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();
}
private bool disposedValue = false; // To detect redundant calls
protected virtual void Dispose(bool disposing)
{
if (!disposedValue)
{
if (disposing)
{
imdlr.Dispose();
}
imdlr = null;
disposedValue = true;
}
}
static void Main()
{
{
#region
using (var srm = new FileStream("../zinc-structures/ZINC_subset3_3D_charged_wH_maxmin1000.sdf", FileMode.Open))
{
EnumerableSDFReader reader = new EnumerableSDFReader(srm, ChemObjectBuilder.Instance);
foreach (var molecule in reader)
{
// do something
}
}
#endregion
}
}
public void TestMultipleEntryFields()
{
var filename = "NCDK.Data.MDL.test.sdf";
var ins = ResourceLoader.GetAsStream(filename);
using (var reader = new EnumerableSDFReader(ins, CDK.Builder))
{
var tor = reader.GetEnumerator();
tor.MoveNext();
IAtomContainer m = (IAtomContainer)tor.Current;
Assert.AreEqual("553-97-9", m.GetProperty <string>("E_CAS"));
tor.MoveNext();
m = tor.Current;
Assert.AreEqual("120-78-5", m.GetProperty <string>("E_CAS"));
}
}
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();
}
public EnumerableMDLConformerReader(Stream ins, IChemObjectBuilder builder)
{
imdlr = new EnumerableSDFReader(ins, builder);
}
public IEnumerableMDLConformerReader(TextReader ins, IChemObjectBuilder builder)
{
imdlr = new EnumerableSDFReader(ins, builder);
}