/// <summary>
/// Create a pattern which can be used to find molecules which contain the
/// <paramref name="query"/> structure.
/// </summary>
/// <param name="query">the substructure to find</param>
/// <returns>a pattern for finding the <paramref name="query"/></returns>
public static new Pattern CreateSubstructureFinder(IAtomContainer query)
{
bool isQuery = query is IQueryAtomContainer;
return(new Ullmann(query, isQuery ? AtomMatcher.CreateQueryMatcher() : AtomMatcher.CreateElementMatcher(),
isQuery ? BondMatcher.CreateQueryMatcher() : BondMatcher.CreateOrderMatcher()));
}
public void HasNext()
{
var state = CreateNaphthaleneToBenzene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
var it = new StateStream(state);
Assert.IsFalse(it.Any());
}
public void Next()
{
var state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
var it = new StateStream(state).GetEnumerator();
it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 0, 1, 2, 7, 8, 9 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 0, 9, 8, 7, 2, 1 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 1, 0, 9, 8, 7, 2 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 1, 2, 7, 8, 9, 0 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 2, 1, 0, 9, 8, 7 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 2, 3, 4, 5, 6, 7 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 2, 7, 6, 5, 4, 3 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 2, 7, 8, 9, 0, 1 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 3, 2, 7, 6, 5, 4 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 3, 4, 5, 6, 7, 2 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 4, 3, 2, 7, 6, 5 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 4, 5, 6, 7, 2, 3 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 5, 4, 3, 2, 7, 6 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 5, 6, 7, 2, 3, 4 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 6, 5, 4, 3, 2, 7 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 6, 7, 2, 3, 4, 5 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 7, 2, 1, 0, 9, 8 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 7, 2, 3, 4, 5, 6 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 7, 6, 5, 4, 3, 2 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 7, 8, 9, 0, 1, 2 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 8, 7, 2, 1, 0, 9 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 8, 9, 0, 1, 2, 7 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 9, 0, 1, 2, 7, 8 }, it.Current)); it.MoveNext();
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 9, 8, 7, 2, 1, 0 }, it.Current)); it.MoveNext();
}
/// <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>
/// Create a pattern which can be used to find molecules which are the same
/// as the <paramref name="query"/> structure.
/// </summary>
/// <param name="query">the substructure to find</param>
/// <returns>a pattern for finding the <paramref name="query"/></returns>
public static new Pattern CreateIdenticalFinder(IAtomContainer query)
{
bool isQuery = query is IQueryAtomContainer;
return(CreateIdenticalFinder(query,
isQuery ? AtomMatcher.CreateQueryMatcher() : AtomMatcher.CreateElementMatcher(),
isQuery ? BondMatcher.CreateQueryMatcher() : BondMatcher.CreateOrderMatcher()));
}
/// <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);
}
/// <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>
/// 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>
/// 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;
}
public void QueryMatch()
{
BondMatcher matcher = BondMatcher.CreateQueryMatcher();
var m_bond1 = new Mock <IQueryBond>(); IQueryBond bond1 = m_bond1.Object;
var m_bond2 = new Mock <IBond>(); IBond bond2 = m_bond2.Object;
var m_bond3 = new Mock <IBond>(); IBond bond3 = m_bond3.Object;
m_bond1.Setup(n => n.Matches(bond2)).Returns(true);
m_bond1.Setup(n => n.Matches(bond3)).Returns(false);
Assert.IsTrue(matcher.Matches(bond1, bond2));
Assert.IsFalse(matcher.Matches(bond1, bond3));
}
public void AliphaticStrictMatch()
{
BondMatcher matcher = BondMatcher.CreateStrictOrderMatcher();
var m_bond1 = new Mock <IBond>(); IBond bond1 = m_bond1.Object;
var m_bond2 = new Mock <IBond>(); IBond bond2 = m_bond2.Object;
m_bond1.SetupGet(n => n.IsAromatic).Returns(false);
m_bond2.SetupGet(n => n.IsAromatic).Returns(false);
m_bond1.SetupGet(n => n.Order).Returns(BondOrder.Single);
m_bond2.SetupGet(n => n.Order).Returns(BondOrder.Single);
Assert.IsTrue(matcher.Matches(bond1, bond2));
Assert.IsTrue(matcher.Matches(bond2, bond1));
}
public void AnyMatch()
{
BondMatcher matcher = BondMatcher.CreateAnyMatcher();
IBond bond1 = new Mock <IBond>().Object;
IBond bond2 = new Mock <IBond>().Object;
IBond bond3 = new Mock <IBond>().Object;
Assert.IsTrue(matcher.Matches(bond1, bond2));
Assert.IsTrue(matcher.Matches(bond2, bond1));
Assert.IsTrue(matcher.Matches(bond1, bond3));
Assert.IsTrue(matcher.Matches(bond1, null));
Assert.IsTrue(matcher.Matches(null, null));
}
public void HasNext2()
{
var state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
int cnt = 0;
var it = new StateStream(state);
foreach (var i in it)
{
Assert.IsNotNull(i);
cnt++;
}
Assert.AreEqual(24, cnt);
}
/// <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;
}
public void InfeasibleBonds()
{
var m = new Mock <BondMatcher>(); BondMatcher mock = m.Object;
