public void TestIsomoltane_Bug3088164()
{
var sg = SmilesGenerator.Unique.Aromatic();
var mol = smilesParser.ParseSmiles("CC(C)NCC(O)COC1=C(C=CC=C1)N1C=CC=C1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
var f = fragmenter.GetFrameworks().ToReadOnlyList();
var fc = fragmenter.GetFrameworksAsContainers().ToReadOnlyList();
Assert.AreEqual(1, f.Count);
Assert.AreEqual(f.Count, fc.Count);
Assert.AreEqual("c1ccc(cc1)-n2cccc2", f[0]);
for (int i = 0; i < f.Count; i++)
{
Aromaticity.CDKLegacy.Apply(fc[i]);
string newsmiles = sg.Create(fc[i]);
Assert.IsTrue(f[i].Equals(newsmiles), f[i] + " did not match the container, " + newsmiles);
}
}
public void TestPirenperone_Bug3088164()
{
var sg = SmilesGenerator.Unique.Aromatic();
var mol = smilesParser.ParseSmiles("Fc1ccc(cc1)C(=O)C4CCN(CCC\\3=C(\\N=C2\\C=C/C=C\\N2C/3=O)C)CC4");
AtomContainerManipulator.ClearAtomConfigurations(mol);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
var f = fragmenter.GetFrameworks().ToReadOnlyList();
var fc = fragmenter.GetFrameworksAsContainers().ToReadOnlyList();
Assert.AreEqual(1, f.Count);
Assert.AreEqual(f.Count, fc.Count);
AtomContainerManipulator.ClearAtomConfigurations(mol);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
CDK.HydrogenAdder.AddImplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
Assert.AreEqual("N=1C=C(CN2C=CC=CC12)CCN3CCC(Cc4ccccc4)CC3", f[0]);
for (int i = 0; i < f.Count; i++)
{
string newsmiles = sg.Create(fc[i]);
Assert.IsTrue(f[i].Equals(newsmiles), f[i] + " did not match the container, " + newsmiles);
}
}
public void TestCHEMBL529226()
{
var smiles = "CC1=CN([C@@H]2O[C@@]3(COP(=S)(O)O[C@H]4[C@H]5OC[C@]4(COP(=S)(O)O[C@H]6C[C@@H](O[C@@H]6COP(=S)(O)O[C@H]7[C@@H](O)[C@@H](O[C@@H]7COP(=S)(O)O[C@H]8[C@@H](O)[C@@H](O[C@@H]8COP(=S)(O)O[C@H]9[C@@H](O)[C@@H](O[C@@H]9COP(=S)(O)O[C@H]%10[C@@H](O)[C@@H](O[C@@H]%10COP(=S)(O)O[C@H]%11[C@@H](O)[C@@H](O[C@@H]%11COP(=S)(O)O[C@H]%12[C@@H](O)[C@@H](O[C@@H]%12COP(=S)(O)O[C@H]%13[C@@H](O)[C@@H](O[C@@H]%13COP(=S)(O)O[C@H]%14[C@@H](O)[C@@H](O[C@@H]%14COP(=S)(O)O[C@H]%15[C@@H](O)[C@@H](O[C@@H]%15COP(=S)(O)O[C@H]%16[C@H]%17OC[C@]%16(COP(=S)(O)O[C@H]%18[C@H]%19OC[C@]%18(CO)O[C@H]%19N%20C=C(C)C(=O)NC%20=O)O[C@H]%17N%21C=C(C)C(=NC%21=O)N)N%22C=CC(=NC%22=O)N)n%23cnc%24C(=O)NC(=Nc%23%24)N)n%25cnc%26C(=O)NC(=Nc%25%26)N)N%27C=C(C)C(=O)NC%27=O)N%28C=CC(=NC%28=O)N)n%29cnc%30c(N)ncnc%29%30)N%31C=CC(=NC%31=O)N)n%32cnc%33C(=O)NC(=Nc%32%33)N)n%34cnc%35C(N)NC=Nc%34%35)N%36C=C(C)C(=O)NC%36=O)O[C@H]5N%37C=C(C)C(=O)NC%37=O)CO[C@@H]2[C@@H]3O)C(=O)N=C1N";
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smiles);
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
Assert.AreEqual(1, fragmenter.GetFrameworks().Count());
}
public void TestSingleFramework()
{
var mol = smilesParser.ParseSmiles("C1(c2ccccc2)(CC(CC1)CCc1ccccc1)CC1C=CC=C1");
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
var frameworks = fragmenter.GetFrameworks();
Assert.AreEqual(1, frameworks.Count());
}
public void TestBug1848591()
{
var mol = smilesParser.ParseSmiles("c1(ccc(cc1C)CCC(C(CCC)C2C(C2)CC)C3C=C(C=C3)CC)C");
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
var frameworks = fragmenter.GetFrameworks();
Assert.AreEqual(1, frameworks.Count());
Assert.AreEqual("c1ccc(cc1)CCC(CC2CC2)C3C=CC=C3", frameworks.ElementAt(0));
}
public void TestMF1()
{
var mol = smilesParser.ParseSmiles("c1ccccc1PP(B)c1cccc(N(N)N)c1SC1CCC1");
var fragmenter = new MurckoFragmenter(false, 2);
fragmenter.GenerateFragments(mol);
var frameworks = fragmenter.GetFrameworks();
Assert.AreEqual(3, frameworks.Count());
var rings = fragmenter.GetRingSystems();
Assert.AreEqual(2, rings.Count());
}
public void TestGetFragmentsAsContainers()
{
var biphenyl = TestMoleculeFactory.MakeBiphenyl();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(biphenyl);
Aromaticity.CDKLegacy.Apply(biphenyl);
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(biphenyl);
var fragments = fragmenter.GetFragmentsAsContainers().ToReadOnlyList();
Assert.AreEqual(2, fragments.Count);
Assert.AreEqual(12, fragments[0].Atoms.Count);
Assert.AreEqual(6, fragments[1].Atoms.Count);
}
public void TestMacrocycle()
{
var mol = smilesParser.ParseSmiles("C1=C(C=C(C(=C1O)O)O)C(=O)OC2=CC(=CC(=C2O)O)C(=O)OCC3C(C(C(C(O3)OC(=O)C4=CC(=C(C(=C4)OC(=O)C5=CC(=C(C(=C5)O)O)O)O)O)OC(=O)C6=CC(=C(C(=C6)OC(=O)C7=CC(=C(C(=C7)O)O)O)O)O)OC(=O)C8=CC(=C(C(=C8)OC(=O)C9=CC(=C(C(=C9)O)O)O)O)O)OC(=O)C1=CC(=C(C(=C1)OC(=O)C1=CC(=C(C(=C1)O)O)O)O)O");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var fragmenter = new MurckoFragmenter(true, 6);
fragmenter.GenerateFragments(mol);
var f = fragmenter.GetFrameworks();
Assert.AreEqual(1, f.Count());
var rs = fragmenter.GetRingSystems();
Assert.AreEqual(2, rs.Count());
var fs = fragmenter.GetFragments();
Assert.AreEqual(3, fs.Count());
}