private static ISet <IBond> FindCutBonds(IAtomContainer mol, EdgeToBondMap bmap, int[][] adjlist)
{
var cuts = new HashSet <IBond>();
var numAtoms = mol.Atoms.Count;
for (int i = 0; i < numAtoms; i++)
{
var atom = mol.Atoms[i];
var deg = adjlist[i].Length;
var elem = atom.AtomicNumber;
if (elem == 6 && deg <= 2 || deg < 2)
{
continue;
}
foreach (var w in adjlist[i])
{
var bond = bmap[i, w];
if (adjlist[w].Length >= 2 && !bond.IsInRing)
{
cuts.Add(bond);
}
}
}
return(cuts);
}
private static List <IAtomContainer> GenerateFragments(IAtomContainer mol)
{
var bmap = EdgeToBondMap.WithSpaceFor(mol);
var adjlist = GraphUtil.ToAdjList(mol, bmap);
Cycles.MarkRingAtomsAndBonds(mol, adjlist, bmap);
var cuts = FindCutBonds(mol, bmap, adjlist);
var atmidx = new Dictionary <IAtom, int>();
foreach (var atom in mol.Atoms)
{
atmidx[atom] = atmidx.Count;
}
// frags are ordered by biggest to smallest
var frags = new List <IAtomContainer>();
foreach (var cut in cuts)
{
if (frags.Count >= MaxFragment)
{
break;
}
frags.AddRange(MakeCut(cut, mol, atmidx, adjlist));
}
frags.Sort(delegate(IAtomContainer a, IAtomContainer b)
{
return(-a.Bonds.Count.CompareTo(b.Bonds.Count));
});
return(frags);
}
/// <summary>
/// Computes <see cref="SMARTSAtomInvariants"/> and stores on the <see cref="Key"/> or
/// each <see cref="IAtom"/> in the <paramref name="container"/>. The <see cref="IMolecularEntity.IsInRing"/>
/// is also set for each bond. This configuration
/// includes the ring information as used by the Daylight implementation.
/// That is the Smallest Set of Smallest Rings (SSSR) is used and only the
/// smallest ring is stored for the <see cref="RingSize"/> .
/// </summary>
/// <example>
/// <code>
/// IAtomContainer container = ...;
/// SMARTSAtomInvariants.ConfigureDaylightWithRingInfo(container);
/// foreach (var atom in container.Atoms) {
/// SMARTSAtomInvariants inv = atom.GetProperty<SMARTSAtomInvariants>(SMARTSAtomInvariants.Key);
/// }
/// </code>
/// </example>
/// <param name="container">the container to configure</param>
public static void ConfigureDaylightWithRingInfo(IAtomContainer container)
{
var map = EdgeToBondMap.WithSpaceFor(container);
var graph = GraphUtil.ToAdjList(container, map);
ConfigureDaylight(container, graph, map, true);
}
/// <summary>
/// Obtain the MMFF symbolic types to the atoms of the provided structure.
/// </summary>
/// <param name="container">container structure representation</param>
/// <returns>MMFF symbolic types for each atom index</returns>
public string[] SymbolicTypes(IAtomContainer container)
{
var bonds = EdgeToBondMap.WithSpaceFor(container);
var graph = GraphUtil.ToAdjList(container, bonds);
return(SymbolicTypes(container, graph, bonds, new HashSet <IBond>()));
}
/// <summary>
/// Create a state for matching subgraphs using the Ullmann refinement
/// procedure.
/// </summary>
/// <param name="container1">query container</param>
/// <param name="container2">target container</param>
/// <param name="g1">query container adjacency list</param>
/// <param name="g2">target container adjacency list</param>
/// <param name="bonds1">query container bond map</param>
/// <param name="bonds2">target container bond map</param>
/// <param name="atomMatcher">method of matching atom semantics</param>
/// <param name="bondMatcher">method of matching bond semantics</param>
public UllmannState(IAtomContainer container1, IAtomContainer container2, int[][] g1, int[][] g2,
EdgeToBondMap bonds1, EdgeToBondMap bonds2, AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
this.bondMatcher = bondMatcher;
this.g1 = g1;
this.g2 = g2;
this.bond1 = bonds1;
this.bonds2 = bonds2;
this.m1 = new int[g1.Length];
this.m2 = new int[g2.Length];
Arrays.Fill(m1, UNMAPPED);
Arrays.Fill(m2, UNMAPPED);
// build up compatibility matrix
matrix = new CompatibilityMatrix(g1.Length, g2.Length);
for (int i = 0; i < g1.Length; i++)
{
for (int j = 0; j < g2.Length; j++)
{
if (g1[i].Length <= g2[j].Length && atomMatcher.Matches(container1.Atoms[i], container2.Atoms[j]))
{
matrix.Set1(i, j);
}
}
}
}
/// <summary>
/// Use the provided query and target to obtain the bond instances.
