public void TestFindAllRings_IAtomContainer_bool()
{
AllRingsFinder arf = new AllRingsFinder();
IAtomContainer molecule = TestMoleculeFactory.MakeEthylPropylPhenantren();
arf.FindAllRings(molecule);
}
public void TestRingFlags2()
{
var sp = CDK.SmilesParser;
var molecule = sp.ParseSmiles("C1CCCC1CC");
foreach (var a in molecule.Atoms)
{
a.IsInRing = false;
}
AllRingsFinder arf = new AllRingsFinder();
arf.FindAllRings(molecule);
int count = 0;
foreach (var atom in molecule.Atoms)
{
if (atom.IsInRing)
{
count++;
}
}
Assert.AreEqual(5, count, "All atoms in 1-ethyl-cyclopentane were not marked as being in a ring");
}
public void TestBug777488()
{
//var filename = "data/Bug646.cml";
var filename = "NCDK.Data.CML.testBug777488-1-AllRingsFinder.cml";
//var filename = "data/NCI_diversity_528.mol.cml";
//var filename = "data/NCI_diversity_978.mol.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer mol = model.MoleculeSet[0];
if (standAlone)
{
Console.Out.WriteLine("Constructed Molecule");
}
if (standAlone)
{
Console.Out.WriteLine("Starting AllRingsFinder");
}
IRingSet ringSet = new AllRingsFinder().FindAllRings(mol);
if (standAlone)
{
Console.Out.WriteLine("Finished AllRingsFinder");
}
if (standAlone)
{
Console.Out.WriteLine("Found " + ringSet.Count + " rings.");
}
//Display(mol);
}
public void TestBigMoleculeWithIsolatedRings()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
var filename = "NCDK.Data.CML.isolated_ringsystems.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer mol = model.MoleculeSet[0];
//Debug.WriteLine("Constructed Molecule");
//Debug.WriteLine("Starting AllRingsFinder");
ringSet = new AllRingsFinder().FindAllRings(mol);
//Debug.WriteLine("Finished AllRingsFinder");
Assert.AreEqual(24, ringSet.Count);
//Display(mol);
// check sizes of rings
int[] ringSize = new int[mol.Atoms.Count];
foreach (var ring in ringSet)
{
ringSize[ring.Atoms.Count]++;
}
Assert.AreEqual(18, ringSize[6]);
Assert.AreEqual(6, ringSize[10]);
}
public void TestFindAllRings_IAtomContainer()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
IAtomContainer molecule = TestMoleculeFactory.MakeEthylPropylPhenantren();
ringSet = arf.FindAllRings(molecule);
Assert.AreEqual(6, ringSet.Count);
}
public void TestBigRingSystem_MaxRingSize6_03419()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
var filename = "NCDK.Data.MDL.ring_03419.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer molecule = model.MoleculeSet[0];
ringSet = arf.FindAllRings(molecule, 6);
Assert.AreEqual(12, ringSet.Count);
}
public void TestBigRingSystem_MaxRingSize4_fourRing5x10()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
var filename = "NCDK.Data.MDL.four-ring-5x10.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer molecule = model.MoleculeSet[0];
// there are 5x10 squares (four-rings) in the 5x10 molecule
ringSet = arf.FindAllRings(molecule, 4);
Assert.AreEqual(50, ringSet.Count);
}
public void TestCholoylCoA()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
var filename = "NCDK.Data.MDL.choloylcoa.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer molecule = model.MoleculeSet[0];
ringSet = arf.FindAllRings(molecule);
Assert.AreEqual(14, ringSet.Count);
}
public void TestBigRingSystem()
{
IRingSet ringSet = null;
AllRingsFinder arf = AllRingsFinder.UsingThreshold(Threshold.PubChem994);
var filename = "NCDK.Data.MDL.ring_03419.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer molecule = model.MoleculeSet[0];
ringSet = arf.FindAllRings(molecule);
// the 1976 value was empirically derived, and might not be accurate
Assert.AreEqual(1976, ringSet.Count);
}
public void TestBondsWithinRing()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
IAtomContainer molecule = TestMoleculeFactory.MakeEthylPropylPhenantren();
ringSet = arf.FindAllRings(molecule);
foreach (var ring in ringSet)
{
foreach (var ec in ring.Bonds)
{
var atom1 = ec.Begin;
var atom2 = ec.End;
Assert.IsTrue(ring.Contains(atom1));
Assert.IsTrue(ring.Contains(atom2));
}
}
}
public void TestBigRingSystem_MaxRingSize6_fourRing5x10()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
var filename = "NCDK.Data.MDL.four-ring-5x10.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer molecule = model.MoleculeSet[0];
// there are 5x10 four-rings (squares ) = 50
// there are (9x5) + (4x10) six-rings = 85
// combined 135
ringSet = arf.FindAllRings(molecule, 6);
Assert.AreEqual(135, ringSet.Count);
}
public void TestAllRingsFinder()
{
AllRingsFinder arf = new AllRingsFinder();
Assert.IsNotNull(arf);
}