public void TestPirenperone_Bug3088164()
{
var sg = SmilesGenerator.Unique.Aromatic();
var mol = smilesParser.ParseSmiles("Fc1ccc(cc1)C(=O)C4CCN(CCC\\3=C(\\N=C2\\C=C/C=C\\N2C/3=O)C)CC4");
AtomContainerManipulator.ClearAtomConfigurations(mol);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
var f = fragmenter.GetFrameworks().ToReadOnlyList();
var fc = fragmenter.GetFrameworksAsContainers().ToReadOnlyList();
Assert.AreEqual(1, f.Count);
Assert.AreEqual(f.Count, fc.Count);
AtomContainerManipulator.ClearAtomConfigurations(mol);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
CDK.HydrogenAdder.AddImplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
Assert.AreEqual("N=1C=C(CN2C=CC=CC12)CCN3CCC(Cc4ccccc4)CC3", f[0]);
for (int i = 0; i < f.Count; i++)
{
string newsmiles = sg.Create(fc[i]);
Assert.IsTrue(f[i].Equals(newsmiles), f[i] + " did not match the container, " + newsmiles);
}
}
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);
}