/// </summary>
/// <param name="query">the structure to be found</param>
/// <param name="target">the structure being searched</param>
public BondMaper(IAtomContainer query, IAtomContainer target)
{
this.bonds1 = EdgeToBondMap.WithSpaceFor(query);
this.bonds2 = EdgeToBondMap.WithSpaceFor(target);
this.g1 = GraphUtil.ToAdjList(query, bonds1);
GraphUtil.ToAdjList(target, bonds2);
}
/// <summary>
/// Given the assigned preliminary MMFF atom types (symbs[]) update these to the aromatic types.
/// To begin, all the 5 and 6 member aromatic cycles are discovered. The symbolic types of five
/// and six member cycles are then update with <see cref="UpdateAromaticTypesInFiveMemberRing(int[], string[])"/>
/// and <see cref="UpdateAromaticTypesInSixMemberRing(int[], string[])"/>.
/// </summary>
/// <param name="container">structure representation</param>
/// <param name="symbs">vector of symbolic types for the whole structure</param>
/// <param name="bonds">edge to bond map lookup</param>
/// <param name="graph">adjacency list graph representation of structure</param>
/// <param name="mmffArom">set of bonds that are aromatic</param>
public void Assign(IAtomContainer container, string[] symbs, EdgeToBondMap bonds, int[][] graph, ISet <IBond> mmffArom)
{
var contribution = new int[graph.Length];
var doubleBonds = new int[graph.Length];
Arrays.Fill(doubleBonds, -1);
SetupContributionAndDoubleBonds(container, bonds, graph, contribution, doubleBonds);
var cycles = FindAromaticRings(CyclesOfSizeFiveOrSix(container, graph), contribution, doubleBonds);
foreach (var cycle in cycles)
{
int len = cycle.Length - 1;
if (len == 6)
{
UpdateAromaticTypesInSixMemberRing(cycle, symbs);
}
if (len == 5 && NormaliseCycle(cycle, contribution))
{
UpdateAromaticTypesInFiveMemberRing(cycle, symbs);
}
// mark aromatic bonds
for (int i = 1; i < cycle.Length; i++)
{
mmffArom.Add(bonds[cycle[i], cycle[i - 1]]);
}
}
}
public void RecogniseLeftHandedGlyceraldehyde()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, 0.80d, 1.24d));
m.Atoms.Add(Atom("C", 0, 0.80d, 0.42d));
m.Atoms.Add(Atom("O", 1, 0.09d, 1.66d));
m.Atoms.Add(Atom("O", 0, 1.52d, 1.66d));
m.Atoms.Add(Atom("O", 0, -0.02d, 0.42d));
m.Atoms.Add(Atom("C", 2, 0.80d, -0.41d));
m.Atoms.Add(Atom("H", 1, 1.63d, 0.42d));
m.Atoms.Add(Atom("O", 1, 1.52d, -0.82d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[3], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[1], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[7], BondOrder.Single);
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
FischerRecognition recogniser = new FischerRecognition(m,
graph,
bondMap,
Stereocenters.Of(m));
var elements = recogniser.Recognise(new[] { Projection.Fischer }).ToReadOnlyList();
Assert.AreEqual(1, elements.Count);
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.AntiClockwise,
m.Atoms[0], m.Atoms[6], m.Atoms[5], m.Atoms[4]);
}
/// <summary>
/// Find the bonds of a <paramref name="molecule"/> which this model determined were aromatic.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Aromaticities.Aromaticity_Example.cs+FindBonds"]/*' />
/// </example>
/// <param name="molecule">the molecule to apply the model to</param>
/// <returns>the set of bonds which are aromatic</returns>
/// <exception cref="CDKException">a problem occurred with the cycle perception - one can retry with a simpler cycle set</exception>
public IEnumerable <IBond> FindBonds(IAtomContainer molecule)
{
// build graph data-structures for fast cycle perception
var bondMap = EdgeToBondMap.WithSpaceFor(molecule);
var graph = GraphUtil.ToAdjList(molecule, bondMap);
// initial ring/cycle search and get the contribution from each atom
RingSearch ringSearch = new RingSearch(molecule, graph);
var electrons = model.Contribution(molecule, ringSearch);
// obtain the subset of electron contributions which are >= 0 (i.e.
