public void TestGetSize()
{
IFingerprinter fingerprinter = new ExtendedFingerprinter(512);
Assert.IsNotNull(fingerprinter);
Assert.AreEqual(512, fingerprinter.Length);
}
public void TestDifferentRingFinders()
{
var fingerprinter = new ExtendedFingerprinter();
var ac1 = builder.NewAtomContainer();
var atom1 = builder.NewAtom("C");
var atom2 = builder.NewAtom("C");
var atom3 = builder.NewAtom("C");
var atom4 = builder.NewAtom("C");
var atom5 = builder.NewAtom("C");
var atom6 = builder.NewAtom("C");
ac1.Atoms.Add(atom1);
ac1.Atoms.Add(atom2);
ac1.Atoms.Add(atom3);
ac1.Atoms.Add(atom4);
ac1.Atoms.Add(atom5);
ac1.Atoms.Add(atom6);
var bond1 = builder.NewBond(atom1, atom2);
var bond2 = builder.NewBond(atom2, atom3);
var bond3 = builder.NewBond(atom3, atom4);
var bond4 = builder.NewBond(atom4, atom5);
var bond5 = builder.NewBond(atom5, atom6);
var bond6 = builder.NewBond(atom6, atom1);
ac1.Bonds.Add(bond1);
ac1.Bonds.Add(bond2);
ac1.Bonds.Add(bond3);
ac1.Bonds.Add(bond4);
ac1.Bonds.Add(bond5);
ac1.Bonds.Add(bond6);
var ac2 = builder.NewAtomContainer();
ac2.Atoms.Add(atom1);
ac2.Atoms.Add(atom2);
ac2.Atoms.Add(atom3);
ac2.Atoms.Add(atom4);
ac2.Atoms.Add(atom5);
ac2.Atoms.Add(atom6);
var bond7 = builder.NewBond(atom3, atom1);
ac2.Bonds.Add(bond1);
ac2.Bonds.Add(bond2);
ac2.Bonds.Add(bond3);
ac2.Bonds.Add(bond4);
ac2.Bonds.Add(bond5);
ac2.Bonds.Add(bond6);
ac2.Bonds.Add(bond7);
var bs = fingerprinter.GetBitFingerprint(ac1).AsBitSet();
var bs1 = fingerprinter.GetBitFingerprint(ac2).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs1, bs));
Assert.IsFalse(FingerprinterTool.IsSubset(bs, bs1));
}
public void TestExtendedFingerprinter_int()
{
IFingerprinter fingerprinter = new ExtendedFingerprinter(512);
Assert.IsNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.MakeIndole();
BitArray bs = fingerprinter.GetBitFingerprint(mol).AsBitSet();
IAtomContainer frag1 = TestMoleculeFactory.MakePyrrole();
BitArray bs1 = fingerprinter.GetBitFingerprint(frag1).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs, bs1));
Assert.IsFalse(FingerprinterTool.IsSubset(bs1, bs));
}
public void TestgetBitFingerprintIAtomContainerIRingSetList()
{
var fingerprinter = new ExtendedFingerprinter();
Assert.IsNotNull(fingerprinter);
var mol = TestMoleculeFactory.MakeIndole();
var rs = Cycles.FindSSSR(mol).ToRingSet();
var rslist = RingPartitioner.PartitionRings(rs);
var bs = fingerprinter.GetBitFingerprint(mol, rs, rslist).AsBitSet();
var frag1 = TestMoleculeFactory.MakePyrrole();
var bs1 = fingerprinter.GetBitFingerprint(frag1).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs, bs1));
Assert.IsFalse(FingerprinterTool.IsSubset(bs1, bs));
}
public void TestMoleculeInvariance()
{
var mol = TestMoleculeFactory.MakePyrrole();
var clone = (IAtomContainer)mol.Clone();
// should pass since we have not explicitly detected aromaticity
foreach (var atom in mol.Atoms)
{
Assert.IsFalse(atom.IsAromatic);
}
var diff1 = AtomContainerDiff.Diff(mol, clone);
Assert.AreEqual("", diff1);
var fprinter = new ExtendedFingerprinter();
var fp = fprinter.GetBitFingerprint(mol).AsBitSet();
Assert.IsNotNull(fp);
var diff2 = AtomContainerDiff.Diff(mol, clone);