m.Setup(n => n.Matches(It.IsAny <IBond>(), It.IsAny <IBond>())).Returns(false);
VFSubState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), mock);
state.m1[0] = 0;
state.m1[1] = 1;
state.m1[2] = 2;
state.m1[3] = 3;
state.m1[4] = 4;
for (int i = 0; i < 4; i++)
{
for (int j = 0; j < 4; j++)
{
Assert.IsFalse(state.Feasible(i, j));
}
}
}
public void TestNextM()
{
UllmannState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
Assert.AreEqual(state.NextM(0, -1), 0);
Assert.AreEqual(state.NextM(0, 0), 1);
Assert.AreEqual(state.NextM(0, 1), 2);
state.m2[1] = 0; // 1 has been mapped and should be skipped over
Assert.AreEqual(state.NextM(0, 0), 2);
}
public void Add()
{
UllmannState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }
},
state.matrix.Fix()
));
Assert.IsTrue(state.Add(0, 0));
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, 1 },
new[] { 1, -1, 1, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, 1, -1, 1, -1, -1, -1, 1, -1, 1 },
new[] { 1, -1, 1, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, 1 }
},
state.matrix.Fix()));
Assert.IsTrue(state.Add(1, 9));
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
new[] { -1, -2, -1, -1, -1, -1, -1, -1, -1, 1 },
new[] { 1, -1, -2, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, 1, -1, -2, -1, -1, -1, 1, -1, 1 },
new[] { 1, -1, 1, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, 1 }
},
state.matrix.Fix()));
Assert.IsTrue(state.Add(2, 8));
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
new[] { -1, -2, -1, -1, -1, -1, -1, -1, -1, 1 },
new[] { -3, -1, -2, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, -3, -1, -2, -1, -1, -1, 1, -1, 1 },
new[] { 1, -1, 1, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, 1 }
},
state.matrix.Fix()));
Assert.IsTrue(state.Add(3, 7));
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
new[] { -1, -2, -1, -1, -1, -1, -1, -1, -1, 1 },
new[] { -3, -1, -2, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, -3, -1, -2, -1, -1, -1, 1, -1, -4 },
new[] { -4, -1, 1, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, 1 }
},
state.matrix.Fix()));
Assert.IsTrue(state.Add(4, 2));
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
new[] { -1, -2, -1, -1, -1, -1, -1, -1, -1, 1 },
new[] { -3, -1, -2, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, -3, -1, -2, -1, -1, -1, 1, -1, -4 },
new[] { -4, -1, 1, -1, -1, -1, -1, -1, -5, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, -5 }
},
state.matrix.Fix()));
Assert.IsTrue(state.Add(5, 1));
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
new[] { -1, -2, -1, -1, -1, -1, -1, -1, -1, 1 },
new[] { -3, -1, -2, -1, -1, -1, -1, -1, 1, -1 },
new[] { -1, -3, -1, -2, -1, -1, -1, 1, -1, -4 },
new[] { -4, -1, 1, -1, -1, -1, -1, -1, -5, -1 },
new[] { -1, 1, -1, -1, -1, -1, -1, -1, -1, -5 }
},
state.matrix.Fix()));
}
public void InfeasibleTerminalCount()
{
VFState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
Assert.IsTrue(state.Feasible(4, 4)); // 4, 4 is feasible
state.Add(0, 0);
state.Add(1, 1);
state.Add(2, 2);
state.Add(3, 3);
Assert.IsFalse(state.Feasible(4, 4)); // 4, 4 is infeasible
}
public void TestNextN()
{
UllmannState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
Assert.AreEqual(state.NextN(0), 0);
state.size = 1;
Assert.AreEqual(state.NextN(0), 1);
state.size = 2;
Assert.AreEqual(state.NextN(0), 2);
}
public void Accessors()
{
UllmannState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
state.size = 1;
Assert.AreEqual(state.Count, 1);
Assert.AreEqual(state.NMax(), state.g1.Length);
Assert.AreEqual(state.MMax(), state.g2.Length);
}
public void Mapping()
{
UllmannState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
state.m1[0] = 1;
state.m1[1] = 2;
Assert.IsTrue(Compares.AreDeepEqual(state.m1, state.Mapping()));
Assert.AreNotSame(state.m1, state.Mapping());
}
public void InfeasibleRemainCount()
{
VFSubState state = CreateBenzeneToNaphthalene(AtomMatcher.CreateAnyMatcher(), BondMatcher.CreateAnyMatcher());
Assert.IsTrue(state.Feasible(0, 0)); // 0,0 is feasible
// XXX: depends on molecule order not changing
state.m1[1] = 1;
state.m1[5] = 5;
state.t2[1] = 1;
state.t2[9] = 1;
Assert.IsFalse(state.Feasible(0, 0)); // 0,0 is infeasible
}
/// <summary>
/// Create a pattern which can be used to find molecules which contain the
/// <paramref name="query"/> structure.
/// </summary>
/// <param name="query">the substructure to find</param>
/// <param name="atomMatcher">how atoms are matched</param>
/// <param name="bondMatcher">how bonds are matched</param>
/// <returns>a pattern for finding the <paramref name="query"/></returns>
public static Pattern CreateSubstructureFinder(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
return(new VentoFoggia(query, atomMatcher, bondMatcher, true));
}
/// <summary>
/// Create a pattern which can be used to find molecules which are the same
/// as the <paramref name="query"/> structure.
/// </summary>
/// <param name="query">the substructure to find</param>
/// <param name="atomMatcher">how atoms are matched</param>
/// <param name="bondMatcher">how bonds are matched</param>
/// <returns>a pattern for finding the <paramref name="query"/></returns>
public static Pattern CreateIdenticalFinder(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
return(new VentoFoggia(query, atomMatcher, bondMatcher, false));
}