// allowed to be aromatic) - we then find the cycles in this subgraph
// and 'lift' the indices back to the original graph using the subset
// as a lookup
var subset = Subset(electrons);
var subgraph = GraphUtil.Subgraph(graph, subset);
// for each cycle if the electron sum is valid add the bonds of the
// cycle to the set or aromatic bonds
foreach (var cycle in cycles.Find(molecule, subgraph, subgraph.Length).GetPaths())
{
if (CheckElectronSum(cycle, electrons, subset))
{
for (int i = 1; i < cycle.Length; i++)
{
yield return(bondMap[subset[cycle[i]], subset[cycle[i - 1]]]);
}
}
}
yield break;
}
public void RequireAtLeastTwoProjectedSubstituents()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("O", 0, -0.71d, 1.24d));
m.Atoms.Add(Atom("C", 0, 0.00d, 0.83d));
m.Atoms.Add(Atom("O", 0, 0.71d, 1.24d));
m.Atoms.Add(Atom("C", 1, 0.00d, 0.00d));
m.Atoms.Add(Atom("C", 2, -0.67d, -0.48d));
m.Atoms.Add(Atom("C", 2, -0.41d, -1.27d));
m.Atoms.Add(Atom("C", 2, 0.41d, -1.27d));
m.Atoms.Add(Atom("N", 1, 0.67d, -0.48d));
m.AddBond(m.Atoms[6], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[0], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[2], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
Stereocenters stereocenters = new Stereocenters(m, graph, bondMap);
stereocenters.CheckSymmetry();
CyclicCarbohydrateRecognition recon = new CyclicCarbohydrateRecognition(m, graph, bondMap,
stereocenters);
var elements = recon.Recognise(new[] { Projection.Haworth }).ToReadOnlyList();
Assert.IsTrue(elements.Count == 0);
}
internal AdjListCache(IAtomContainer mol)
{
this.bmap = EdgeToBondMap.WithSpaceFor(mol);
this.g = GraphUtil.ToAdjList(mol, bmap);
this.numAtoms = mol.Atoms.Count;
this.numBonds = mol.Bonds.Count;
this.tInit = DateTime.Now.Ticks;
}
public override Mappings MatchAll(IAtomContainer target)
{
var bonds2 = EdgeToBondMap.WithSpaceFor(target);
var g2 = GraphUtil.ToAdjList(target, bonds2);
var iterable = new UllmannIterable(query, target, g1, g2, bonds1, bonds2, atomMatcher, bondMatcher);
var mappings = new Mappings(query, target, iterable);
return(Filter(mappings, query, target));
}
/// <summary>
/// Determine the stereocenter atoms in the provided container based on connectivity.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Stereo.Stereocenters_Example.cs+Of"]/*' />
/// </example>
/// <param name="container">input container</param>
/// <returns>the stereocenters</returns>
public static Stereocenters Of(IAtomContainer container)
{
var bondMap = EdgeToBondMap.WithSpaceFor(container);
var g = GraphUtil.ToAdjList(container, bondMap);
var stereocenters = new Stereocenters(container, g, bondMap);
stereocenters.CheckSymmetry();
return(stereocenters);
}
/// <summary>
/// Non-public constructor for-now the atom/bond semantics are fixed.
