public void UnrecognisedAtomTypes()
{
IAtomContainer container;
using (var mol2Reader = new Mol2Reader(ResourceLoader.GetAsStream(this.GetType(), "CLMW1.mol2")))
{
container = mol2Reader.Read(builder.NewAtomContainer());
}
foreach (var atom in container.Atoms)
{
Assert.IsNotNull(atom.AtomicNumber);
}
}
private static void CheckMol(string str)
{
IChemFile mol;
using (var reader = new Mol2Reader(new StringReader(str)))
{
mol = reader.Read(CDK.Builder.NewChemFile());
}
Assert.IsTrue(mol.Count > 0);
Assert.IsTrue(mol[0].Count > 0);
Assert.IsTrue(mol[0][0].MoleculeSet.Count > 0);
Assert.IsTrue(mol[0][0].MoleculeSet[0].Atoms.Count > 0);
}
public void TestIAtomContainer()
{
var filename = "NCDK.Data.Mol2.fromWebsite.mol2";
IAtomContainer mol;
using (var reader = new Mol2Reader(ResourceLoader.GetAsStream(filename)))
{
mol = (IAtomContainer)reader.Read(builder.NewAtomContainer());
}
Assert.IsNotNull(mol);
Assert.AreEqual(12, mol.Atoms.Count);
Assert.AreEqual(12, mol.Bonds.Count);
}
public void TestReadingIDs()
{
var filename = "NCDK.Data.Mol2.fromWebsite.mol2";
IAtomContainer molecule;
using (var reader = new Mol2Reader(ResourceLoader.GetAsStream(filename)))
{
molecule = reader.Read(builder.NewAtomContainer());
}
Assert.IsNotNull(molecule);
var reference = (IAtomContainer)molecule.Clone();
Assert.AreEqual("C1", reference.Atoms[0].Id);
}
public void TestMultiMolButSingle()
{
var filename = "NCDK.Data.Mol2.fromWebsite.mol2";
Trace.TraceInformation("Testing: ", filename);
IChemFile chemFile;
using (var reader = new Mol2Reader(ResourceLoader.GetAsStream(filename)))
{
chemFile = reader.Read(builder.NewChemFile());
}
var mols = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
Assert.AreEqual(1, mols.Count);
Assert.AreEqual(12, mols[0].Atoms.Count);
}
public void TestExampleFromWebsite()
{
var filename = "NCDK.Data.Mol2.fromWebsite.mol2";
Trace.TraceInformation("Testing: ", filename);
IChemFile chemFile;
using (var reader = new Mol2Reader(ResourceLoader.GetAsStream(filename)))
{
chemFile = reader.Read(builder.NewChemFile());
}
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
var som = model.MoleculeSet;
Assert.IsNotNull(som);
Assert.AreEqual(1, som.Count);
var m = som[0];
Assert.IsNotNull(m);
Assert.AreEqual(12, m.Atoms.Count);
Assert.AreEqual(12, m.Bonds.Count);
Assert.AreEqual("C.ar", m.Atoms[0].AtomTypeName);
Assert.AreEqual("C", m.Atoms[0].Symbol);
Assert.AreEqual("H", m.Atoms[6].AtomTypeName);
Assert.AreEqual("H", m.Atoms[6].Symbol);
}
public void TestBug1714794()
{
