public void TestSalt()
{
var filename = "NCDK.Data.CML.COONa.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
//Debug.WriteLine($"NO sequences: {chemFile.Count}");
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
//Debug.WriteLine($"NO models: {seq.Count}");
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(1, model.MoleculeSet.Count);
// test the molecule
IAtomContainer mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual(4, mol.Atoms.Count);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
}
public void TestAceticAcid()
{
var filename = "NCDK.Data.PMP.aceticacid.pmp";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new PMPReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
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 crystal = model.Crystal;
Assert.IsNotNull(crystal);
Assert.AreEqual(32, crystal.Atoms.Count);
Assert.AreEqual(28, crystal.Bonds.Count);
Assert.AreEqual("O", crystal.Atoms[6].Symbol);
Assert.AreEqual(1.4921997, crystal.Atoms[6].Point3D.Value.X, 0.00001);
Assert.AreEqual("O", crystal.Atoms[7].Symbol);
Assert.AreEqual(1.4922556, crystal.Atoms[7].Point3D.Value.X, 0.00001);
}
public void TestGuanine()
{
var filename = "NCDK.Data.InChI.guanine.inchi";
Trace.TraceInformation("Testing: ", filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new InChIPlainTextReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
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 moleculeSet = model.MoleculeSet;
Assert.IsNotNull(moleculeSet);
var molecule = moleculeSet[0];
Assert.IsNotNull(molecule);
Assert.AreEqual(11, molecule.Atoms.Count);
Assert.AreEqual(12, molecule.Bonds.Count);
}
public void SetUp()
{
molecule1 = builder.NewAtomContainer();
atomInMol1 = builder.NewAtom("Cl");
molecule1.Atoms.Add(atomInMol1);
molecule1.Atoms.Add(builder.NewAtom("Cl"));
bondInMol1 = builder.NewBond(atomInMol1, molecule1.Atoms[1]);
molecule1.Bonds.Add(bondInMol1);
molecule2 = builder.NewAtomContainer();
atomInMol2 = builder.NewAtom("O");
atomInMol2.ImplicitHydrogenCount = 2;
molecule2.Atoms.Add(atomInMol2);
moleculeSet = builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Add(molecule1);
moleculeSet.Add(molecule2);
reaction = builder.NewReaction();
reaction.Reactants.Add(molecule1);
reaction.Products.Add(molecule2);
reactionSet = builder.NewReactionSet();
reactionSet.Add(reaction);
chemModel = builder.NewChemModel();
chemModel.MoleculeSet = moleculeSet;
chemModel.ReactionSet = reactionSet;
chemSequence1 = builder.NewChemSequence();
chemSequence1.Add(chemModel);
chemSequence2 = builder.NewChemSequence();
chemFile = builder.NewChemFile();
chemFile.Add(chemSequence1);
chemFile.Add(chemSequence2);
}
public void TestCuran()
{
var filename = "NCDK.Data.CML.curan.xml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(model.MoleculeSet.Count, 1);
// test the molecule
IAtomContainer mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual(mol.Atoms.Count, 24);
Assert.AreEqual(mol.Bonds.Count, 28);
Assert.IsFalse(GeometryUtil.Has3DCoordinates(mol));
Assert.IsTrue(GeometryUtil.Has2DCoordinates(mol));
}
/// <summary>
/// Convert a Molecule to CML and back to a Molecule again.
/// Given that CML reading is working, the problem is with the CMLWriter.