/// </summary>
/// <param name="query">the query structure</param>
/// <param name="atomMatcher">how atoms should be matched</param>
/// <param name="bondMatcher">how bonds should be matched</param>
private Ullmann(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
this.query = query;
this.atomMatcher = atomMatcher;
this.bondMatcher = bondMatcher;
this.bonds1 = EdgeToBondMap.WithSpaceFor(query);
this.g1 = GraphUtil.ToAdjList(query, bonds1);
DetermineFilters(query);
}
public void Mannitol()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 2, -0.53d, 6.25d));
m.Atoms.Add(Atom("C", 1, -0.53d, 5.42d));
m.Atoms.Add(Atom("O", 1, 0.18d, 6.66d));
m.Atoms.Add(Atom("O", 1, -1.36d, 5.42d));
m.Atoms.Add(Atom("C", 1, -0.53d, 4.60d));
m.Atoms.Add(Atom("O", 1, -1.36d, 4.60d));
m.Atoms.Add(Atom("C", 1, -0.53d, 3.77d));
m.Atoms.Add(Atom("O", 1, 0.29d, 3.77d));
m.Atoms.Add(Atom("C", 1, -0.53d, 2.95d));
m.Atoms.Add(Atom("O", 1, 0.29d, 2.95d));
m.Atoms.Add(Atom("C", 2, -0.53d, 2.12d));
m.Atoms.Add(Atom("O", 1, 0.05d, 1.54d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[10], BondOrder.Single);
m.AddBond(m.Atoms[10], m.Atoms[11], BondOrder.Single);
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
FischerRecognition recogniser = new FischerRecognition(m,
graph,
bondMap,
Stereocenters.Of(m));
var elements = recogniser.Recognise(new[] { Projection.Fischer }).ToReadOnlyList();
Assert.AreEqual(4, elements.Count);
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.AntiClockwise,
m.Atoms[0], m.Atoms[1], m.Atoms[4], m.Atoms[3]);
AssertTetrahedralCenter(elements[1],
m.Atoms[4],
TetrahedralStereo.AntiClockwise,
m.Atoms[1], m.Atoms[4], m.Atoms[6], m.Atoms[5]);
AssertTetrahedralCenter(elements[2],
m.Atoms[6],
TetrahedralStereo.AntiClockwise,
m.Atoms[4], m.Atoms[7], m.Atoms[8], m.Atoms[6]);
AssertTetrahedralCenter(elements[3],
m.Atoms[8],
TetrahedralStereo.AntiClockwise,
m.Atoms[6], m.Atoms[9], m.Atoms[10], m.Atoms[8]);
m.SetStereoElements(elements);
}
/// <summary>
/// Assign MMFF Symbolic atom types. The symbolic type can be accessed with
/// <see cref="IAtomType.AtomTypeName"/>. An atom of unknown type is assigned the
/// symbolic type <c>"UNK"</c>.
/// All atoms, including hydrogens must be explicitly represented.
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>all atoms had a type assigned</returns>
public virtual bool AssignAtomTypes(IAtomContainer mol)
{
// preconditions need explicit hydrogens
foreach (var atom in mol.Atoms)
{
if (atom.ImplicitHydrogenCount == null || atom.ImplicitHydrogenCount > 0)
{
throw new ArgumentException("Hydrogens must be explicit nodes, each must have a zero (non-null) impl H count.");
}
}
// conversion to faster data structures
var edgeMap = EdgeToBondMap.WithSpaceFor(mol);
var adjList = GraphUtil.ToAdjList(mol, edgeMap);
mol.SetProperty(MMFF_ADJLIST_CACHE, adjList);
mol.SetProperty(MMFF_EDGEMAP_CACHE, edgeMap);
var aromBonds = new HashSet <IBond>();
var oldArom = GetAromatics(mol);
// note: for MMFF we need to remove current aromatic flags for type
// assignment (they are restored after)
foreach (var chemObj in oldArom)
{
chemObj.IsAromatic = false;
}
var atomTypes = mmffAtomTyper.SymbolicTypes(mol, adjList, edgeMap, aromBonds);
bool hasUnkType = false;
for (int i = 0; i < mol.Atoms.Count; i++)
{
if (atomTypes[i] == null)
{
mol.Atoms[i].AtomTypeName = "UNK";
hasUnkType = true;
}
else
{
mol.Atoms[i].AtomTypeName = atomTypes[i];
}
}
// restore aromatic flags and mark the MMFF aromatic bonds
foreach (var chemObj in oldArom)
{
chemObj.IsAromatic = true;
}
foreach (var bond in aromBonds)
{
bond.SetProperty(MMFF_AROM, true);
}
return(!hasUnkType);
}
/// <summary>
/// Required information to recognise stereochemistry.
/// </summary>
/// <param name="container">input structure</param>
/// <param name="graph">adjacency list representation</param>
/// <param name="bonds">edge to bond index</param>
/// <param name="stereocenters">location and type of asymmetries</param>
public FischerRecognition(IAtomContainer container,
int[][] graph,
EdgeToBondMap bonds,
Stereocenters stereocenters)
{
this.container = container;
this.graph = graph;
this.bonds = bonds;
this.stereocenters = stereocenters;
}
/// <summary>
/// Create a perception method for the provided container, graph
/// representation and bond map.