var problematicMol2 = "@<TRIPOS>MOLECULE\n" + "mol_197219.smi\n" + " 129 135 0 0 0\n" + "SMALL\n"
+ "GASTEIGER\n" + "Energy = 0\n" + "\n" + "@<TRIPOS>ATOM\n"
+ " 1 N1 0.0000 0.0000 0.0000 N.am 1 <1> -0.2782\n"
+ " 2 H1 0.0000 0.0000 0.0000 H 1 <1> 0.1552\n"
+ " 3 C1 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0886\n"
+ " 4 C2 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1500\n"
+ " 5 C3 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0714\n"
+ " 6 C4 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0456\n"
+ " 7 C5 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0788\n"
+ " 8 C6 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1435\n"
+ " 9 C7 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0342\n"
+ " 10 C8 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1346\n"
+ " 11 O1 0.0000 0.0000 0.0000 O.3 1 <1> -0.5057\n"
+ " 12 H2 0.0000 0.0000 0.0000 H 1 <1> 0.2922\n"
+ " 13 C9 0.0000 0.0000 0.0000 C.3 1 <1> -0.0327\n"
+ " 14 H3 0.0000 0.0000 0.0000 H 1 <1> 0.0280\n"
+ " 15 H4 0.0000 0.0000 0.0000 H 1 <1> 0.0280\n"
+ " 16 H5 0.0000 0.0000 0.0000 H 1 <1> 0.0280\n"
+ " 17 O2 0.0000 0.0000 0.0000 O.3 1 <1> -0.4436\n"
+ " 18 C10 0.0000 0.0000 0.0000 C.3 1 <1> 0.3143\n"
+ " 19 O3 0.0000 0.0000 0.0000 O.2 1 <1> -0.4528\n"
+ " 20 C11 0.0000 0.0000 0.0000 C.2 1 <1> 0.0882\n"
+ " 21 H6 0.0000 0.0000 0.0000 H 1 <1> 0.1022\n"
+ " 22 C12 0.0000 0.0000 0.0000 C.2 1 <1> -0.0208\n"
+ " 23 H7 0.0000 0.0000 0.0000 H 1 <1> 0.0628\n"
+ " 24 C13 0.0000 0.0000 0.0000 C.3 1 <1> 0.0854\n"
+ " 25 H8 0.0000 0.0000 0.0000 H 1 <1> 0.0645\n"
+ " 26 C14 0.0000 0.0000 0.0000 C.3 1 <1> 0.0236\n"
+ " 27 H9 0.0000 0.0000 0.0000 H 1 <1> 0.0362\n"
+ " 28 C15 0.0000 0.0000 0.0000 C.3 1 <1> 0.1131\n"
+ " 29 H10 0.0000 0.0000 0.0000 H 1 <1> 0.0741\n"
+ " 30 C16 0.0000 0.0000 0.0000 C.3 1 <1> 0.0200\n"
+ " 31 H11 0.0000 0.0000 0.0000 H 1 <1> 0.0359\n"
+ " 32 C17 0.0000 0.0000 0.0000 C.3 1 <1> 0.0661\n"
+ " 33 H12 0.0000 0.0000 0.0000 H 1 <1> 0.0600\n"
+ " 34 C18 0.0000 0.0000 0.0000 C.3 1 <1> 0.0091\n"
+ " 35 H13 0.0000 0.0000 0.0000 H 1 <1> 0.0348\n"
+ " 36 C19 0.0000 0.0000 0.0000 C.3 1 <1> 0.0661\n"
+ " 37 H14 0.0000 0.0000 0.0000 H 1 <1> 0.0602\n"
+ " 38 C20 0.0000 0.0000 0.0000 C.3 1 <1> 0.0009\n"
+ " 39 H15 0.0000 0.0000 0.0000 H 1 <1> 0.0365\n"
+ " 40 C21 0.0000 0.0000 0.0000 C.2 1 <1> -0.0787\n"
+ " 41 H16 0.0000 0.0000 0.0000 H 1 <1> 0.0576\n"
+ " 42 C22 0.0000 0.0000 0.0000 C.2 1 <1> -0.0649\n"
+ " 43 H17 0.0000 0.0000 0.0000 H 1 <1> 0.0615\n"
+ " 44 C23 0.0000 0.0000 0.0000 C.2 1 <1> -0.0542\n"
+ " 45 H18 0.0000 0.0000 0.0000 H 1 <1> 0.0622\n"
