public static IReaction RoundTripReaction(Convertor convertor, IReaction reaction)
{
string cmlString = "<!-- failed -->";
var cmlDOM = convertor.CDKReactionToCMLReaction(reaction);
cmlString = cmlDOM.ToString();
IReaction roundTrippedReaction = null;
Debug.WriteLine("CML string: ", cmlString);
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlString)));
IChemFile file = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
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);
IReactionSet reactionSet = chemModel.ReactionSet;
Assert.IsNotNull(reactionSet);
Assert.AreEqual(1, reactionSet.Count);
roundTrippedReaction = reactionSet[0];
Assert.IsNotNull(roundTrippedReaction);
return(roundTrippedReaction);
}
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 void TestCMLReactionList()
{
var filename = "NCDK.Data.CML.reactionList.1.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(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(2, model.ReactionSet.Count);
Assert.AreEqual("1.3.2", model.ReactionSet[0].Id);
// test the reaction
IReaction reaction = model.ReactionSet[0];
Assert.IsNotNull(reaction);
Assert.AreEqual("actey", reaction.Reactants[0].Id);
Assert.AreEqual("a14293164", reaction.Reactants[0].Atoms[0].Id);
Assert.AreEqual(6, reaction.Products[0].Atoms.Count);
Assert.AreEqual(6, reaction.Reactants[0].Atoms.Count);
}
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 TestNucleustest()
{
var filename = "NCDK.Data.CML.nucleustest.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(11, mol.Atoms.Count, "Incorrect number of atoms");
Assert.AreEqual(12, mol.Bonds.Count, "Incorrect number of bonds");
Assert.IsFalse(GeometryUtil.Has3DCoordinates(mol), "File does not have 3D coordinates");
Assert.IsFalse(GeometryUtil.Has2DCoordinates(mol), "File does not have 2D coordinates");
}
/// <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 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 static IChemModel RoundTripChemModel(Convertor convertor, IChemModel model)
{
string cmlString = "<!-- failed -->";
var cmlDOM = convertor.CDKChemModelToCMLList(model);
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(model.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);
return(chemModel);
}
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]);
}
private IAtomContainer ReadCMLMolecule(string filename)
{
IAtomContainer mol = null;
Debug.WriteLine($"Filename: {filename}");
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
IChemFile 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);
mol = moleculeSet[0];
Assert.IsNotNull(mol);
return(mol);
}
public void TestCephNS()
{
var filename = "NCDK.Data.CML.ceph-ns.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, 15);
Assert.AreEqual(mol.Bonds.Count, 16);
Assert.IsFalse(GeometryUtil.Has3DCoordinates(mol));
Assert.IsTrue(GeometryUtil.Has2DCoordinates(mol));
}
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 TestMethanolOne()
{
var filename = "NCDK.Data.CML.methanol1.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);
var som = model.MoleculeSet;
Assert.AreEqual(1, som.Count);
// test the molecule
IAtomContainer mol = som[0];
Assert.IsNotNull(mol);
Assert.AreEqual(mol.Atoms.Count, 6);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
}
[TestMethod(), Ignore()] // It is broken, but not used, AFAIK
public void TestAnimation()
{
var filename = "NCDK.Data.CML.SN1_reaction.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);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(34, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
var som = model.MoleculeSet;
Assert.IsNotNull(som);
Assert.AreEqual(1, som.Count);
// test the molecule
IAtomContainer mol = som[0];
Assert.IsNotNull(mol);
Assert.AreEqual(mol.Atoms.Count, 25);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
}
public void TestCMLConciseFormula2()
{
var filename = "NCDK.Data.CML.cmlConciseFormula2.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(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
var mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
// FIXME: REACT: It should return two different formulas
Assert.AreEqual("[C 18 H 21 Cl 2 Mn 1 N 5 O 1, C 4 H 10]",
Strings.ToJavaString(mol.GetProperty <IList <string> >(CDKPropertyName.Formula)));
}
public void TestCMLWithFormula()
{
var filename = "NCDK.Data.CML.cmlWithFormula.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(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
var mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual("a", mol.Id);
Assert.AreEqual("a1", mol.Atoms[0].Id);
Assert.AreEqual(27, mol.Atoms.Count);
Assert.AreEqual(32, mol.Bonds.Count);
}
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 TestBug2697568()
{
var filename = "NCDK.Data.CML.AlanineTreeReverse.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = builder.NewChemFile();
chemFile = (IChemFile)reader.Read(chemFile);
reader.Close();
Assert.AreSame(chemFile[0][0].MoleculeSet[0], chemFile
[0][0].ReactionSet[0].Reactants[0]);
