public static PropertiesListener Join(PropertiesListener listener1, PropertyListener listener2)
{
return(new PropertiesListener(listener1,
listener1.propertyTypes.Concat(new[] { listener2.PropertyType }).ToArray(),
listener1.propertyNames.Select(x => x.Key).Concat(new[] { listener2.PropertyName }).ToArray(),
listener1.getValues.Concat(new[] { listener2.GetValue }).ToArray()));
}
public void TestAromaticBondType4()
{
IAtomContainer benzene = TestMoleculeFactory.MakeBenzene();
foreach (var atom in benzene.Atoms)
{
atom.IsAromatic = true;
}
foreach (var bond in benzene.Bonds)
{
bond.IsAromatic = true;
}
StringWriter writer = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(benzene);
mdlWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("1 2 1 0 0 0 0") != -1);
writer = new StringWriter();
mdlWriter = new MDLV2000Writer(writer);
var prop = new NameValueCollection
{
["WriteAromaticBondTypes"] = "true"
};
PropertiesListener listener = new PropertiesListener(prop);
mdlWriter.Listeners.Add(listener);
mdlWriter.CustomizeJob();
mdlWriter.Write(benzene);
mdlWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("1 2 4 0 0 0 0") != -1);
}
public void TestForce2DCoordinates()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer();
IAtom atom = builder.NewAtom("C");
atom.Point2D = new Vector2(1.0, 2.0);
atom.Point3D = new Vector3(3.0, 4.0, 5.0);
molecule.Atoms.Add(atom);
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
var prop = new NameValueCollection
{
["ForceWriteAs2DCoordinates"] = "true"
};
PropertiesListener listener = new PropertiesListener(prop);
mdlWriter.Listeners.Add(listener);
mdlWriter.CustomizeJob();
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
// the current behavior is that if both 2D and 3D coordinates
// are available, the 3D is outputed, and the 2D not
Assert.IsTrue(output.Contains("1.0"));
Assert.IsTrue(output.Contains("2.0"));
}
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 TestWriteAromatic()
{
StringWriter stringWriter = new StringWriter();
IAtomContainer benzene = TestMoleculeFactory.MakeBenzene();
AddImplicitHydrogens(benzene);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(benzene);
Aromaticity.CDKLegacy.Apply(benzene);
SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
var prop = new NameValueCollection();
prop["UseAromaticity"] = "true";
PropertiesListener listener = new PropertiesListener(prop);
smilesWriter.Listeners.Add(listener);
smilesWriter.CustomizeJob();
smilesWriter.Write(benzene);
smilesWriter.Close();
Assert.IsFalse(stringWriter.ToString().Contains("C=C"));
Assert.IsTrue(stringWriter.ToString().Contains("ccc"));
}
static void Main()
{
{
IAtomContainer molecule = null;
#region
using (var writer = new MDLV2000Writer(new FileStream("output.mol", FileMode.Create)))
{
writer.Write((IAtomContainer)molecule);
}
#endregion
}
{
MDLV2000Writer writer = null;
#region listener
var customSettings = new NameValueCollection
{
["ForceWriteAs2DCoordinates"] = "true"
};
var listener = new PropertiesListener(customSettings);
writer.Listeners.Add(listener);
#endregion
}
}