/// </summary>
/// <param name="convertor"></param>
/// <param name="mol"></param>
/// <returns></returns>
/// <seealso cref="CMLFragmentsTest"/>
public static IAtomContainer RoundTripMolecule(Convertor convertor, IAtomContainer mol)
{
string cmlString = "<!-- failed -->";
var cmlDOM = convertor.CDKAtomContainerToCMLMolecule(mol);
cmlString = cmlDOM.ToString();
Debug.WriteLine("CML string: ", cmlString);
IChemFile file;
using (var reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlString))))
{
file = (IChemFile)reader.Read(builder.NewChemFile());
}
Assert.IsNotNull(file);
Assert.AreEqual(1, file.Count);
IChemSequence sequence = file[0];
Assert.IsNotNull(sequence);
Assert.AreEqual(1, sequence.Count);
IChemModel chemModel = sequence[0];
Assert.IsNotNull(chemModel);
var moleculeSet = chemModel.MoleculeSet;
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(1, moleculeSet.Count);
var roundTrippedMol = moleculeSet[0];
Assert.IsNotNull(roundTrippedMol);
return(roundTrippedMol);
}
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 TestSFBug1085912_1()
{
string filename_pdb = "NCDK.Data.PDB.1CKV.pdb";
var ins1 = ResourceLoader.GetAsStream(this.GetType(), filename_pdb);
ISimpleChemObjectReader reader = new PDBReader(ins1);
IChemFile chemFile1 = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
IChemSequence seq1 = chemFile1[0];
IChemModel model1 = seq1[0];
IAtomContainer container = model1.MoleculeSet[0];
IBioPolymer polymer1 = (IBioPolymer)container;
int countchemFile1 = chemFile1.Count;
int countmodel1 = model1.MoleculeSet.Count;
int countpolymer1 = polymer1.Atoms.Count;
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer1);
cmlWriter.Close();
string cmlContent1 = writer.ToString();
CMLReader reader2 = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlContent1)));
var chemFil2 = reader2.Read(builder.NewChemFile());
reader2.Close();
IChemSequence seq2 = chemFil2[0];
IChemModel model2 = seq2[0];
var polymer2 = (IPDBPolymer)model2.MoleculeSet[0];
int countchemFile2 = chemFil2.Count;
int countmodel2 = model2.MoleculeSet.Count;
int countpolymer2 = polymer2.Atoms.Count;
Assert.AreEqual(countchemFile1, countchemFile2);
Assert.AreEqual(countmodel1, countmodel2);
Assert.AreEqual(countpolymer1, countpolymer2);
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer2);
cmlWriter.Close();
string cmlContent2 = writer.ToString();
string conte1 = cmlContent1.Substring(0, 1000);
string conte2 = cmlContent2.Substring(0, 1000);
Assert.AreEqual(conte1, conte2);
}
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 TestNewChemFile()
{
IChemObjectBuilder builder = RootObject.Builder;
IChemFile file = builder.NewChemFile();
Assert.IsNotNull(file);
}
public void TestEthene()
{
var filename = "NCDK.Data.Ghemical.ethene.mm1gp";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new GhemicalMMReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
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(6, m.Atoms.Count);
Assert.AreEqual(5, m.Bonds.Count);
}
public void TestReading()
{
var filename = "NCDK.Data.VASP.LiMoS2_optimisation_ISIF3.vasp";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new VASPReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
var sequence = chemFile[0];
Assert.IsNotNull(sequence);
Assert.AreEqual(6, sequence.Count);
var model = sequence[0];
Assert.IsNotNull(model);
var crystal = model.Crystal;
Assert.IsNotNull(crystal);
Assert.AreEqual(16, crystal.Atoms.Count);
var atom = crystal.Atoms[0];
Assert.IsNotNull(atom);
Assert.IsNotNull(atom.FractionalPoint3D);
}
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 virtual void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
EntryReact entry = (EntryReact)dictionary[entryString.ToLowerInvariant()];
var xmlList = entry.ExampleReactions;
Assert.IsTrue(xmlList.Count != 0, "The representation entry for [" + entryString
+ "] must contain at least one example of reaction.");
Assert.IsTrue(xmlList.Count > 0, "The representation entry for [" + entryString
+ "] must contain at least one example of reaction.");
foreach (var xml in xmlList)
{
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(xml)));
var chemFile = (IChemFile)reader.Read(builder.NewChemFile());
IReaction reactionDict = chemFile[0][0].ReactionSet[0];
var reactants = reactionDict.Reactants;
var agents = reactionDict.Agents;
var products = reactionDict.Products;
if (agents.Count == 0)
{
agents = null;
}
IReactionSet reactions = reaction.Initiate(reactants, agents);
