private void WriteChemFile(IChemFile file)
{
foreach (var container in ChemFileManipulator.GetAllAtomContainers(file))
{
WriteMolecule(container);
}
}
public void Test2Dvs3D()
{
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles("O1C2C34C(C(C1O)CCCc1cc(cc(c1)C(F)(F)F)C(F)(F)F)CCC(C3CCC(O2)(OO4)C)C");
AddExplicitHydrogens(mol);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
double value2D = CreateDescriptor().Calculate(mol).Value;
var filename = "NCDK.Data.MDL.cpsa-uncharged.sdf";
IChemFile content;
using (var reader = new MDLV2000Reader(ResourceLoader.GetAsStream(filename)))
{
content = reader.Read(CDK.Builder.NewChemFile());
}
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
mol = cList[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var value3D = CreateDescriptor().Calculate(mol).Value;
Assert.AreEqual(value2D, value3D, 0.001);
}
public void TestSulfurCompound_ImplicitHydrogens()
{
var filename = "NCDK.Data.MDL.sulfurCompound.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
Assert.AreEqual(1, containersList.Count);
var atomContainer_0 = (IAtomContainer)containersList[0];
Assert.AreEqual(10, atomContainer_0.Atoms.Count);
var sulfur = atomContainer_0.Atoms[1];
FindAndConfigureAtomTypesForAllAtoms(atomContainer_0);
adder.AddImplicitHydrogens(atomContainer_0);
Assert.AreEqual("S", sulfur.Symbol);
Assert.IsNotNull(sulfur.ImplicitHydrogenCount);
Assert.AreEqual(0, sulfur.ImplicitHydrogenCount.Value);
Assert.AreEqual(3, atomContainer_0.GetConnectedBonds(sulfur).Count());
Assert.AreEqual(10, atomContainer_0.Atoms.Count);
Assert.IsNotNull(sulfur.ImplicitHydrogenCount);
Assert.AreEqual(0, sulfur.ImplicitHydrogenCount.Value);
Assert.AreEqual(3, atomContainer_0.GetConnectedBonds(sulfur).Count());
}
public void TestBug1274()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol-multipleBondStereo.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// we check here that the charContent is not used and also that more then
// one stereo isn't set
Assert.AreEqual(BondStereo.None, container.Bonds[0].Stereo, "expected non-stereo bond");
Assert.AreEqual(BondStereo.Down, container.Bonds[1].Stereo, "expected Hatch (Down) Bond");
Assert.AreEqual(BondStereo.None, container.Bonds[2].Stereo, "expected non-stereo bond");
}
finally
{
reader.Close();
}
}
public void TestBug1245()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
foreach (var atom in container.Atoms)
{
Assert.AreEqual(
PeriodicTable.GetAtomicNumber(atom.Symbol),
atom.AtomicNumber,
"Incorrect atomic number");
}
}
finally
{
reader.Close();
}
}
public void TestBug1275()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol-malformedDictRef.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// we check here that the malformed dictRef doesn't throw an exception
Assert.AreEqual(BondStereo.None, container.Bonds[0].Stereo, "expected non-stereo bond");
Assert.AreEqual(BondStereo.Up, container.Bonds[1].Stereo, "expected Wedge (Up) Bond");
Assert.AreEqual(BondStereo.None, container.Bonds[2].Stereo, "expected non-stereo bond");
}
finally
{
reader.Close();
}
}
public void TestExtraEigenvalues()
{
var filename = "NCDK.Data.HIN.gravindex.hin";
IChemFile content;
using (var reader = new HINReader(ResourceLoader.GetAsStream(filename)))
{
content = reader.Read(CDK.Builder.NewChemFile());
}
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
var ac = cList[0];
var descriptor = CreateDescriptor(true);
var descriptorValue = descriptor.Calculate(ac, 0, 25);
var retval = descriptorValue.Values;
int nheavy = 20;
Assert.AreEqual(75, retval.Count);
foreach (var v in retval)
{
Assert.IsTrue(v != double.NaN);
}
for (int i = nheavy; i < nheavy + 5; i++)
{
Assert.IsTrue(double.IsNaN(retval[i]), "Extra eigenvalue should have been NaN");
}
}
public void TestBug1248()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
IBond bond = container.Bonds[2];
Assert.IsNotNull(bond, "Null bond");
Assert.AreEqual(BondStereo.Up, bond.Stereo, "Expected Wedge (Up) Bond");
}
finally
{
reader.Close();
}
}
public void TestSmilesFiles()
{
var atomTypeMatcher = CDK.AtomTypeMatcher;
// Read the first file
var filename = "NCDK.Data.CML.smiles1.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
IAtomContainer mol1 = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