Assert.IsTrue(diff2.Length == 0, "There was a difference\n" + diff2);
}
public void TestChebi()
{
IAtomContainer searchmol = null;
IAtomContainer findmol = null;
var filename = "NCDK.Data.MDL.chebisearch.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
searchmol = reader.Read(builder.NewAtomContainer());
reader.Close();
filename = "NCDK.Data.MDL.chebifind.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins);
findmol = reader.Read(builder.NewAtomContainer());
reader.Close();
var fingerprinter = new ExtendedFingerprinter();
var superBS = fingerprinter.GetBitFingerprint(findmol).AsBitSet();
var subBS = fingerprinter.GetBitFingerprint(searchmol).AsBitSet();
var isSubset = FingerprinterTool.IsSubset(superBS, subBS);
var isSubset2 = FingerprinterTool.IsSubset(subBS, superBS);
Assert.IsFalse(isSubset);
Assert.IsFalse(isSubset2);
}
public void TestExtendedFingerprinter()
{
IFingerprinter fingerprinter = new ExtendedFingerprinter();
Assert.IsNotNull(fingerprinter);
}
public void TestCondensedSingle()
{
var molcondensed = builder.NewAtomContainer();
var a1 = molcondensed.Builder.NewAtom("C");
a1.Point2D = new Vector2(421.99999999999994, 860.0);
molcondensed.Atoms.Add(a1);
var a2 = molcondensed.Builder.NewAtom("C");
a2.Point2D = new Vector2(390.8230854637602, 878.0);
molcondensed.Atoms.Add(a2);
var a3 = molcondensed.Builder.NewAtom("C");
a3.Point2D = new Vector2(390.8230854637602, 914.0);
molcondensed.Atoms.Add(a3);
var a4 = molcondensed.Builder.NewAtom("C");
a4.Point2D = new Vector2(422.0, 932.0);
molcondensed.Atoms.Add(a4);
var a5 = molcondensed.Builder.NewAtom("C");
a5.Point2D = new Vector2(453.1769145362398, 914.0);
molcondensed.Atoms.Add(a5);
var a6 = molcondensed.Builder.NewAtom("C");
a6.Point2D = new Vector2(453.1769145362398, 878.0);
molcondensed.Atoms.Add(a6);
var a7 = molcondensed.Builder.NewAtom("C");
a7.Point2D = new Vector2(484.3538290724796, 860.0);
molcondensed.Atoms.Add(a7);
var a8 = molcondensed.Builder.NewAtom("C");
a8.Point2D = new Vector2(515.5307436087194, 878.0);
molcondensed.Atoms.Add(a8);
var a9 = molcondensed.Builder.NewAtom("C");
a9.Point2D = new Vector2(515.5307436087194, 914.0);
molcondensed.Atoms.Add(a9);
var a10 = molcondensed.Builder.NewAtom("C");
a10.Point2D = new Vector2(484.3538290724796, 932.0);
molcondensed.Atoms.Add(a10);
var a11 = molcondensed.Builder.NewAtom("C");
a11.Point2D = new Vector2(546.7076581449592, 932.0);
molcondensed.Atoms.Add(a11);
var a12 = molcondensed.Builder.NewAtom("C");
a12.Point2D = new Vector2(577.884572681199, 914.0);
molcondensed.Atoms.Add(a12);
var a13 = molcondensed.Builder.NewAtom("C");
a13.Point2D = new Vector2(577.884572681199, 878.0);
molcondensed.Atoms.Add(a13);
var a14 = molcondensed.Builder.NewAtom("C");
a14.Point2D = new Vector2(546.7076581449592, 860.0);
molcondensed.Atoms.Add(a14);
var a15 = molcondensed.Builder.NewAtom("C");
a15.Point2D = new Vector2(359.6461709275204, 860.0);
molcondensed.Atoms.Add(a15);
var a16 = molcondensed.Builder.NewAtom("C");
a16.Point2D = new Vector2(609.0614872174388, 860.0);
molcondensed.Atoms.Add(a16);
var b1 = molcondensed.Builder.NewBond(a1, a2, BondOrder.Single);
molcondensed.Bonds.Add(b1);
var b2 = molcondensed.Builder.NewBond(a2, a3, BondOrder.Single);