Assert.IsTrue(reactions.Count > 0, "The products for [" + entryString + "] reaction is at least one reaction expected.");
Assert.AreEqual(products[0].Atoms.Count,
reactions[0].Products[0].Atoms.Count,
"The products for [" + entryString + "] reaction is not the expected.");
}
}
public override void StartDocument()
{
ChemFile = builder.NewChemFile();
chemSequence = builder.NewChemSequence();
chemModel = builder.NewChemModel();
setOfMolecules = builder.NewChemObjectSet <IAtomContainer>();
}
public void TestBug1649526()
{
//Read the original
var filename = "NCDK.Data.MDL.bug-1649526.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins);
var mol = reader.Read(builder.NewAtomContainer());
reader.Close();
//Write it as cml
var writer = new StringWriter();
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(mol);
cmlWriter.Close();
//Read this again
var cmlreader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(writer.ToString())));
var file = (IChemFile)cmlreader.Read(builder.NewChemFile());
cmlreader.Close();
//And finally write as mol
var writermdl = new StringWriter();
var mdlWriter = new MDLV2000Writer(writermdl);
mdlWriter.Write(file);
mdlWriter.Close();
var output = writermdl.ToString().Replace("\r\n", "\n");
//if there would be 3 instances (as in the bug), the only instance wouldnt't be right at the end
Assert.AreEqual(2994, output.IndexOf("M END"));
//there would need some $$$$ to be in
Assert.AreEqual(-1, output.IndexOf("$$$$"));
//check atom/bond count
Assert.AreEqual(25, output.IndexOf(" 31 33 0 0 0 0"));
}
public SpanningTreeTest()
{
if (azulene == null)
{
// load azulene
var filename = "NCDK.Data.MDL.azulene.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
IAtomContainer azuleneMolecule = model.MoleculeSet[0];
Assert.AreEqual(10, azuleneMolecule.Atoms.Count);
Assert.AreEqual(11, azuleneMolecule.Bonds.Count);
azulene = new SpanningTree(azuleneMolecule);
}
if (ethane == null)
{
// create ethane
IAtomContainer ethaneMolecule = builder.NewAtomContainer();
ethaneMolecule.Atoms.Add(builder.NewAtom("C"));
ethaneMolecule.Atoms.Add(builder.NewAtom("C"));
ethaneMolecule.AddBond(ethaneMolecule.Atoms[0], ethaneMolecule.Atoms[1], BondOrder.Single);
ethane = new SpanningTree(ethaneMolecule);
}
}
public void TestStabilityAfterRoundtrip()
{
var filename = "NCDK.Data.MDL.bug1014344-1.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins, ChemObjectReaderMode.Strict);
var mol1 = reader.Read(builder.NewAtomContainer());
AddImplicitHydrogens(mol1);
var output = new StringWriter();
var cmlWriter = new CMLWriter(output);
cmlWriter.Write(mol1);
var cmlreader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(output.ToString())));
var mol2 = ((IChemFile)cmlreader.Read(builder.NewChemFile()))[0][0].MoleculeSet[0];
AddImplicitHydrogens(mol2);
labeler.CanonLabel(mol1);
labeler.CanonLabel(mol2);
var atoms1 = mol1.Atoms.GetEnumerator();
var atoms2 = mol2.Atoms.GetEnumerator();
while (atoms1.MoveNext())
{
atoms2.MoveNext();
var atom1 = atoms1.Current;
var atom2 = atoms2.Current;
Assert.AreEqual(atom1.GetProperty <long>(InvPair.CanonicalLabelPropertyKey), atom2.GetProperty <long>(InvPair.CanonicalLabelPropertyKey));
}
}
public void TestRDFChemFile()
{
var filename = "NCDK.Data.MDL.qsar-reaction-test.rdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
MDLRXNReader reader = new MDLRXNReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
Assert.AreEqual(2, chemFile[0][0].ReactionSet.Count);
Assert.AreEqual(2, chemFile[0][0].ReactionSet[0]
.Reactants.Count);
Assert.AreEqual(3, chemFile[0][0].ReactionSet[0]
.Reactants[0].Atoms.Count);
Assert.AreEqual(2, chemFile[0][0].ReactionSet[0]
.Reactants[1].Atoms.Count);
Assert.AreEqual(2, chemFile[0][0].ReactionSet[0]
.Products.Count);
Assert.AreEqual(2, chemFile[0][0].ReactionSet[0]
.Products[0].Atoms.Count);
Assert.AreEqual(2, chemFile[0][0].ReactionSet[0]
.Products[1].Atoms.Count);
Assert.AreEqual(1, chemFile[0][0].ReactionSet[1]
.Reactants.Count);
Assert.AreEqual(3, chemFile[0][0].ReactionSet[1]
.Reactants[0].Atoms.Count);
Assert.AreEqual(1, chemFile[0][0].ReactionSet[1]
.Products.Count);
Assert.AreEqual(2, chemFile[0][0].ReactionSet[1]
.Products[0].Atoms.Count);
}
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 TestNonConnectedPiSystems()
{
Trace.TraceInformation("Entering testNonConnectedPiSystems.");
IAtomContainer mol = null;
var filename = "NCDK.Data.MDL.nonConnectedPiSystems.mol";
var ins = ResourceLoader.GetAsStream(filename);
MDLReader reader = new MDLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