}
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 TestReactionProperties()
{
var filename = "NCDK.Data.CML.reaction.2.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = builder.NewChemFile();
chemFile = (IChemFile)reader.Read(chemFile);
reader.Close();
IReaction reaction = chemFile[0][0].ReactionSet[0];
Assert.AreEqual("3", reaction.GetProperty <string>("Ka"));
}
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 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 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 TestCMLSchemeMoleculeSet()
{
var filename = "NCDK.Data.CML.reactionSchemeMoleculeSet.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(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
// test reaction
Assert.AreEqual(1, model.ReactionSet.Count);
string[] idReaction = { "react_1" };
string[] idReactants = { "A" };
string[] idProducts = { "B", "C" };
IReaction reaction = model.ReactionSet[0];
Assert.AreEqual(idReaction[0], reaction.Id);
// test molecule
Assert.AreEqual(2, reaction.Products.Count());
Assert.AreEqual(idProducts[0], reaction.Products[0].Id);
Assert.AreEqual("C 9 H 20 N 1",
reaction.Products[0].GetProperty <IList <string> >(CDKPropertyName.Formula)[0]);
Assert.AreEqual(idProducts[1], reaction.Products[1].Id);
Assert.AreEqual(1, reaction.Reactants.Count());
Assert.AreEqual(idReactants[0], reaction.Reactants[0].Id);
Assert.AreEqual("C 28 H 60 N 1",
reaction.Reactants[0].GetProperty <IList <string> >(CDKPropertyName.Formula)[0]);
}
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 TestCOONa()
{
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(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
var mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual(4, mol.Atoms.Count);
Assert.AreEqual(2, mol.Bonds.Count);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
Assert.IsTrue(!GeometryUtil.Has2DCoordinates(mol));
foreach (var atom in mol.Atoms)
{
if (atom.Symbol.Equals("Na"))
{
Assert.AreEqual(+1, atom.FormalCharge.Value);
}
}
}
public void TestCMLStepList()
{
var filename = "NCDK.Data.CML.reactionStepList.1.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(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
// test reaction
Assert.AreEqual(3, model.ReactionSet.Count);
string[] idReaction = { "r1", "r2", "r3" };
string[] idReactants = { "A", "B", "C" };
string[] idProducts = { "B", "C", "D" };
for (int i = 0; i < idReaction.Length; i++)
{
IReaction reaction = model.ReactionSet[i];
Assert.AreEqual(idReaction[i], reaction.Id);
// test molecule
Assert.AreEqual(1, reaction.Products.Count());
Assert.AreEqual(idProducts[i], reaction.Products[0].Id);
Assert.AreEqual(1, reaction.Reactants.Count());
Assert.AreEqual(idReactants[i], reaction.Reactants[0].Id);
}
}
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());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
var mol = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
for (int i = 0; i <= 3; i++)
{
Assert.IsFalse(mol.Bonds[i].IsAromatic, "Bond " + (i + 1) + " is not aromatic in the file");
}
for (int i = 4; i <= 9; i++)
{
Assert.IsTrue(mol.Bonds[i].IsAromatic, "Bond " + (i + 1) + " is aromatic in the file");
}
}
static void Main(string[] args)
{
var container = Builder.NewAtomContainer();
container.Add(Builder.NewAtom("C"));
container.Add(Builder.NewAtom("C"));
container.Add(Builder.NewBond(container.Atoms[0], container.Atoms[1], BondOrder.Unset));
using (var file = new FileStream("./cml.cml", FileMode.Create, FileAccess.Write))
{
using (var writer = new CMLWriter(file))
{
writer.Write(container);
}
}
using (var cmlFile = new FileStream("./cml.cml", FileMode.Open, FileAccess.Read))
{
var reader = new CMLReader(cmlFile);
var chemFile = reader.Read(Builder.NewChemFile());
Console.WriteLine(chemFile[0][0].MoleculeSet[0].Bonds[0].Order);
}
}
/// <summary>
/// Loads all existing templates into memory. To add templates to be used in
/// SDG, place a drawing with the new template in org/openscience/cdk/layout/templates and add the
/// template filename to org/openscience/cdk/layout/templates/template.list
/// </summary>
public void LoadTemplates()
{
try
{
using (var reader = new StreamReader(ResourceLoader.GetAsStream("NCDK.Layout.Templates.templates.list")))
{
string line;
while ((line = reader.ReadLine()) != null)
{
line = "NCDK.Layout.Templates." + line;
Debug.WriteLine($"Attempting to read template {line}");
try
{
CMLReader structureReader = new CMLReader(ResourceLoader.GetAsStream(line));
IChemFile file = structureReader.Read(builder.NewChemFile());
var files = ChemFileManipulator.GetAllAtomContainers(file);
foreach (var f in files)
{
AddMolecule(f);
}
Debug.WriteLine($"Successfully read template {line}");
}
catch (CDKException e)
{
Trace.TraceWarning($"Could not read template {line}, reason: {e.Message}");
Debug.WriteLine(e.Message);
}
}
}
}
catch (IOException e)
{
Trace.TraceWarning($"Could not read (all of the) templates, reason: {e.Message}");
Debug.WriteLine(e.Message);
}
}
