/// <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);
}