// Read the second file
filename = "NCDK.Data.CML.smiles2.cml";
ins = ResourceLoader.GetAsStream(filename);
reader = new CMLReader(ins);
chemFile = reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
IAtomContainer mol2 = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
var types1 = atomTypeMatcher.FindMatchingAtomTypes(mol1).ToReadOnlyList();
var types2 = atomTypeMatcher.FindMatchingAtomTypes(mol2).ToReadOnlyList();
for (int i = 0; i < mol1.Atoms.Count; i++)
{
Assert.IsNotNull(types1[i], "Atom typing in mol1 failed for atom " + (i + 1));
Assert.IsNotNull(types2[i], "Atom typing in mol2 failed for atom " + (i + 1));
Assert.AreEqual(types1[i].AtomTypeName, types2[i].AtomTypeName,
"Atom type mismatch for the " + (i + 1) + " atom");
}
}
public void TestFindHeavyAtomsInChain_IAtomContainer_IAtomContainer()
{
var filename = "NCDK.Data.MDL.allmol232.mol";
var ins = ResourceLoader.GetAsStream(filename);
// TODO: shk3-cleanuptests: best to use the STRICT IO mode here
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile);
var ac = new Silent.AtomContainer(containersList.First());
AddExplicitHydrogens(ac);
var chain = ac.Builder.NewAtomContainer();
for (int i = 16; i < 25; i++)
{
chain.Atoms.Add(ac.Atoms[i]);
}
chain.Atoms.Add(ac.Atoms[29]);
chain.Atoms.Add(ac.Atoms[30]);
int[] result = new AtomPlacer3D().FindHeavyAtomsInChain(ac, chain);
Assert.AreEqual(16, result[0]);
Assert.AreEqual(11, result[1]);
}
public void TestSFBug1085912_1()
{
string cmlContent = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>"
+ "<molecule convention=\"PDB\" dictRef=\"pdb:model\" xmlns=\"http://www.xml-cml.org/schema\">"
+ " <molecule dictRef=\"pdb:sequence\" id=\"ALAA116\">"
+ " <atomArray>"
+ " <atom id=\"a9794931\" elementType=\"N\" x3=\"-10.311\" y3=\"2.77\" z3=\"-9.837\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a5369354\" elementType=\"C\" x3=\"-9.75\" y3=\"4.026\" z3=\"-9.35\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a14877152\" elementType=\"C\" x3=\"-10.818\" y3=\"5.095\" z3=\"-9.151\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a26221736\" elementType=\"O\" x3=\"-11.558\" y3=\"5.433\" z3=\"-10.074\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a4811470\" elementType=\"C\" x3=\"-8.678\" y3=\"4.536\" z3=\"-10.304\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a211489\" elementType=\"H\" x3=\"-10.574\" y3=\"2.695\" z3=\"-10.778\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a31287617\" elementType=\"H\" x3=\"-9.279\" y3=\"3.829\" z3=\"-8.398\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a19487109\" elementType=\"H\" x3=\"-8.523\" y3=\"3.813\" z3=\"-11.09\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a28589522\" elementType=\"H\" x3=\"-8.994\" y3=\"5.477\" z3=\"-10.737\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a4638116\" elementType=\"H\" x3=\"-7.754\" y3=\"4.682\" z3=\"-9.763\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>" + " </atomArray>" + " </molecule>" + "</molecule>";
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlContent)));
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// OK, now test that the residue identifier is properly read
Assert.AreEqual("ALAA116", container.Id);
}
finally
{
reader.Close();
}
}
public void TestAlign()
{
{
IAtomContainer ac;
var filename = "NCDK.Data.HIN.gravindex.hin";
var ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = new HINReader(ins);
ChemFile content = (ChemFile)reader.Read((ChemObject) new ChemFile());
var cList = ChemFileManipulator.GetAllAtomContainers(content);
ac = cList.First();
KabschAlignment ka = new KabschAlignment(ac, ac);
Assert.IsNotNull(ka);
ka.Align();
double rmsd = ka.RMSD;
Assert.IsTrue(1e-8 > rmsd);
Assert.IsNotNull(ka.RotationMatrix);
}
{
double[][] p1 = new[] { new[] { 16.754, 20.462, 45.049 }, new[] { 19.609, 18.145, 46.011 }, new[] { 17.101, 17.256, 48.707 },
new[] { 13.963, 18.314, 46.820 }, new[] { 14.151, 15.343, 44.482 }, new[] { 14.959, 12.459, 46.880 }, new[] { 11.987, 13.842, 48.862 },
new[] { 9.586, 12.770, 46.123 }, new[] { 11.006, 9.245, 46.116 }, new[] { 10.755, 9.090, 49.885 } };
double[][] p2 = new[] { new[] { 70.246, 317.510, 188.263 }, new[] { 73.457, 317.369, 190.340 }, new[] { 71.257, 318.976, 193.018 },
