/// <summary> /// Search and place branches of a chain or ring. /// </summary> /// <param name="chain">AtomContainer if atoms in an aliphatic chain or ring system</param> private void SearchAndPlaceBranches(IAtomContainer molecule, IAtomContainer chain, AtomPlacer3D ap3d, AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer) { //Debug.WriteLine("****** SEARCH AND PLACE ****** Chain length: "+chain.Atoms.Count); IAtomContainer branchAtoms = molecule.Builder.NewAtomContainer(); IAtomContainer connectedAtoms = molecule.Builder.NewAtomContainer(); for (int i = 0; i < chain.Atoms.Count; i++) { var atoms = molecule.GetConnectedAtoms(chain.Atoms[i]); foreach (var atom in atoms) { if (!atom.AtomicNumber.Equals(AtomicNumbers.H) & !atom.IsPlaced & !atom.IsInRing) { connectedAtoms.Add(ap3d.GetPlacedHeavyAtoms(molecule, chain.Atoms[i])); try { SetBranchAtom(molecule, atom, chain.Atoms[i], connectedAtoms, ap3d, atlp3d); } catch (CDKException ex2) { Trace.TraceError($"SearchAndPlaceBranchERROR: Cannot find enough neighbour atoms due to {ex2.ToString()}"); throw new CDKException($"SearchAndPlaceBranchERROR: Cannot find enough neighbour atoms: {ex2.Message}", ex2); } branchAtoms.Atoms.Add(atom); connectedAtoms.RemoveAllElements(); } } }//for ac.getAtomCount PlaceLinearChains3D(molecule, branchAtoms, ap3d, atlp3d, atomPlacer); }
public override void TestGetPlacedHeavyAtoms_IAtomContainer_IAtom() { AtomPlacer3D atmplacer = new AtomPlacer3D(); IAtomContainer molecule = TestMoleculeFactory.MakeBenzene(); for (int j = 0; j < 3; j++) { (molecule.Atoms[j]).IsPlaced = true; } IAtomContainer placedAndConnectedTo1 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[1]); IAtomContainer placedAndConnectedTo2 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[2]); IAtomContainer placedAndConnectedTo4 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[4]); Assert.AreEqual(2, placedAndConnectedTo1.Atoms.Count); Assert.AreEqual(1, placedAndConnectedTo2.Atoms.Count); Assert.AreEqual(0, placedAndConnectedTo4.Atoms.Count); }
/// <summary> /// Layout the molecule, starts with ring systems and than aliphatic chains. /// </summary> /// <param name="ringSetMolecule">ringSystems of the molecule</param> private void LayoutMolecule(IReadOnlyList <IRingSet> ringSetMolecule, IAtomContainer molecule, AtomPlacer3D ap3d, AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer) { //Debug.WriteLine("****** LAYOUT MOLECULE MAIN *******"); IAtomContainer ac = null; int safetyCounter = 0; IAtom atom = null; //Place rest Chains/Atoms do { safetyCounter++; atom = ap3d.GetNextPlacedHeavyAtomWithUnplacedRingNeighbour(molecule); if (atom != null) { //Debug.WriteLine("layout RingSystem..."); var unplacedAtom = ap3d.GetUnplacedRingHeavyAtom(molecule, atom); var ringSetA = GetRingSetOfAtom(ringSetMolecule, unplacedAtom); var ringSetAContainer = RingSetManipulator.GetAllInOneContainer(ringSetA); templateHandler.MapTemplates(ringSetAContainer, ringSetAContainer.Atoms.Count); if (CheckAllRingAtomsHasCoordinates(ringSetAContainer)) { } else { throw new IOException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout. Sorry"); } Vector3 firstAtomOriginalCoord = unplacedAtom.Point3D.Value; Vector3 centerPlacedMolecule = ap3d.GeometricCenterAllPlacedAtoms(molecule); SetBranchAtom(molecule, unplacedAtom, atom, ap3d.GetPlacedHeavyAtoms(molecule, atom), ap3d, atlp3d); LayoutRingSystem(firstAtomOriginalCoord, unplacedAtom, ringSetA, centerPlacedMolecule, atom, ap3d); SearchAndPlaceBranches(molecule, ringSetAContainer, ap3d, atlp3d, atomPlacer); //Debug.WriteLine("Ready layout Ring System"); ringSetA = null; unplacedAtom = null; } else { //Debug.WriteLine("layout chains..."); SetAtomsToUnVisited(molecule); atom = ap3d.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(molecule); if (atom != null) { ac = atom.Builder.NewAtomContainer(); ac.Atoms.Add(atom); SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer); ac = null; } } } while (!ap3d.AllHeavyAtomsPlaced(molecule) || safetyCounter > molecule.Atoms.Count); }