/// </summary>
/// <param name="container">native CDK structure representation</param>
/// <param name="graph">graph representation (adjacency list)</param>
/// <param name="bondMap">fast lookup bonds by atom index</param>
internal Stereocenters(IAtomContainer container, int[][] graph, EdgeToBondMap bondMap)
{
this.container = container;
this.bondMap = bondMap;
this.g = graph;
this.ringSearch = new RingSearch(container, graph);
this.elements = new StereoElement[g.Length];
this.stereocenters = new CenterType[g.Length];
this.numStereoElements = CreateElements();
}
/// <summary>
/// Non-public constructor for-now the atom/bond semantics are fixed.
/// </summary>
/// <param name="query">the query structure</param>
/// <param name="atomMatcher">how atoms should be matched</param>
/// <param name="bondMatcher">how bonds should be matched</param>
/// <param name="substructure">substructure search</param>
private VentoFoggia(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher, bool substructure)
{
this.query = query;
this.atomMatcher = atomMatcher;
this.bondMatcher = bondMatcher;
this.bonds1 = EdgeToBondMap.WithSpaceFor(query);
this.g1 = GraphUtil.ToAdjList(query, bonds1);
this.subgraph = substructure;
DetermineFilters(query);
}
/// <summary>
/// Determine the set of atoms that are available to have a double-bond.
/// </summary>
/// <param name="graph">adjacent list representation</param>
/// <param name="atoms">array of atoms</param>
/// <param name="bonds">map of atom indices to bonds</param>
/// <returns>atoms that can require a double-bond</returns>
private static BitArray IsAvailable(int[][] graph, IAtom[] atoms, EdgeToBondMap bonds)
{
var available = new BitArray(atoms.Length);
// for all atoms, select those that require a double-bond
for (int i = 0; i < atoms.Length; i++)
{
var atom = atoms[i];
// preconditions
if (atom.FormalCharge == null)
{
throw new ArgumentException($"atom {i + 1} had unset formal charge");
}
if (atom.ImplicitHydrogenCount == null)
{
throw new ArgumentException($"atom {i + 1} had unset implicit hydrogen count");
}
if (!atom.IsAromatic)
{
continue;
}
// count preexisting pi-bonds, a higher bond order causes a skip
int nPiBonds = 0;
foreach (var w in graph[i])
{
var order = bonds[i, w].Order;
if (order == BondOrder.Double)
{
nPiBonds++;
}
else if (order.Numeric() > 2)
{
goto continue_ATOMS;
}
}
// check if a pi bond can be assigned
var element = atom.AtomicNumber;
var charge = atom.FormalCharge.Value;
var valence = graph[i].Length + atom.ImplicitHydrogenCount.Value + nPiBonds;
if (IsAvailable(element, charge, valence))
{
available.Set(i, true);
}
continue_ATOMS:
;
}
return(available);
}
/// <summary>
/// Create a VF state for matching isomorphisms. The query is passed first
/// and should read as, find container1 in container2.
/// </summary>
/// <param name="container1">the molecule to search for (query)</param>
/// <param name="container2">the molecule to search in (target)</param>
/// <param name="g1">adjacency list of the query</param>
/// <param name="g2">adjacency list of the target</param>
/// <param name="bonds1">bond lookup of the query</param>
/// <param name="bonds2">bond lookup of the target</param>
/// <param name="atomMatcher">what semantic attributes (symbol, charge, query) determines atoms to be compatible</param>
/// <param name="bondMatcher">what semantic attributes (order/aromatic, query) determines bonds to be compatible</param>
public VFState(IAtomContainer container1, IAtomContainer container2, int[][] g1, int[][] g2, EdgeToBondMap bonds1,
EdgeToBondMap bonds2, AtomMatcher atomMatcher, BondMatcher bondMatcher)
: base(g1, g2)
{
this.container1 = container1;
this.container2 = container2;
this.bonds1 = bonds1;
this.bonds2 = bonds2;
this.atomMatcher = atomMatcher;
this.bondMatcher = bondMatcher;
}
/// <summary>
/// Helper method to obtain the neighbouring bonds from an adjacency list
/// graph and edge->bond map.