new[] { 68.053, 317.543, 191.651 }, new[] { 68.786, 313.954, 192.637 }, new[] { 70.248, 314.486, 196.151 },
new[] { 67.115, 316.584, 196.561 }, new[] { 64.806, 313.610, 196.423 }, new[] { 66.804, 311.735, 199.035 },
new[] { 66.863, 314.832, 201.113 } };
Atom[] a1 = new Atom[10];
Atom[] a2 = new Atom[10];
for (int i = 0; i < 10; i++)
{
a1[i] = new Atom("C");
Vector3 newCoord = new Vector3
{
X = p1[i][0],
Y = p1[i][1],
Z = p1[i][2]
};
a1[i].Point3D = newCoord;
a2[i] = new Atom("C");
newCoord = new Vector3
{
X = p2[i][0],
Y = p2[i][1],
Z = p2[i][2]
};
a2[i].Point3D = newCoord;
}
var ka = new KabschAlignment(a1, a2);
ka.Align();
var rmsd = ka.RMSD;
Assert.AreEqual(0.13479726, rmsd, 0.00000001);
}
}
public void TestBug2846213()
{
var filename = "NCDK.Data.MDL.bug2846213.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
ChemFile chemFile = (ChemFile)reader.Read((ChemObject) new ChemFile());
IAtomContainer ac = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
long[] morganNumbers = MorganNumbersTools.GetMorganNumbers(ac);
Assert.IsFalse(morganNumbers[7] == morganNumbers[8]);
}
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");
}
private IAtomContainer LoadMolecule(string path)
{
var ins = ResourceLoader.GetAsStream(path);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
return((IAtomContainer)containersList[0]);
}
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 TestAromaticRingsLine()
{
var filename = "NCDK.Data.HIN.bug2984581.hin";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new HINReader(ins);
var content = reader.Read(builder.NewChemFile());
reader.Close();
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
Assert.AreEqual(1, cList.Count);
}
public void TestWeightedPathDescriptor()
{
var sp = CDK.SmilesParser;
{
var mol = sp.ParseSmiles("CCCC");
var result = CreateDescriptor().Calculate(mol);
var values = result.Values;
Assert.AreEqual(6.871320, values[0], 0.000001);
Assert.AreEqual(1.717830, values[1], 0.000001);
Assert.AreEqual(0.0, values[2], 0.000001);
Assert.AreEqual(0.0, values[3], 0.000001);
Assert.AreEqual(0.0, values[4], 0.000001);
}
{
var filename = "NCDK.Data.MDL.wpo.sdf";
IChemFile content;
using (var reader = new MDLV2000Reader(ResourceLoader.GetAsStream(filename)))
{
content = reader.Read(CDK.Builder.NewChemFile());
}
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
var mol = cList[0];
mol = AtomContainerManipulator.RemoveHydrogens(mol);
var result = CreateDescriptor().Calculate(mol);
var values = result.Values;
Assert.AreEqual(18.42026, values[0], 0.00001);
Assert.AreEqual(1.842026, values[1], 0.00001);
Assert.AreEqual(13.45733, values[2], 0.00001);
Assert.AreEqual(13.45733, values[3], 0.00001);
Assert.AreEqual(0, values[4], 0.00001);
}
{
var filename = "NCDK.Data.MDL.wpn.sdf";
IChemFile content;
using (var reader = new MDLV2000Reader(ResourceLoader.GetAsStream(filename)))
{
content = reader.Read(CDK.Builder.NewChemFile());
}
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
var mol = cList[0];
mol = AtomContainerManipulator.RemoveHydrogens(mol);
var result = CreateDescriptor().Calculate(mol);
var values = result.Values;
Assert.AreEqual(26.14844, values[0], 0.00001);
Assert.AreEqual(1.867746, values[1], 0.00001);
Assert.AreEqual(19.02049, values[2], 0.00001);
Assert.AreEqual(0, values[3], 0.000001);
Assert.AreEqual(19.02049, values[4], 0.00001);
}
}
public void Properties()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.bug1356.sdf");
var reader = new MDLReader(ins);
var chemfile = builder.NewChemFile();
chemfile = reader.Read(chemfile);
var container = ChemFileManipulator.GetAllAtomContainers(chemfile).First();
Assert.IsNotNull(container.GetProperty <object>("first"));
Assert.IsNotNull(container.GetProperty <object>("second"));
reader.Close();
}
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());
reader.Close();
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
var ac = cList[0];
Assert.AreEqual(57, ac.Atoms.Count);
Assert.AreEqual(59, ac.Bonds.Count);
}
public void TestBCUT()
{
var filename = "NCDK.Data.HIN.gravindex.hin";
IChemFile content;
using (var reader = new HINReader(ResourceLoader.GetAsStream(filename)))
{
content = reader.Read(CDK.Builder.NewChemFile());
}
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
var ac = cList[0];
