public void TestIsConnectedArtemisinin1()
{
var sp = CDK.SmilesParser;
var container = sp.ParseSmiles("C1CN2CCN(CCCN(CCN(C1)Cc1ccccn1)CC2)C");
Assert.IsTrue(ConnectivityChecker.IsConnected(container));
}
public void TestPartitionExtendedTetrahedral()
{
SmilesParser smipar = CDK.SmilesParser;
var container = smipar.ParseSmiles("CC=[C@]=CC.C");
IChemObjectSet <IAtomContainer> containerSet = ConnectivityChecker.PartitionIntoMolecules(container);
Assert.AreEqual(2, containerSet.Count);
Assert.IsTrue(containerSet[0].StereoElements.GetEnumerator().MoveNext());
}
public void TestIsConnectedFromSDFile()
{
var filename = "NCDK.Data.MDL.mdeotest.sdf";
var ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content = (ChemFile)reader.Read((ChemObject) new ChemFile());
var cList = ChemFileManipulator.GetAllAtomContainers(content);
IAtomContainer ac = cList.First();
Assert.IsTrue(ConnectivityChecker.IsConnected(ac), "Molecule appears not to be connected");
}
public void TestIsConnectedFromHINFile()
{
var filename = "NCDK.Data.HIN.connectivity1.hin";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new HINReader(ins);
var content = reader.Read(builder.NewChemFile());
var cList = ChemFileManipulator.GetAllAtomContainers(content);
IAtomContainer ac = cList.First();
Assert.IsTrue(ConnectivityChecker.IsConnected(ac), "Molecule appears not to be connected");
}
public void TestPartitionIntoMolecules_IAtomContainer()
{
//Debug.WriteLine(atomCon);
AtomContainer atomCon = new AtomContainer();
atomCon.Add(TestMoleculeFactory.Make4x3CondensedRings());
atomCon.Add(TestMoleculeFactory.MakeAlphaPinene());
atomCon.Add(TestMoleculeFactory.MakeSpiroRings());
IChemObjectSet <IAtomContainer> moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon);
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(3, moleculeSet.Count);
}
public void TestPartitionIntoMolecules_IAtomContainer()
{
//Debug.WriteLine(atomCon);
var atomCon = builder.NewAtomContainer();
atomCon.Add(TestMoleculeFactory.Make4x3CondensedRings());
atomCon.Add(TestMoleculeFactory.MakeAlphaPinene());
atomCon.Add(TestMoleculeFactory.MakeSpiroRings());
var moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon).ToReadOnlyList();
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(3, moleculeSet.Count);
}
public void Main()
{
var container = TestMoleculeFactory.MakeBenzene();
#region 1
bool isConnected = ConnectivityChecker.IsConnected(container);
#endregion
var disconnectedContainer = TestMoleculeFactory.MakeBenzene();
#region 2
var fragments = ConnectivityChecker.PartitionIntoMolecules(disconnectedContainer);
int fragmentCount = fragments.Count;
#endregion
}
public void TestDontDeleteSingleElectrons()
{
AtomContainer atomCon = new AtomContainer();
// make two molecules; one with an LonePair, the other with a SingleElectron
IAtomContainer mol1 = new AtomContainer();
Atom atom1 = new Atom("C");
mol1.Atoms.Add(atom1);
LonePair lp1 = new LonePair(atom1);
mol1.LonePairs.Add(lp1);
// mol2
IAtomContainer mol2 = new AtomContainer();
Atom atom2 = new Atom("C");
mol2.Atoms.Add(atom2);
SingleElectron se2 = new SingleElectron(atom2);
mol2.SingleElectrons.Add(se2);
atomCon.Add(mol1);
atomCon.Add(mol2);
// now partition
IChemObjectSet <IAtomContainer> moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon);
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(2, moleculeSet.Count);
Assert.IsTrue(ConnectivityChecker.IsConnected(moleculeSet[0]));
Assert.IsTrue(ConnectivityChecker.IsConnected(moleculeSet[1]));
// make sure
Assert.AreEqual(1, moleculeSet[0].Atoms.Count);
Assert.AreEqual(1, moleculeSet[0].GetElectronContainers().Count());
Assert.AreEqual(1, moleculeSet[1].Atoms.Count);
Assert.AreEqual(1, moleculeSet[1].GetElectronContainers().Count());
// we don't know which partition contains the LP and which the electron
Assert.IsTrue(moleculeSet[0].GetConnectedSingleElectrons(
moleculeSet[0].Atoms[0]).Count() == 0 ||
moleculeSet[1].GetConnectedSingleElectrons(
moleculeSet[1].Atoms[0]).Count() == 0);
Assert.IsTrue(moleculeSet[0].GetConnectedLonePairs(
moleculeSet[0].Atoms[0]).Count() == 0 ||
moleculeSet[1].GetConnectedLonePairs(
moleculeSet[1].Atoms[0]).Count() == 0);
}
public void TestPartitionIntoMoleculesKeepsAtomIDs()
{
AtomContainer atomCon = new AtomContainer();
Atom atom1 = new Atom("C");
atom1.Id = "atom1";
Atom atom2 = new Atom("C");
atom2.Id = "atom2";
atomCon.Atoms.Add(atom1);
atomCon.Atoms.Add(atom2);
IChemObjectSet <IAtomContainer> moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon);
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(2, moleculeSet.Count);
IAtom copy1 = moleculeSet[0].Atoms[0];
IAtom copy2 = moleculeSet[1].Atoms[0];
Assert.AreEqual(atom1.Id, copy1.Id);
Assert.AreEqual(atom2.Id, copy2.Id);
}
public void TestPartitionIntoMoleculesKeepsAtomIDs()
{
var atomCon = builder.NewAtomContainer();
var atom1 = builder.NewAtom("C");
atom1.Id = "atom1";
var atom2 = builder.NewAtom("C");
atom2.Id = "atom2";
atomCon.Atoms.Add(atom1);
atomCon.Atoms.Add(atom2);
var moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon).ToReadOnlyList();
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(2, moleculeSet.Count);
IAtom copy1 = moleculeSet[0].Atoms[0];
IAtom copy2 = moleculeSet[1].Atoms[0];
Assert.AreEqual(atom1.Id, copy1.Id);
Assert.AreEqual(atom2.Id, copy2.Id);
}
public void TestNoAtomsIsConnected()
{
IAtomContainer container = new AtomContainer();
Assert.IsTrue(ConnectivityChecker.IsConnected(container), "Molecule appears not to be connected");
}
public void TestIsConnected_IAtomContainer()
{
IAtomContainer spiro = TestMoleculeFactory.MakeSpiroRings();
Assert.IsTrue(ConnectivityChecker.IsConnected(spiro));
}