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 void WrongFormat()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.bug1356.sdf");
var reader = new MDLReader(ins, ChemObjectReaderMode.Strict);
var chemfile = builder.NewChemFile();
chemfile = reader.Read(chemfile);
}
public void TestEmptyString()
{
var emptyString = "";
var reader = new MDLReader(new StringReader(emptyString), ChemObjectReaderMode.Strict);
var mol = reader.Read(builder.NewAtomContainer());
reader.Close();
Assert.IsNull(mol);
}
public void TestMissingAtomProperties()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.bug3485634.mol");
var reader = new MDLReader(ins);
var molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
Assert.AreEqual(9, molecule.Atoms.Count);
}
public void TestHas2DCoordinates_With000()
{
var filenameMol = "NCDK.Data.MDL.with000coordinate.mol";
var ins = ResourceLoader.GetAsStream(filenameMol);
var reader = new MDLReader(ins, ChemObjectReaderMode.Relaxed);
var molOne = reader.Read(builder.NewAtomContainer());
reader.Close();
Assert.IsNull(molOne.Atoms[0].Point2D);
}
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 TestUndefinedStereo()
{
var filename = "NCDK.Data.MDL.ChEBI_26120.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins, ChemObjectReaderMode.Relaxed);
var mol = reader.Read(builder.NewAtomContainer());
reader.Close();
Assert.AreEqual(BondStereo.EOrZ, mol.Bonds[1].Stereo);
Assert.AreEqual(BondStereo.EOrZ, mol.Bonds[6].Stereo);
Assert.AreEqual(BondStereo.EOrZ, mol.Bonds[7].Stereo);
Assert.AreEqual(BondStereo.EOrZ, mol.Bonds[11].Stereo);
}
public void TestReadProton()
{
string mdl = "proton.mol\n" + "\n" + "\n" + " 1 0 0 0 0 1\n"
+ " -0.0073 -0.5272 0.9655 H 0 3 0 0 0\n";
var reader = new MDLReader(new StringReader(mdl), ChemObjectReaderMode.Strict);
var mol = reader.Read(builder.NewAtomContainer());
reader.Close();
Assert.IsNotNull(mol);
Assert.AreEqual(1, mol.Atoms.Count);
Assert.AreEqual(0, mol.Bonds.Count);
var atom = mol.Atoms[0];
Assert.AreEqual(1, atom.FormalCharge.Value);
}
public void TestBug1542467()
{
var filename = "NCDK.Data.MDL.Strychnine_nichtOK.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
Assert.AreEqual(1, containersList.Count);
Assert.IsTrue((containersList[0]).Atoms.Count > 0);
Assert.IsTrue((containersList[0]).Bonds.Count > 0);
}
public void TestStereoReadZeroDefault()
{
var filename = "NCDK.Data.MDL.prev2000.sd";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
Assert.AreEqual(2, containersList.Count);
var container = containersList[0];
Assert.AreEqual(BondStereo.None, container.Bonds[0].Stereo);
}
public void TestReadFromStringReader()
{
var mdl = "cyclopropane.mol\n" + "\n" + "\n" + " 9 9 0 0\n"
+ " -0.0073 -0.5272 0.9655 C 0 0 0 0 0\n"
+ " -0.6776 -0.7930 -0.3498 C 0 0 0 0 0\n"
+ " 0.2103 0.4053 -0.1891 C 0 0 0 0 0\n"
+ " 0.8019 -1.1711 1.2970 H 0 0 0 0 0\n"
+ " -0.6000 -0.2021 1.8155 H 0 0 0 0 0\n"
+ " -1.7511 -0.6586 -0.4435 H 0 0 0 0 0\n"
+ " -0.3492 -1.6277 -0.9620 H 0 0 0 0 0\n"
+ " 1.1755 0.4303 -0.6860 H 0 0 0 0 0\n"
+ " -0.2264 1.3994 -0.1675 H 0 0 0 0 0\n" + " 1 2 1 6 0 0\n"
+ " 1 3 1 6 0 0\n" + " 1 4 1 0 0 0\n" + " 1 5 1 1 0 0\n" + " 2 3 1 0 0 0\n"
+ " 2 6 1 0 0 0\n" + " 2 7 1 6 0 0\n" + " 3 8 1 6 0 0\n" + " 3 9 1 0 0 0\n";
var reader = new MDLReader(new StringReader(mdl), ChemObjectReaderMode.Strict);
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(9, m.Atoms.Count);
Assert.AreEqual(9, m.Bonds.Count);
}
/// <summary>
/// Read a Reaction from a file in MDL RXN format
///
/// <returns>The Reaction that was read from the MDL file.</returns>
/// </summary>
private IReaction ReadReaction(IChemObjectBuilder builder)
{
Debug.WriteLine("Reading new reaction");
int linecount = 0;