+ " 46 C24 0.0000 0.0000 0.0000 C.2 1 <1> 0.0115\n"
+ " 47 C25 0.0000 0.0000 0.0000 C.2 1 <1> 0.2441\n"
+ " 48 O4 0.0000 0.0000 0.0000 O.2 1 <1> -0.2702\n"
+ " 49 C26 0.0000 0.0000 0.0000 C.3 1 <1> -0.0348\n"
+ " 50 H19 0.0000 0.0000 0.0000 H 1 <1> 0.0279\n"
+ " 51 H20 0.0000 0.0000 0.0000 H 1 <1> 0.0279\n"
+ " 52 H21 0.0000 0.0000 0.0000 H 1 <1> 0.0279\n"
+ " 53 C27 0.0000 0.0000 0.0000 C.3 1 <1> -0.0566\n"
+ " 54 H22 0.0000 0.0000 0.0000 H 1 <1> 0.0236\n"
+ " 55 H23 0.0000 0.0000 0.0000 H 1 <1> 0.0236\n"
+ " 56 H24 0.0000 0.0000 0.0000 H 1 <1> 0.0236\n"
+ " 57 O5 0.0000 0.0000 0.0000 O.3 1 <1> -0.3909\n"
+ " 58 H25 0.0000 0.0000 0.0000 H 1 <1> 0.2098\n"
+ " 59 C28 0.0000 0.0000 0.0000 C.3 1 <1> -0.0577\n"
+ " 60 H26 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 61 H27 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 62 H28 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 63 O6 0.0000 0.0000 0.0000 O.3 1 <1> -0.3910\n"
+ " 64 H29 0.0000 0.0000 0.0000 H 1 <1> 0.2098\n"
+ " 65 C29 0.0000 0.0000 0.0000 C.3 1 <1> -0.0567\n"
+ " 66 H30 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 67 H31 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 68 H32 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 69 O7 0.0000 0.0000 0.0000 O.3 1 <1> -0.4608\n"
+ " 70 C30 0.0000 0.0000 0.0000 C.2 1 <1> 0.3042\n"
+ " 71 O8 0.0000 0.0000 0.0000 O.2 1 <1> -0.2512\n"
+ " 72 C31 0.0000 0.0000 0.0000 C.3 1 <1> 0.0332\n"
+ " 73 H33 0.0000 0.0000 0.0000 H 1 <1> 0.0342\n"
+ " 74 H34 0.0000 0.0000 0.0000 H 1 <1> 0.0342\n"
+ " 75 H35 0.0000 0.0000 0.0000 H 1 <1> 0.0342\n"
+ " 76 C32 0.0000 0.0000 0.0000 C.3 1 <1> -0.0564\n"
+ " 77 H36 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 78 H37 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 79 H38 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 80 O9 0.0000 0.0000 0.0000 O.3 1 <1> -0.3753\n"
+ " 81 C33 0.0000 0.0000 0.0000 C.3 1 <1> 0.0372\n"
+ " 82 H39 0.0000 0.0000 0.0000 H 1 <1> 0.0524\n"
+ " 83 H40 0.0000 0.0000 0.0000 H 1 <1> 0.0524\n"
+ " 84 H41 0.0000 0.0000 0.0000 H 1 <1> 0.0524\n"
+ " 85 C34 0.0000 0.0000 0.0000 C.2 1 <1> 0.2505\n"
+ " 86 O10 0.0000 0.0000 0.0000 O.2 1 <1> -0.2836\n"
+ " 87 C35 0.0000 0.0000 0.0000 C.3 1 <1> 0.0210\n"
+ " 88 H42 0.0000 0.0000 0.0000 H 1 <1> 0.0309\n"
+ " 89 H43 0.0000 0.0000 0.0000 H 1 <1> 0.0309\n"
+ " 90 H44 0.0000 0.0000 0.0000 H 1 <1> 0.0309\n"
+ " 91 C36 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1361\n"
+ " 92 C37 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0613\n"
