public void ChooseFormatToWrite2()
{
StringWriter writer = new StringWriter();
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.SetAlwaysV3000(true);
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("CH4"));
sdfWriter.Write(molecule);
molecule = new AtomContainer();
for (int i = 0; i < 1000; i++)
{
molecule.Atoms.Add(new Atom("CH4"));
}
sdfWriter.Write(molecule);
molecule = new AtomContainer();
molecule.Atoms.Add(new Atom("CH4"));
sdfWriter.Write(molecule);
sdfWriter.Close();
string result = writer.ToString();
Assert.IsFalse(result.Contains("V2000"));
Assert.IsTrue(result.Contains("V3000"));
}
public void TestIOPropPropagation()
{
IAtomContainer mol = TestMoleculeFactory.MakeBenzene();
foreach (var atom in mol.Atoms)
{
atom.IsAromatic = true;
}
foreach (var bond in mol.Bonds)
{
bond.IsAromatic = true;
}
StringWriter strWriter = new StringWriter();
SDFWriter writer = new SDFWriter(strWriter);
var sdfWriterProps = new NameValueCollection();
sdfWriterProps["WriteAromaticBondTypes"] = "true";
writer.Listeners.Add(new PropertiesListener(sdfWriterProps));
writer.CustomizeJob();
writer.Write(mol);
writer.Close();
string output = strWriter.ToString();
Assert.IsTrue(output.Contains("4 0 0 0 0"));
}
public void SetProgramName()
{
var sw = new StringWriter();
using (var sdfw = new SDFWriter(sw))
{
try
{
sdfw.IOSettings[MDLV2000Writer.OptWriteDefaultProperties].Setting = "false";
sdfw.IOSettings[MDLV2000Writer.OptProgramName].Setting = "Bioclipse";
sdfw.Write(TestMoleculeFactory.Make123Triazole());
sdfw.IOSettings[SDFWriter.OptAlwaysV3000].Setting = "true";
sdfw.Write(TestMoleculeFactory.Make123Triazole());
}
catch (Exception e)
{
Console.WriteLine(e.StackTrace);
}
}
var sdf = sw.ToString();
foreach (var mol in sdf.Split("\\$\\$\\$\\$", 2))
{
Assert.IsTrue(mol.Contains("Bioclip"));
}
}
public void TestAccepts()
{
SDFWriter reader = new SDFWriter(new StringWriter());
Assert.IsTrue(reader.Accepts(typeof(ChemFile)));
Assert.IsTrue(reader.Accepts(typeof(ChemModel)));
Assert.IsTrue(reader.Accepts(typeof(ChemObjectSet <IAtomContainer>)));
}
public void InvalidSDfileHeaderTags()
{
StringWriter writer = new StringWriter();
SDFWriter sdfWriter = new SDFWriter(writer);
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("http://not-valid.com", "URL");
sdfWriter.Write(molecule);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().Contains("> <http://not_valid_com>"));
}
public void TestWrite_IAtomContainerSet()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = builder.NewAtomContainerSet();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.Write(molSet);
sdfWriter.Close();
Assert.AreNotSame(0, writer.ToString().Length);
}
public void TestPropertyOutput_none()
{
IAtomContainer adenine = TestMoleculeFactory.MakeAdenine();
StringWriter sw = new StringWriter();
SDFWriter sdf = new SDFWriter(sw, Array.Empty <string>());
adenine.SetProperty("one", "a");
adenine.SetProperty("two", "b");
sdf.Write(adenine);
sdf.Close();
string output = sw.ToString();
Assert.IsFalse(output.Contains("> <two>"));
Assert.IsFalse(output.Contains("> <one>"));
}
public void TestWrite_IAtomContainerSet_SingleMolecule()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = new ChemObjectSet <IAtomContainer>();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.Write(molSet);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("$$$$") != -1);
}
public void TestWrite_IAtomContainerSet_CDKProperties()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = new ChemObjectSet <IAtomContainer>();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty(InvPair.CanonicalLabelPropertyKey, "bar");
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.Write(molSet);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf(InvPair.CanonicalLabelPropertyKey) == -1);
}
public void TestWrite_IAtomContainerSet_Properties_Off()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = new ChemObjectSet <IAtomContainer>();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("foo", "bar");
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
var sdfWriterProps = new NameValueCollection();
sdfWriterProps["writeProperties"] = "false";
sdfWriter.Listeners.Add(new PropertiesListener(sdfWriterProps));
sdfWriter.CustomizeJob();
sdfWriter.Write(molSet);
sdfWriter.Close();
string result = writer.ToString();
Assert.IsFalse(result.Contains("<foo>"));
}
public void TestWrite_IAtomContainer_MultIAtomContainer()
{
StringWriter writer = new StringWriter();
SDFWriter sdfWriter = new SDFWriter(writer);
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("foo", "bar");
sdfWriter.Write(molecule);
molecule = new AtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("toys", "r-us");
sdfWriter.Write(molecule);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("foo") != -1);
Assert.IsTrue(writer.ToString().IndexOf("bar") != -1);
Assert.IsTrue(writer.ToString().IndexOf("toys") != -1);
Assert.IsTrue(writer.ToString().IndexOf("r-us") != -1);
Assert.IsTrue(writer.ToString().IndexOf("$$$$") != -1);
}