mol = chemFile[0][0].MoleculeSet[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(2, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(4, ac1.Atoms.Count);
Assert.AreEqual(3, ac1.Bonds.Count);
for (int i = 0; i < ac1.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Atoms[i]));
}
for (int i = 0; i < ac1.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Bonds[i]));
}
IAtomContainer ac2 = acSet[1];
Assert.AreEqual(4, ac2.Atoms.Count);
Assert.AreEqual(3, ac2.Bonds.Count);
for (int i = 0; i < ac2.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac2.Atoms[i]));
}
for (int i = 0; i < ac2.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac2.Bonds[i]));
}
}
public void TestModelBuilder3D_232()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
var filename = "NCDK.Data.MDL.allmol232.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]);
AddExplicitHydrogens(ac);
ac = mb3d.Generate3DCoordinates(ac, false);
Assert.IsNotNull(ac.Atoms[0].Point3D);
CheckAverageBondLength(ac);
}
private IChemFile ParseCMLString(string cmlString)
{
IChemFile chemFile = null;
using (var reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlString))))
{
chemFile = reader.Read(builder.NewChemFile());
}
return(chemFile);
}
public void TestCPSA()
{
var filename = "NCDK.Data.HIN.benzene.hin";
IChemFile content;
using (var reader = new HINReader(ResourceLoader.GetAsStream(filename)))
{
content = reader.Read(builder.NewChemFile());
}
var cList = ChemFileManipulator.GetAllAtomContainers(content).ToReadOnlyList();
var ac = cList[0];
var retval = CreateDescriptor().Calculate(ac).Values;
Assert.AreEqual(0, retval[28], 0.0001);
Assert.AreEqual(1, retval[27], 0.0001);
Assert.AreEqual(0, retval[26], 0.0001);
Assert.AreEqual(356.8849, retval[25], 0.0001);
}
public void TestPorphyrine()
{
IRingSet ringSet = null;
AllRingsFinder arf = new AllRingsFinder();
var filename = "NCDK.Data.MDL.porphyrin.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(20, ringSet.Count);
}
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 TestReadGz()
{
var filename = "NCDK.Data.XYZ.bf3.xyz.gz";
var input = new GZipStream(ResourceLoader.GetAsStream(filename), CompressionMode.Decompress);
// ok, if format ok, try instantiating a reader
ISimpleChemObjectReader reader = factory.CreateReader(input);
Assert.IsNotNull(reader);
Assert.AreEqual(((IChemFormat)XYZFormat.Instance).ReaderClassName, reader.GetType().FullName);
// now try reading something from it
var chemFile = reader.Read(builder.NewChemFile());
var molecule = builder.NewAtomContainer();
foreach (var container in ChemFileManipulator.GetAllAtomContainers(chemFile))
{
molecule.Add(container);
}
Assert.IsNotNull(molecule);
Assert.AreEqual(4, molecule.Atoms.Count);
}
public void TestRoundTrip()
{
StringWriter sWriter = new StringWriter();
PDBWriter writer = new PDBWriter(sWriter);
ICrystal crystal = builder.NewCrystal();
crystal.A = new Vector3(0, 1, 0);
crystal.B = new Vector3(1, 0, 0);
crystal.C = new Vector3(0, 0, 2);
IAtom atom = builder.NewAtom("C");
atom.Point3D = new Vector3(0.1, 0.1, 0.3);
crystal.Atoms.Add(atom);
writer.Write(crystal);
writer.Close();
string output = sWriter.ToString();
Assert.IsNotNull(output);
Assert.IsTrue(output.Length > 0);
PDBReader reader = new PDBReader(new StringReader(""));
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
IChemSequence sequence = chemFile[0];
Assert.AreEqual(1, sequence.Count);
IChemModel chemModel = sequence[0];
Assert.IsNotNull(chemModel);
// can't do further testing as the PDBReader does not read
// Crystal structures :(
}
public void TestEstron()
{
var filename = "NCDK.Data.CML.estron.cml";
Trace.TraceInformation("Testing: " + filename);
IChemFile chemFile;
using (var ins = ResourceLoader.GetAsStream(filename))
using (var reader = new CMLReader(ins))
{
chemFile = reader.Read(builder.NewChemFile());
}
// test the resulting ChemFile content
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);
// test the molecule
ICrystal crystal = model.Crystal;
Assert.IsNotNull(crystal);
Assert.AreEqual(4 * 42, crystal.Atoms.Count);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(crystal));
// test the cell axes
Vector3 a = crystal.A;
Assert.IsTrue(a.X != 0.0);
Vector3 b = crystal.B;
Assert.IsTrue(b.Y != 0.0);
Vector3 c = crystal.C;
Assert.IsTrue(c.Z != 0.0);
}
public void TestBenzene()
{
var filename = "NCDK.Data.HIN.benzene.hin";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new HINReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
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);
// AreEqual(?, m.Bonds.Count);
}