+ " 93 C38 0.0000 0.0000 0.0000 C.2 1 <1> 0.0580\n"
+ " 94 H45 0.0000 0.0000 0.0000 H 1 <1> 0.0853\n"
+ " 95 N2 0.0000 0.0000 0.0000 N.2 1 <1> -0.1915\n"
+ " 96 N3 0.0000 0.0000 0.0000 N.pl3 1 <1> -0.2525\n"
+ " 97 C39 0.0000 0.0000 0.0000 C.3 1 <1> 0.0525\n"
+ " 98 C40 0.0000 0.0000 0.0000 C.3 1 <1> -0.0271\n"
+ " 99 H46 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 100 H47 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 101 C41 0.0000 0.0000 0.0000 C.3 1 <1> -0.0385\n"
+ " 102 H48 0.0000 0.0000 0.0000 H 1 <1> 0.0302\n"
+ " 103 C42 0.0000 0.0000 0.0000 C.3 1 <1> -0.0472\n"
+ " 104 H49 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 105 H50 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 106 C43 0.0000 0.0000 0.0000 C.3 1 <1> -0.0385\n"
+ " 107 H51 0.0000 0.0000 0.0000 H 1 <1> 0.0302\n"
+ " 108 C44 0.0000 0.0000 0.0000 C.3 1 <1> -0.0271\n"
+ " 109 H52 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 110 H53 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 111 C45 0.0000 0.0000 0.0000 C.3 1 <1> -0.0472\n"
+ " 112 H54 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 113 H55 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 114 C46 0.0000 0.0000 0.0000 C.3 1 <1> -0.0385\n"
+ " 115 H56 0.0000 0.0000 0.0000 H 1 <1> 0.0302\n"
+ " 116 C47 0.0000 0.0000 0.0000 C.3 1 <1> -0.0271\n"
+ " 117 H57 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 118 H58 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 119 C48 0.0000 0.0000 0.0000 C.3 1 <1> -0.0472\n"
+ " 120 H59 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 121 H60 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 122 C49 0.0000 0.0000 0.0000 C.3 1 <1> 0.0189\n"
+ " 123 H61 0.0000 0.0000 0.0000 H 1 <1> 0.0444\n"
+ " 124 H62 0.0000 0.0000 0.0000 H 1 <1> 0.0444\n"
+ " 125 H63 0.0000 0.0000 0.0000 H 1 <1> 0.0444\n"
+ " 126 O11 0.0000 0.0000 0.0000 O.3 1 <1> -0.5054\n"
+ " 127 H64 0.0000 0.0000 0.0000 H 1 <1> 0.2922\n"
+ " 128 O12 0.0000 0.0000 0.0000 O.3 1 <1> -0.5042\n"
+ " 129 H65 0.0000 0.0000 0.0000 H 1 <1> 0.2923\n" + "@<TRIPOS>BOND\n"
+ " 1 1 2 1\n" + " 2 1 3 1\n" + " 3 3 4 ar\n"
+ " 4 4 5 ar\n" + " 5 5 6 ar\n" + " 6 6 7 ar\n"
+ " 7 7 8 ar\n" + " 8 8 9 ar\n" + " 9 9 10 ar\n"
+ " 10 5 10 ar\n" + " 11 10 11 1\n" + " 12 11 12 1\n"
+ " 13 9 13 1\n" + " 14 13 14 1\n" + " 15 13 15 1\n"
+ " 16 13 16 1\n" + " 17 8 17 1\n" + " 18 17 18 1\n"
+ " 19 18 19 1\n" + " 20 19 20 1\n" + " 21 20 21 1\n"
+ " 22 20 22 2\n" + " 23 22 23 1\n" + " 24 22 24 1\n"
+ " 25 24 25 1\n" + " 26 24 26 1\n" + " 27 26 27 1\n"