/// </summary>
/// <param name="v">vertex</param>
/// <param name="g">graph (adj list)</param>
/// <param name="bondMap">map of edges to bonds</param>
/// <returns>neighboring bonds</returns>
private static IBond[] Neighbors(int v, int[][] g, EdgeToBondMap bondMap)
{
var ws = g[v];
var bonds = new IBond[ws.Length];
for (int i = 0; i < ws.Length; i++)
{
bonds[i] = bondMap[v, ws[i]];
}
return(bonds);
}
/// <summary>
/// Create a state for matching benzene to naphthalene Benzene:
/// InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H Naphthalene: InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H
/// </summary>
UllmannState CreateBenzeneToNaphthalene(AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
IAtomContainer container1 = TestMoleculeFactory.MakeBenzene();
IAtomContainer container2 = TestMoleculeFactory.MakeNaphthalene();
EdgeToBondMap bonds1 = EdgeToBondMap.WithSpaceFor(container1);
EdgeToBondMap bonds2 = EdgeToBondMap.WithSpaceFor(container2);
int[][] g1 = GraphUtil.ToAdjList(container1, bonds1);
int[][] g2 = GraphUtil.ToAdjList(container2, bonds2);
return(new UllmannState(container1, container2, g1, g2, bonds1, bonds2, atomMatcher, bondMatcher));
}
/// <summary>
/// Create a match for the following parameters.
/// </summary>
/// <param name="container1">query structure</param>
/// <param name="container2">target structure</param>
/// <param name="g1">query adjacency list</param>
/// <param name="g2">target adjacency list</param>
/// <param name="bonds1">query bond map</param>
/// <param name="bonds2">target bond map</param>
/// <param name="atomMatcher">how atoms are matched</param>
/// <param name="bondMatcher">how bonds are matched</param>
public UllmannIterable(IAtomContainer container1, IAtomContainer container2, int[][] g1, int[][] g2,
EdgeToBondMap bonds1, EdgeToBondMap bonds2, AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
this.container1 = container1;
this.container2 = container2;
this.g1 = g1;
this.g2 = g2;
this.bonds1 = bonds1;
this.bonds2 = bonds2;
this.atomMatcher = atomMatcher;
this.bondMatcher = bondMatcher;
}
private static bool IsAromPath(int[] path, EdgeToBondMap bmap)
{
int end = path.Length - 1;
for (int i = 0; i < end; i++)
{
if (!bmap[path[i], path[i + 1]].IsAromatic)
{
return(false);
}
}
return(true);
}
/// <summary>
/// Create a match for the following parameters.
/// </summary>
/// <param name="container1">query structure</param>
/// <param name="container2">target structure</param>
/// <param name="g1">query adjacency list</param>
/// <param name="g2">target adjacency list</param>
/// <param name="bonds1">query bond map</param>
/// <param name="bonds2">target bond map</param>
/// <param name="atomMatcher">how atoms are matched</param>
/// <param name="bondMatcher">how bonds are matched</param>
/// <param name="subgraph">perform subgraph search</param>
public VFIterable(IAtomContainer container1, IAtomContainer container2, int[][] g1, int[][] g2,
EdgeToBondMap bonds1, EdgeToBondMap bonds2, AtomMatcher atomMatcher, BondMatcher bondMatcher,
bool subgraph)
{
this.container1 = container1;
this.container2 = container2;
this.g1 = g1;
this.g2 = g2;
this.bonds1 = bonds1;
this.bonds2 = bonds2;
this.atomMatcher = atomMatcher;
this.bondMatcher = bondMatcher;
this.subgraph = subgraph;
}
/// <summary>
/// Convert a cycle in <see cref="int"/>[] representation to an <see cref="IRing"/>
/// but first map back using the given <paramref name="mapping"/>.
/// </summary>
/// <param name="container">atom container</param>
/// <param name="edges">edge map</param>
/// <param name="cycle">vertex walk forming the cycle, first and last vertex the same</param>
/// <returns>a new ring</returns>
private static IRing ToRing(IAtomContainer container, EdgeToBondMap edges, int[] cycle, int[] mapping)
{
var len = cycle.Length - 1;
var atoms = new IAtom[len];
var bonds = new IBond[len];
for (int i = 0; i < len; i++)
{
atoms[i] = container.Atoms[mapping[cycle[i]]];
bonds[i] = edges[mapping[cycle[i]], mapping[cycle[i + 1]]];
atoms[i].IsInRing = true;
}
var ring = container.Builder.NewRing(atoms, bonds);
return(ring);
}
/// <summary>
/// Create a new layout refiner for the provided molecule.