var descriptor = CreateDescriptor(true);
var descriptorValue = descriptor.Calculate(ac, 2, 2);
var retval = descriptorValue.Values;
Assert.IsNotNull(retval);
foreach (var v in retval)
{
Assert.IsTrue(Math.Abs(0.0 - v) > 0.0000001, "The returned value must be non-zero");
}
var names = descriptorValue.Keys;
foreach (var name in names)
{
Assert.IsNotNull(name);
}
// Assert.AreEqual(1756.5060703860984,
// ((Double)retval[0]).Value, 0.00000001);
// Assert.AreEqual(41.91069159994975,
// ((Double)retval[1]).Value, 0.00000001);
// Assert.AreEqual(12.06562671430088,
// ((Double)retval[2]).Value, 0.00000001);
// Assert.AreEqual(1976.6432599699767,
// ((Double)retval[3]).Value, 0.00000001);
// Assert.AreEqual(44.45945636161082,
// ((Double)retval[4]).Value, 0.00000001);
// Assert.AreEqual(12.549972243701887,
// ((Double)retval[5]).Value, 0.00000001);
// Assert.AreEqual(4333.097373073368,
// ((Double)retval[6]).Value, 0.00000001);
// Assert.AreEqual(65.82626658920714,
// ((Double)retval[7]).Value, 0.00000001);
// Assert.AreEqual(16.302948232909483,
// ((Double)retval[8]).Value, 0.00000001);
}
public void TestFile3()
{
var filename = "NCDK.Data.CML.3.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
IAtomContainer mol = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
string[] expectedTypes = { "C.sp2", "N.sp2", "C.sp2", "N.sp3", "C.sp2", "N.sp2", "O.sp3", "C.sp2", "C.sp2",
"C.sp2" };
AssertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
public void TestBug3141611()
{
var filename = "NCDK.Data.MDL.error.sdf";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
IAtomContainer mol = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
string[] expectedTypes = { "C.sp3", "C.sp2", "O.sp2", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "P.ate", "O.sp2",
"O.minus" };
AssertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
public void TestModelBuilder3D_bug_1241421()
{
var mb3d = ModelBuilder3D.GetInstance();
var filename = "NCDK.Data.MDL.bug1241421.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
IAtomContainer ac = new Silent.AtomContainer(containersList[0]);
ac = mb3d.Generate3DCoordinates(ac, false);
CheckAverageBondLength(ac);
}
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 TestCMLTestCase()
{
var filename = "NCDK.Data.CML.olaCmlAtomType.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = builder.NewChemFile();
chemFile = (IChemFile)reader.Read(chemFile);
reader.Close();
var container = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
foreach (var atom in container.Atoms)
{
Assert.AreEqual(null, atom.ImplicitHydrogenCount);
}
}
public void TestCranbinSurface()
{
var bldr = CDK.Builder;
IChemFile chemFile;
var path = "NCDK.Data.PDB.1CRN.pdb";
using (var pdbr = new PDBReader(ResourceLoader.GetAsStream(path)))
{
chemFile = pdbr.Read(bldr.NewChemFile());
var mol = ChemFileManipulator.GetAllAtomContainers(chemFile).ElementAt(0);
var surface = new NumericalSurface(mol);
var map = surface.GetAtomSurfaceMap();
Assert.AreEqual(222, map.Count);
Assert.AreEqual(327, mol.Atoms.Count);
}
}
public void TestMixedNamespaces()
{
var ins = ResourceLoader.GetAsStream(this.GetType(), "US06358966-20020319-C00001-enr.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.AreEqual(34, ChemFileManipulator.GetAtomCount(cfile));
Assert.AreEqual(39, ChemFileManipulator.GetBondCount(cfile));
}
finally
{
reader.Close();
}
}
public void TestAtomProperties()
{
var filename = "NCDK.Data.CML.custompropertiestest.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
ChemFile chemFile = (ChemFile)reader.Read((ChemFile) new ChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
IAtomContainer container = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
for (int i = 0; i < container.Atoms.Count; i++)
{
Assert.AreEqual(2, container.Atoms[i].GetProperties().Count);
}
}
public void Testbug2917084()
{
string filename1 = "NCDK.Data.MDL.boronBuckyBall.mol";
Trace.TraceInformation("Testing: " + filename1);
var ins1 = ResourceLoader.GetAsStream(filename1);
var reader = new MDLV2000Reader(ins1, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
var mol = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
Fingerprinter fingerprinter = new Fingerprinter(1024, 8);
Assert.IsNotNull(fingerprinter.GetBitFingerprint(mol));
}