+ " 28 26 28 1\n" + " 29 28 29 1\n" + " 30 28 30 1\n"
+ " 31 30 31 1\n" + " 32 30 32 1\n" + " 33 32 33 1\n"
+ " 34 32 34 1\n" + " 35 34 35 1\n" + " 36 34 36 1\n"
+ " 37 36 37 1\n" + " 38 36 38 1\n" + " 39 38 39 1\n"
+ " 40 38 40 1\n" + " 41 40 41 1\n" + " 42 40 42 2\n"
+ " 43 42 43 1\n" + " 44 42 44 1\n" + " 45 44 45 1\n"
+ " 46 44 46 2\n" + " 47 46 47 1\n" + " 48 1 47 am\n"
+ " 49 47 48 2\n" + " 50 46 49 1\n" + " 51 49 50 1\n"
+ " 52 49 51 1\n" + " 53 49 52 1\n" + " 54 38 53 1\n"
+ " 55 53 54 1\n" + " 56 53 55 1\n" + " 57 53 56 1\n"
+ " 58 36 57 1\n" + " 59 57 58 1\n" + " 60 34 59 1\n"
+ " 61 59 60 1\n" + " 62 59 61 1\n" + " 63 59 62 1\n"
+ " 64 32 63 1\n" + " 65 63 64 1\n" + " 66 30 65 1\n"
+ " 67 65 66 1\n" + " 68 65 67 1\n" + " 69 65 68 1\n"
+ " 70 28 69 1\n" + " 71 69 70 1\n" + " 72 70 71 2\n"
+ " 73 70 72 1\n" + " 74 72 73 1\n" + " 75 72 74 1\n"
+ " 76 72 75 1\n" + " 77 26 76 1\n" + " 78 76 77 1\n"
+ " 79 76 78 1\n" + " 80 76 79 1\n" + " 81 24 80 1\n"
+ " 82 80 81 1\n" + " 83 81 82 1\n" + " 84 81 83 1\n"
+ " 85 81 84 1\n" + " 86 18 85 1\n" + " 87 7 85 1\n"
+ " 88 85 86 2\n" + " 89 18 87 1\n" + " 90 87 88 1\n"
+ " 91 87 89 1\n" + " 92 87 90 1\n" + " 93 6 91 ar\n"
+ " 94 91 92 ar\n" + " 95 3 92 ar\n" + " 96 92 93 1\n"
+ " 97 93 94 1\n" + " 98 93 95 2\n" + " 99 95 96 1\n"
+ " 100 96 97 1\n" + " 101 97 98 1\n" + " 102 98 99 1\n"
+ " 103 98 100 1\n" + " 104 98 101 1\n" + " 105 101 102 1\n"
+ " 106 101 103 1\n" + " 107 103 104 1\n" + " 108 103 105 1\n"
+ " 109 103 106 1\n" + " 110 106 107 1\n" + " 111 106 108 1\n"
+ " 112 108 109 1\n" + " 113 108 110 1\n" + " 114 97 108 1\n"
+ " 115 106 111 1\n" + " 116 111 112 1\n" + " 117 111 113 1\n"
+ " 118 111 114 1\n" + " 119 114 115 1\n" + " 120 114 116 1\n"
+ " 121 116 117 1\n" + " 122 116 118 1\n" + " 123 97 116 1\n"
+ " 124 114 119 1\n" + " 125 119 120 1\n" + " 126 119 121 1\n"
+ " 127 101 119 1\n" + " 128 96 122 1\n" + " 129 122 123 1\n"
+ " 130 122 124 1\n" + " 131 122 125 1\n" + " 132 91 126 1\n"
+ " 133 126 127 1\n" + " 134 4 128 1\n" + " 135 128 129 1\n";
IChemModel model;
using (var r = new Mol2Reader(new StringReader(problematicMol2)))
{
model = (IChemModel)r.Read(CDK.Builder.NewChemModel());
}
Assert.IsNotNull(model);
var containers = ChemModelManipulator.GetAllAtomContainers(model);
Assert.AreEqual(1, containers.Count());
var molecule = containers.FirstOrDefault();
Assert.IsNotNull(molecule);
Assert.AreEqual(129, molecule.Atoms.Count);
Assert.AreEqual(135, molecule.Bonds.Count);
foreach (var atom in molecule.Atoms)
{
Assert.IsNotNull(atom.AtomTypeName);
}
}
