public void Issue602()
{
using (var reader = new MDLV3000Reader(ResourceLoader.GetAsStream(GetType(), "issue602.mol")))
{
var mol = reader.Read(builder.NewAtomContainer());
Assert.AreEqual(31, mol.Atoms.Count);
}
}
public void PositionalVariationRoundTrip()
{
using (var mdlr = new MDLV3000Reader(GetType().Assembly.GetManifestResourceStream(GetType(), "multicenterBond.mol")))
{
var mol = mdlr.Read(builder.NewAtomContainer());
var res = WriteToStr(mol);
Assert.IsTrue(res.Contains("M V30 8 1 8 9 ATTACH=Any ENDPTS=(5 2 3 4 5 6)\n"));
}
}
public void RadicalsInCH3()
{
using (MDLV3000Reader reader = new MDLV3000Reader(GetType().Assembly.GetManifestResourceStream(GetType(), "CH3.mol")))
{
IAtomContainer container = reader.Read(builder.NewAtomContainer());
Assert.AreEqual(1, container.SingleElectrons.Count);
Assert.AreEqual(3, container.Atoms[0].ImplicitHydrogenCount);
}
}
public void PseuDoAtomReplacement()
{
using (MDLV3000Reader reader = new MDLV3000Reader(GetType().Assembly.GetManifestResourceStream(GetType(), "pseudoAtomReplacement.mol")))
{
IAtomContainer container = reader.Read(builder.NewAtomContainer());
foreach (var atom in container.Bonds[9].Atoms)
{
Assert.IsTrue(container.Contains(atom));
}
}
}
public void PositionalVariation()
{
using (MDLV3000Reader reader = new MDLV3000Reader(GetType().Assembly.GetManifestResourceStream(GetType(), "multicenterBond.mol")))
{
IAtomContainer container = reader.Read(builder.NewAtomContainer());
Assert.AreEqual(8, container.Bonds.Count);
var sgroups = container.GetCtabSgroups();
Assert.IsNotNull(sgroups);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual(SgroupType.ExtMulticenter, sgroups[0].Type);
}
}
public void TestPseudoAtomLabels()
{
using (var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.pseudoatomsv3000.mol"))
using (MDLV3000Reader reader = new MDLV3000Reader(ins))
{
IAtomContainer molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
Assert.IsTrue(molecule.Atoms[9] is IPseudoAtom);
Assert.AreEqual("R", molecule.Atoms[9].Symbol);
IPseudoAtom pa = (IPseudoAtom)molecule.Atoms[9];
Assert.AreEqual("Leu", pa.Label);
}
}
public void TestEmptyString()
{
string emptyString = "";
try
{
using (MDLV3000Reader reader = new MDLV3000Reader(new StringReader(emptyString)))
{
reader.Read(builder.NewAtomContainer());
reader.Close();
Assert.Fail("Should have received a CDK Exception");
}
}
catch (CDKException cdkEx)
{
Assert.AreEqual("Expected a header line, but found nothing.", cdkEx.Message);
}
}
public void TestBug1571207()
{
var filename = "NCDK.Data.MDL.molV3000.mol";
Trace.TraceInformation("Testing: " + filename);
using (var ins = ResourceLoader.GetAsStream(filename))
{
MDLV3000Reader reader = new MDLV3000Reader(ins);
IAtomContainer m = reader.Read(builder.NewAtomContainer());
reader.Close();
Assert.IsNotNull(m);
Assert.AreEqual(31, m.Atoms.Count);
Assert.AreEqual(34, m.Bonds.Count);
IAtom atom = m.Atoms[0];
Assert.IsNotNull(atom);
Assert.IsNotNull(atom.Point2D);
Assert.AreEqual(10.4341, atom.Point2D.Value.X, 0.0001);
Assert.AreEqual(5.1053, atom.Point2D.Value.Y, 0.0001);
}
}
public void TestAccepts()
{
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(""));
Assert.IsTrue(reader.Accepts(typeOfAtomContainer));
}
private IReaction ReadReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.NewReaction();
ReadLine(); // first line should be $RXN
ReadLine(); // second line
ReadLine(); // third line
ReadLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
bool foundCOUNTS = false;
while (!foundCOUNTS)
{
string command = ReadCommand();
if (command.StartsWith("COUNTS", StringComparison.Ordinal))
{
var tokenizer = Strings.Tokenize(command);
try
{
reactantCount = int.Parse(tokenizer[1], NumberFormatInfo.InvariantInfo);
Trace.TraceInformation($"Expecting {reactantCount} reactants in file");
productCount = int.Parse(tokenizer[2], NumberFormatInfo.InvariantInfo);
Trace.TraceInformation($"Expecting {productCount } products in file");
}
catch (Exception exception)
{
Debug.WriteLine(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
foundCOUNTS = true;
}
else
{
Trace.TraceWarning("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++)
{
var molFile = new StringBuilder();
string announceMDLFileLine = ReadCommand();
if (!string.Equals(announceMDLFileLine, "BEGIN REACTANT", StringComparison.Ordinal))
{
string error = "Excepted start of reactant, but found: " + announceMDLFileLine;
Trace.TraceError(error);
throw new CDKException(error);
}
string molFileLine = "";
while (!molFileLine.EndsWith("END REACTANT", StringComparison.Ordinal))
{
molFileLine = ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
}
;
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.ToString()), base.ReaderMode);
IAtomContainer reactant = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add reactant
reaction.Reactants.Add(reactant);
}
catch (Exception exception)
{
if (!(exception is ArgumentException ||
exception is CDKException ||
exception is IOException))
{
throw;
}
string error = "Error while reading reactant: " + exception.Message;
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++)
{
var molFile = new StringBuilder();
string announceMDLFileLine = ReadCommand();
if (!string.Equals(announceMDLFileLine, "BEGIN PRODUCT", StringComparison.Ordinal))
{
string error = "Excepted start of product, but found: " + announceMDLFileLine;
Trace.TraceError(error);
throw new CDKException(error);
}
string molFileLine = "";
while (!molFileLine.EndsWith("END PRODUCT", StringComparison.Ordinal))
{
molFileLine = ReadLine();
molFile.Append(molFileLine);
molFile.Append('\n');
}
;
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.ToString()));
IAtomContainer product = (IAtomContainer)reader.Read(builder.NewAtomContainer());
reader.Close();
// add product
reaction.Products.Add(product);
}
catch (Exception exception)
{
if (!(exception is ArgumentException ||
exception is CDKException ||
exception is IOException))
{
throw;
}
string error = "Error while reading product: " + exception.Message;
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
}
return(reaction);
}