molcondensed.Bonds.Add(b2);
var b3 = molcondensed.Builder.NewBond(a3, a4, BondOrder.Single);
molcondensed.Bonds.Add(b3);
var b4 = molcondensed.Builder.NewBond(a4, a5, BondOrder.Single);
molcondensed.Bonds.Add(b4);
var b5 = molcondensed.Builder.NewBond(a5, a6, BondOrder.Single);
molcondensed.Bonds.Add(b5);
var b6 = molcondensed.Builder.NewBond(a6, a1, BondOrder.Single);
molcondensed.Bonds.Add(b6);
var b7 = molcondensed.Builder.NewBond(a6, a7, BondOrder.Single);
molcondensed.Bonds.Add(b7);
var b8 = molcondensed.Builder.NewBond(a7, a8, BondOrder.Single);
molcondensed.Bonds.Add(b8);
var b9 = molcondensed.Builder.NewBond(a8, a9, BondOrder.Single);
molcondensed.Bonds.Add(b9);
var b10 = molcondensed.Builder.NewBond(a9, a10, BondOrder.Single);
molcondensed.Bonds.Add(b10);
var b11 = molcondensed.Builder.NewBond(a10, a5, BondOrder.Single);
molcondensed.Bonds.Add(b11);
var b12 = molcondensed.Builder.NewBond(a9, a11, BondOrder.Single);
molcondensed.Bonds.Add(b12);
var b13 = molcondensed.Builder.NewBond(a11, a12, BondOrder.Single);
molcondensed.Bonds.Add(b13);
var b14 = molcondensed.Builder.NewBond(a12, a13, BondOrder.Single);
molcondensed.Bonds.Add(b14);
var b15 = molcondensed.Builder.NewBond(a13, a14, BondOrder.Single);
molcondensed.Bonds.Add(b15);
var b16 = molcondensed.Builder.NewBond(a14, a8, BondOrder.Single);
molcondensed.Bonds.Add(b16);
var b17 = molcondensed.Builder.NewBond(a2, a15, BondOrder.Single);
molcondensed.Bonds.Add(b17);
var b18 = molcondensed.Builder.NewBond(a13, a16, BondOrder.Single);
molcondensed.Bonds.Add(b18);
var molsingle = builder.NewAtomContainer();
var a1s = molsingle.Builder.NewAtom("C");
a1s.Point2D = new Vector2(421.99999999999994, 860.0);
molsingle.Atoms.Add(a1s);
var a2s = molsingle.Builder.NewAtom("C");
a2s.Point2D = new Vector2(390.8230854637602, 878.0);
molsingle.Atoms.Add(a2s);
var a6s = molsingle.Builder.NewAtom("C");
a6s.Point2D = new Vector2(453.1769145362398, 878.0);
molsingle.Atoms.Add(a6s);
var a3s = molsingle.Builder.NewAtom("C");
a3s.Point2D = new Vector2(390.8230854637602, 914.0);
molsingle.Atoms.Add(a3s);
var a15s = molsingle.Builder.NewAtom("C");
a15s.Point2D = new Vector2(359.6461709275204, 860.0);
molsingle.Atoms.Add(a15s);
var a5s = molsingle.Builder.NewAtom("C");
a5s.Point2D = new Vector2(453.1769145362398, 914.0);
molsingle.Atoms.Add(a5s);
var a7s = molsingle.Builder.NewAtom("C");
a7s.Point2D = new Vector2(492.8230854637602, 881.0);
molsingle.Atoms.Add(a7s);
var a4s = molsingle.Builder.NewAtom("C");
a4s.Point2D = new Vector2(422.0, 932.0);
molsingle.Atoms.Add(a4s);
var a8s = molsingle.Builder.NewAtom("C");
a8s.Point2D = new Vector2(524.0, 863.0);
molsingle.Atoms.Add(a8s);
var a9s = molsingle.Builder.NewAtom("C");
a9s.Point2D = new Vector2(492.8230854637602, 917.0);
molsingle.Atoms.Add(a9s);
var a10s = molsingle.Builder.NewAtom("C");
a10s.Point2D = new Vector2(555.1769145362398, 881.0);
molsingle.Atoms.Add(a10s);
var a11s = molsingle.Builder.NewAtom("C");
a11s.Point2D = new Vector2(524.0, 935.0);
molsingle.Atoms.Add(a11s);
var a12s = molsingle.Builder.NewAtom("C");
a12s.Point2D = new Vector2(555.1769145362398, 917.0);
molsingle.Atoms.Add(a12s);
