/// <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>
/// 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);
}
/// <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 3D coordinates with force field information.
/// </summary>
public IAtomContainer Generate3DCoordinates(IAtomContainer molecule, bool clone)
{
var originalAtomTypeNames = molecule.Atoms.Select(n => n.AtomTypeName).ToArray();
Debug.WriteLine("******** GENERATE COORDINATES ********");
foreach (var atom in molecule.Atoms)
{
atom.IsPlaced = false;
atom.IsVisited = false;
}
//CHECK FOR CONNECTIVITY!
Debug.WriteLine($"#atoms>{molecule.Atoms.Count}");
if (!ConnectivityChecker.IsConnected(molecule))
{
throw new CDKException("Molecule is NOT connected, could not layout.");
}
// setup helper classes
AtomPlacer atomPlacer = new AtomPlacer();
AtomPlacer3D ap3d = new AtomPlacer3D(parameterSet);
AtomTetrahedralLigandPlacer3D atlp3d = new AtomTetrahedralLigandPlacer3D(parameterSet);
if (clone)
{
molecule = (IAtomContainer)molecule.Clone();
}
atomPlacer.Molecule = molecule;
if (ap3d.NumberOfUnplacedHeavyAtoms(molecule) == 1)
{
Debug.WriteLine("Only one Heavy Atom");
ap3d.GetUnplacedHeavyAtom(molecule).Point3D = new Vector3(0.0, 0.0, 0.0);
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message,
ex3);
}
return(molecule);
}
//Assing Atoms to Rings,Aliphatic and Atomtype
IRingSet ringSetMolecule = ffc.AssignAtomTyps(molecule);
IRingSet largestRingSet = null;
int numberOfRingAtoms = 0;
IReadOnlyList <IRingSet> ringSystems = null;
if (ringSetMolecule.Count > 0)
{
if (templateHandler == null)
{
throw new CDKException("You are trying to generate coordinates for a molecule with rings, but you have no template handler set. Please do SetTemplateHandler() before generation!");
}
ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
IAtomContainer largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
numberOfRingAtoms = largestRingSetContainer.Atoms.Count;
templateHandler.MapTemplates(largestRingSetContainer, numberOfRingAtoms);
if (!CheckAllRingAtomsHasCoordinates(largestRingSetContainer))
{
throw new CDKException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout.");
}
SetAtomsToPlace(largestRingSetContainer);
SearchAndPlaceBranches(molecule, largestRingSetContainer, ap3d, atlp3d, atomPlacer);
largestRingSet = null;
}
else
{
//Debug.WriteLine("****** Start of handling aliphatic molecule ******");
IAtomContainer ac = AtomPlacer.GetInitialLongestChain(molecule);
SetAtomsToUnVisited(molecule);
SetAtomsToUnplaced(molecule);
ap3d.PlaceAliphaticHeavyChain(molecule, ac);
//ZMatrixApproach
ap3d.ZMatrixChainToCartesian(molecule, false);
SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer);
}
LayoutMolecule(ringSystems, molecule, ap3d, atlp3d, atomPlacer);
//Debug.WriteLine("******* PLACE SUBSTITUENTS ******");
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message, ex3);
}
// restore the original atom type names
for (int i = 0; i < originalAtomTypeNames.Length; i++)
{
molecule.Atoms[i].AtomTypeName = originalAtomTypeNames[i];
}
return(molecule);
}