual(bonds[4], accumulator[4]);
}
private List <IAtomContainer> Run(IAtomContainer atomContainer)
{
var fragments = new List <IAtomContainer>();
if (atomContainer.Bonds.Count < 3)
{
return(fragments);
}
var splitableBonds = GetSplitableBonds(atomContainer);
if (splitableBonds.Count == 0)
{
return(fragments);
}
Debug.WriteLine("Got " + splitableBonds.Count + " splittable bonds");
string tmpSmiles;
foreach (var bond in splitableBonds)
{
var parts = FragmentUtils.SplitMolecule(atomContainer, bond);
// make sure we don't add the same fragment twice
foreach (var partContainer in parts)
{
AtomContainerManipulator.ClearAtomConfigurations(partContainer);
foreach (var atom in partContainer.Atoms)
{
atom.ImplicitHydrogenCount = null;
}
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(partContainer);
CDK.HydrogenAdder.AddImplicitHydrogens(partContainer);
Aromaticity.CDKLegacy.Apply(partContainer);
tmpSmiles = smilesGenerator.Create(partContainer);
if (partContainer.Atoms.Count >= MinimumFragmentSize && !fragMap.ContainsKey(tmpSmiles))
{
fragments.Add(partContainer);
fragMap[tmpSmiles] = partContainer;
}
}
}
// try and partition the fragments
var tmp = new List <IAtomContainer>(fragments);
foreach (var fragment in fragments)
{
if (fragment.Bonds.Count < 3 || fragment.Atoms.Count < MinimumFragmentSize)
{
continue;
}
if (GetSplitableBonds(fragment).Count == 0)
{
continue;
}
var frags = Run(fragment);
if (frags.Count == 0)
{
continue;
}
foreach (var frag in frags)
{
if (frag.Bonds.Count < 3)
{
continue;
}
AtomContainerManipulator.ClearAtomConfigurations(frag);
foreach (var atom in frag.Atoms)
{
atom.ImplicitHydrogenCount = null;
}
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(frag);
CDK.HydrogenAdder.AddImplicitHydrogens(frag);
Aromaticity.CDKLegacy.Apply(frag);
tmpSmiles = smilesGenerator.Create(frag);
if (frag.Atoms.Count >= MinimumFragmentSize && !fragMap.ContainsKey(tmpSmiles))
{
tmp.Add(frag);
fragMap[tmpSmiles] = frag;
}
}
}
fragments = new List <IAtomContainer>(tmp);
return(fragments);
}