public void TestZeroZCoordinates()
{
var filename = "NCDK.Data.MDL.nozcoord.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var prop = new NameValueCollection
{
["ForceReadAs3DCoordinates"] = "true"
};
PropertiesListener listener = new PropertiesListener(prop);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
reader.Listeners.Add(listener);
reader.CustomizeJob();
int molCount = 0;
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
molCount++;
bool has3d = GeometryUtil.Has3DCoordinates((IAtomContainer)obj);
Assert.IsTrue(has3d);
}
Assert.AreNotSame(0, molCount);
reader.Close();
}
public void TestEmptyEntryIteratingReader()
{
var filename = "NCDK.Data.MDL.emptyStructures.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
int molCount = 0;
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
molCount++;
if (molCount == 2)
{
IAtomContainer mol = (IAtomContainer)obj;
string s = mol.GetProperty <string>("Species");
Assert.AreEqual("rat", s);
}
}
Assert.AreEqual(2, molCount);
reader.Close();
}
public void TestNo3DCoordsButForcedAs()
{
// First test unforced 3D coordinates
var filename = "NCDK.Data.MDL.no3dStructures.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
int molCount = 0;
IAtomContainer mol = null;
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
molCount++;
mol = (IAtomContainer)obj;
}
Assert.AreEqual(2, molCount);
Assert.IsNotNull(mol.Atoms[0].Point2D);
Assert.IsNull(mol.Atoms[0].Point3D);
reader.Close();
// Now test forced 3D coordinates
Trace.TraceInformation("Testing: " + filename);
ins = ResourceLoader.GetAsStream(filename);
reader = new EnumerableSDFReader(ins, CDK.Builder);
reader.Listeners.Add(new MyListener());
reader.CustomizeJob();
molCount = 0;
mol = null;
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
molCount++;
mol = (IAtomContainer)obj;
}
Assert.AreEqual(2, molCount);
Assert.IsNull(mol.Atoms[0].Point2D);
Assert.IsNotNull(mol.Atoms[0].Point3D);
reader.Close();
}
public void TestReadTitle()
{
var filename = "NCDK.Data.MDL.test.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
var etor = reader.GetEnumerator();
Assert.IsTrue(etor.MoveNext());
object obj = etor.Current;
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
Assert.AreEqual("2-methylbenzo-1,4-quinone", ((IAtomContainer)obj).Title);
Assert.AreEqual(MDLV2000Format.Instance, reader.Format);
reader.Close();
}
public void TestOnSingleEntrySDFile()
{
var filename = "NCDK.Data.MDL.singleMol.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
int molCount = 0;
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
molCount++;
}
Assert.AreEqual(1, molCount);
reader.Close();
}
public void TestSDF()
{
var filename = "NCDK.Data.MDL.test2.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
int molCount = 0;
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
molCount++;
Assert.AreEqual(MDLV2000Format.Instance, reader.Format, "Molecule # was not in MDL V2000 format: " + molCount);
}
Assert.AreEqual(6, molCount);
reader.Close();
}
public void TestV3000MolfileFormat()
{
string path = "NCDK.Data.MDL.molV3000.mol";
var ins = ResourceLoader.GetAsStream(path);
var builder = CDK.Builder;
EnumerableSDFReader reader = new EnumerableSDFReader(ins, builder)
{
Skip = true // skip over null entries and keep reading until EOF
};
int count = 0;
foreach (var m in reader)
{
count++;
}
reader.Close();
Assert.AreEqual(1, count);
}
public void TestBrokenSDF()
{
string path = "NCDK.Data.MDL.bug3488307.sdf";
var ins = ResourceLoader.GetAsStream(path);
var builder = CDK.Builder;
EnumerableSDFReader reader = new EnumerableSDFReader(ins, builder)
{
Skip = true // skip over null entries and keep reading until EOF
};
int count = 0;
foreach (var m in reader)
{
count++;
}
reader.Close();
Assert.AreEqual(3, count);
}
public void TestReadDataItems()
{
var filename = "NCDK.Data.MDL.test.sdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSDFReader reader = new EnumerableSDFReader(ins, CDK.Builder);
var etor = reader.GetEnumerator();
Assert.IsTrue(etor.MoveNext());
object obj = etor.Current;
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomContainer);
IAtomContainer m = (IAtomContainer)obj;
Assert.AreEqual("1", m.GetProperty <string>("E_NSC"));
Assert.AreEqual("553-97-9", m.GetProperty <string>("E_CAS"));
reader.Close();
}