IReaction reaction = builder.NewReaction();
try
{
input.ReadLine(); // first line should be $RXN
input.ReadLine(); // second line
input.ReadLine(); // third line
input.ReadLine(); // fourth line
}
catch (IOException exception)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try
{
string countsLine = input.ReadLine();
linecount++;
if (countsLine == null)
{
return(null);
}
Debug.WriteLine("Line " + linecount + ": " + countsLine);
if (countsLine.StartsWith("$$$$", StringComparison.Ordinal))
{
Debug.WriteLine("File is empty, returning empty reaction");
return(reaction);
}
// this line contains the number of reactants and products
var tokens = Strings.Tokenize(countsLine);
reactantCount = int.Parse(tokens[0], NumberFormatInfo.InvariantInfo);
Trace.TraceInformation("Expecting " + reactantCount + " reactants in file");
productCount = int.Parse(tokens[1], NumberFormatInfo.InvariantInfo);
Trace.TraceInformation("Expecting " + productCount + " products in file");
}
catch (Exception exception)
{
if (exception is IOException | exception is FormatException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
throw;
}
// now read the reactants
try
{
for (int i = 1; i <= reactantCount; i++)
{
var molFile = new StringBuilder();
input.ReadLine(); // announceMDLFileLine
string molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
} while (!string.Equals(molFileLine, "M END", StringComparison.Ordinal));
// read MDL molfile content
MDLReader reader = new MDLReader(new StringReader(molFile.ToString()));
IAtomContainer reactant = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Reactants.Add(reactant);
}
}
catch (CDKException)
{
// rethrow exception from MDLReader
throw;
}
catch (Exception exception)
{
if (exception is IOException | exception is ArgumentException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading reactant", exception);
}
throw;
}
// now read the products
try
{
for (int i = 1; i <= productCount; i++)
{
var molFile = new StringBuilder();
input.ReadLine(); // string announceMDLFileLine =
string molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
} while (!string.Equals(molFileLine, "M END", StringComparison.Ordinal));
// read MDL molfile content
MDLReader reader = new MDLReader(new StringReader(molFile.ToString()), base.ReaderMode);
IAtomContainer product = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Products.Add(product);
}
}
catch (CDKException)
{
// rethrow exception from MDLReader
throw;
}
catch (Exception exception)
{
if (exception is IOException | exception is ArgumentException)
{
Debug.WriteLine(exception);
throw new CDKException("Error while reading products", exception);
}
throw;
}
// now try to map things, if wanted
Trace.TraceInformation("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.NewAtomContainer();
foreach (var reactant in reaction.Reactants)
{
reactingSide.Add(reactant);
}
IAtomContainer producedSide = builder.NewAtomContainer();
foreach (var reactant in reaction.Products)
{
producedSide.Add(reactant);
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.GetAtoms();
// IAtom[] producedAtoms = producedSide.GetAtoms();
for (int i = 0; i < reactingSide.Atoms.Count; i++)
{
for (int j = 0; j < producedSide.Atoms.Count; j++)
{
IAtom eductAtom = reactingSide.Atoms[i];
IAtom productAtom = producedSide.Atoms[j];
if (eductAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping) != null &&
eductAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping).Equals(
productAtom.GetProperty <object>(CDKPropertyName.AtomAtomMapping)))
{
reaction.Mappings.Add(builder.NewMapping(eductAtom, productAtom));
mappingCount++;
break;
}
}
}
Trace.TraceInformation("Mapped atom pairs: " + mappingCount);
return(reaction);
}