Пример #1
0
        /// <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);
        }
Пример #2
0
        /// <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);
        }
Пример #3
0
        /// <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 ******");
        }
Пример #4
0
        /// <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);
        }