/// </summary>
/// <param name="mol">molecule to refine</param>
internal LayoutRefiner(IAtomContainer mol, ISet <IAtom> afix, ISet <IBond> bfix)
{
this.mol = mol;
this.afix = afix;
this.bfix = bfix;
this.bondMap = EdgeToBondMap.WithSpaceFor(mol);
this.adjList = GraphUtil.ToAdjList(mol, bondMap);
this.idxs = new Dictionary <IAtom, int>();
foreach (var atom in mol.Atoms)
{
idxs[atom] = idxs.Count;
}
this.atoms = mol.Atoms.ToArray();
// buffers for storing coordinates
this.buffer1 = new Vector2[atoms.Length];
this.buffer2 = new Vector2[atoms.Length];
this.backup = new Vector2[atoms.Length];
for (int i = 0; i < buffer1.Length; i++)
{
buffer1[i] = new Vector2();
buffer2[i] = new Vector2();
backup[i] = new Vector2();
}
this.stackBackup = new IntStack(atoms.Length);
this.visited = new bool[atoms.Length];
this.congestion = new Congestion(mol, adjList);
// note, this is lazy so only does the shortest path when needed
// and does |V| search at maximum
this.apsp = new AllPairsShortestPaths(mol);
// index ring systems, idx -> ring system number (rnum)
int rnum = 1;
this.ringsystems = new int[atoms.Length];
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i].IsInRing && ringsystems[i] == 0)
{
TraverseRing(ringsystems, i, rnum++);
}
}
}
/// <summary>
/// Assign a Kekulé representation to the aromatic systems of a compound.
/// </summary>
/// <param name="ac">structural representation</param>
/// <exception cref="CDKException">a Kekulé form could not be assigned</exception>
public static void Kekulize(IAtomContainer ac)
{
// storage of pairs of atoms that have pi-bonded
var matching = Matching.WithCapacity(ac.Atoms.Count);
// exract data structures for efficient access
var atoms = ac.Atoms.ToArray();
var bonds = EdgeToBondMap.WithSpaceFor(ac);
var graph = GraphUtil.ToAdjList(ac, bonds);
// determine which atoms are available to have a pi bond placed
var available = IsAvailable(graph, atoms, bonds);
// attempt to find a perfect matching such that a pi bond is placed
// next to each available atom. if not found the solution is ambiguous
if (!matching.Perfect(graph, available))
{
throw new CDKException("Cannot assign Kekulé structure without randomly creating radicals.");
}
// propagate bond order information from the matching
foreach (var bond in ac.Bonds)
{
if (bond.Order == BondOrder.Unset && bond.IsAromatic)
{
bond.Order = BondOrder.Single;
}
}
for (int v = BitArrays.NextSetBit(available, 0); v >= 0; v = BitArrays.NextSetBit(available, v + 1))
{
var w = matching.Other(v);
var bond = bonds[v, w];
// sanity check, something wrong if this happens
if (bond.Order.Numeric() > 1)
{
throw new CDKException("Cannot assign Kekulé structure, non-sigma bond order has already been assigned?");
}
bond.Order = BondOrder.Double;
available.Set(w, false);
}
}
/// <summary>
/// Compute all rings up to an including the <paramref name="maxRingSize"/>. No
/// pre-processing is done on the container.
/// </summary>
/// <param name="atomContainer">the molecule to be searched for rings</param>
/// <param name="maxRingSize">Maximum ring size to consider. Provides a possible
/// breakout from recursion for complex compounds.</param>
/// <returns>a RingSet containing the rings in molecule</returns>
/// <exception cref="CDKException">An exception thrown if the threshold was exceeded</exception>
public IRingSet FindAllRingsInIsolatedRingSystem(IAtomContainer atomContainer, int maxRingSize)
{
var edges = EdgeToBondMap.WithSpaceFor(atomContainer);
var graph = GraphUtil.ToAdjList(atomContainer, edges);
var ac = new AllCycles(graph, maxRingSize, threshold.Value);
if (!ac.Completed)
{
throw new CDKException("Threshold exceeded for AllRingsFinder");
}
var ringSet = atomContainer.Builder.NewRingSet();
foreach (var path in ac.GetPaths())
{
ringSet.Add(ToRing(atomContainer, edges, path));
}
return(ringSet);
}
