/// <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);
}
/// <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>
/// Layout all aliphatic chains with ZMatrix.
/// </summary>
/// <param name="startAtoms">AtomContainer of possible start atoms for a chain</param>
private void PlaceLinearChains3D(IAtomContainer molecule, IAtomContainer startAtoms, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** PLACE LINEAR CHAINS ******");
IAtom dihPlacedAtom = null;
IAtom thirdPlacedAtom = null;
IAtomContainer longestUnplacedChain = molecule.Builder.NewAtomContainer();
if (startAtoms.Atoms.Count == 0)
{
//no branch points ->linear chain
//Debug.WriteLine("------ LINEAR CHAIN - FINISH ------");
}
else
{
for (int i = 0; i < startAtoms.Atoms.Count; i++)
{
//Debug.WriteLine("FOUND BRANCHED ALKAN");
//Debug.WriteLine("Atom NOT NULL:" + molecule.Atoms.IndexOf(startAtoms.GetAtomAt(i)));
thirdPlacedAtom = ap3d.GetPlacedHeavyAtom(molecule, startAtoms.Atoms[i]);
dihPlacedAtom = ap3d.GetPlacedHeavyAtom(molecule, thirdPlacedAtom, startAtoms.Atoms[i]);
longestUnplacedChain.Atoms.Add(dihPlacedAtom);
longestUnplacedChain.Atoms.Add(thirdPlacedAtom);
longestUnplacedChain.Atoms.Add(startAtoms.Atoms[i]);
longestUnplacedChain.Add(AtomPlacer.GetLongestUnplacedChain(molecule, startAtoms.Atoms[i]));
SetAtomsToUnVisited(molecule);
if (longestUnplacedChain.Atoms.Count < 4)
{
//di,third,sec
//Debug.WriteLine("------ Single BRANCH METHYLTYP ------");
//break;
}
else
{
//Debug.WriteLine("LongestUnchainLength:"+longestUnplacedChain.Atoms.Count);
ap3d.PlaceAliphaticHeavyChain(molecule, longestUnplacedChain);
ap3d.ZMatrixChainToCartesian(molecule, true);
SearchAndPlaceBranches(molecule, longestUnplacedChain, ap3d, atlp3d, atomPlacer);
}
longestUnplacedChain.RemoveAllElements();
}//for
}
//Debug.WriteLine("****** HANDLE ALIPHATICS END ******");
}
/// <summary>
/// Generate coordinates for all atoms which are singly bonded and have no
/// coordinates. This is useful when hydrogens are present but have no coordinates.
/// It knows about C, O, N, S only and will give tetrahedral or trigonal
/// geometry elsewhere. Bond lengths are computed from covalent radii or taken
/// out of a parameter set if available. Angles are tetrahedral or trigonal
/// </summary>
/// <param name="atomContainer">the set of atoms involved</param>
// @cdk.keyword coordinate calculation
// @cdk.keyword 3D model
public virtual void Add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer)
{
IAtom refAtom = null;
IAtom atomC = null;
int nwanted = 0;
for (int i = 0; i < atomContainer.Atoms.Count; i++)
{
refAtom = atomContainer.Atoms[i];
if (!refAtom.AtomicNumber.Equals(AtomicNumbers.H) && HasUnsetNeighbour(refAtom, atomContainer))
{
IAtomContainer noCoords = GetUnsetAtomsInAtomContainer(refAtom, atomContainer);
IAtomContainer withCoords = GetPlacedAtomsInAtomContainer(refAtom, atomContainer);
if (withCoords.Atoms.Count > 0)
{
atomC = GetPlacedHeavyAtomInAtomContainer(withCoords.Atoms[0], refAtom, atomContainer);
}
if (refAtom.FormalNeighbourCount == 0 && refAtom.AtomicNumber.Equals(AtomicNumbers.C))
{
nwanted = noCoords.Atoms.Count;
}
else if (refAtom.FormalNeighbourCount == 0 && !refAtom.AtomicNumber.Equals(AtomicNumbers.C))
{
nwanted = 4;
}
else
{
nwanted = refAtom.FormalNeighbourCount.Value - withCoords.Atoms.Count;
}
Vector3[] newPoints = Get3DCoordinatesForLigands(refAtom, noCoords, withCoords, atomC, nwanted,
DefaultBondLengthH, -1);
for (int j = 0; j < noCoords.Atoms.Count; j++)
{
IAtom ligand = noCoords.Atoms[j];
Vector3 newPoint = RescaleBondLength(refAtom, ligand, newPoints[j]);
ligand.Point3D = newPoint;
ligand.IsPlaced = true;
}
noCoords.RemoveAllElements();
withCoords.RemoveAllElements();
}
}
}