var a13s = molsingle.Builder.NewAtom("C");
a13s.Point2D = new Vector2(592.8230854637602, 889.0);
molsingle.Atoms.Add(a13s);
var a14s = molsingle.Builder.NewAtom("C");
a14s.Point2D = new Vector2(624.0, 871.0);
molsingle.Atoms.Add(a14s);
var a16s = molsingle.Builder.NewAtom("C");
a16s.Point2D = new Vector2(592.8230854637602, 925.0);
molsingle.Atoms.Add(a16s);
var a17s = molsingle.Builder.NewAtom("C");
a17s.Point2D = new Vector2(655.1769145362398, 889.0);
molsingle.Atoms.Add(a17s);
var a18s = molsingle.Builder.NewAtom("C");
a18s.Point2D = new Vector2(624.0, 943.0);
molsingle.Atoms.Add(a18s);
var a19s = molsingle.Builder.NewAtom("C");
a19s.Point2D = new Vector2(655.1769145362398, 925.0);
molsingle.Atoms.Add(a19s);
var a20s = molsingle.Builder.NewAtom("C");
a20s.Point2D = new Vector2(686.3538290724796, 871.0);
molsingle.Atoms.Add(a20s);
var b1s = molsingle.Builder.NewBond(a1s, a2s, BondOrder.Single);
molsingle.Bonds.Add(b1s);
var b6s = molsingle.Builder.NewBond(a6s, a1s, BondOrder.Single);
molsingle.Bonds.Add(b6s);
var b2s = molsingle.Builder.NewBond(a2s, a3s, BondOrder.Single);
molsingle.Bonds.Add(b2s);
var b17s = molsingle.Builder.NewBond(a2s, a15s, BondOrder.Single);
molsingle.Bonds.Add(b17s);
var b5s = molsingle.Builder.NewBond(a5s, a6s, BondOrder.Single);
molsingle.Bonds.Add(b5s);
var b7s = molsingle.Builder.NewBond(a6s, a7s, BondOrder.Single);
molsingle.Bonds.Add(b7s);
var b3s = molsingle.Builder.NewBond(a3s, a4s, BondOrder.Single);
molsingle.Bonds.Add(b3s);
var b4s = molsingle.Builder.NewBond(a4s, a5s, BondOrder.Single);
molsingle.Bonds.Add(b4s);
var b8s = molsingle.Builder.NewBond(a8s, a7s, BondOrder.Single);
molsingle.Bonds.Add(b8s);
var b9s = molsingle.Builder.NewBond(a7s, a9s, BondOrder.Single);
molsingle.Bonds.Add(b9s);
var b10s = molsingle.Builder.NewBond(a10s, a8s, BondOrder.Single);
molsingle.Bonds.Add(b10s);
var b11s = molsingle.Builder.NewBond(a9s, a11s, BondOrder.Single);
molsingle.Bonds.Add(b11s);
var b12s = molsingle.Builder.NewBond(a12s, a10s, BondOrder.Single);
molsingle.Bonds.Add(b12s);
var b13s = molsingle.Builder.NewBond(a10s, a13s, BondOrder.Single);
molsingle.Bonds.Add(b13s);
var b14s = molsingle.Builder.NewBond(a11s, a12s, BondOrder.Single);
molsingle.Bonds.Add(b14s);
var b15s = molsingle.Builder.NewBond(a14s, a13s, BondOrder.Single);
molsingle.Bonds.Add(b15s);
var b16s = molsingle.Builder.NewBond(a13s, a16s, BondOrder.Single);
molsingle.Bonds.Add(b16s);
var b18s = molsingle.Builder.NewBond(a17s, a14s, BondOrder.Single);
molsingle.Bonds.Add(b18s);
var b19s = molsingle.Builder.NewBond(a16s, a18s, BondOrder.Single);
molsingle.Bonds.Add(b19s);
var b20s = molsingle.Builder.NewBond(a19s, a17s, BondOrder.Single);
molsingle.Bonds.Add(b20s);
var b21s = molsingle.Builder.NewBond(a18s, a19s, BondOrder.Single);
molsingle.Bonds.Add(b21s);
var b22s = molsingle.Builder.NewBond(a17s, a20s, BondOrder.Single);
molsingle.Bonds.Add(b22s);
var fingerprinter = new ExtendedFingerprinter();
var bs1 = fingerprinter.GetBitFingerprint(molsingle).AsBitSet();
var bs2 = fingerprinter.GetBitFingerprint(molcondensed).AsBitSet();
Assert.IsFalse(FingerprinterTool.IsSubset(bs1, bs2));
Assert.IsTrue(FingerprinterTool.IsSubset(bs2, bs1));
}