[TestMethod(), Ignore()] // moved to SMILES2Mol2WriterTest
public void TestWriter1()
{
IAtomContainer molecule = new Mock <IAtomContainer>().Object;
StringWriter swriter = new StringWriter();
Mol2Writer writer = new Mol2Writer(swriter);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(swriter.ToString().IndexOf("1 C1 0.000 0.000 0.000 C.3") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("1 2 1 1") > 0);
}
public void TestWriter1()
{
var sp = CDK.SmilesParser;
var molecule = sp.ParseSmiles("C([H])([H])([H])([H])");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
StringWriter swriter = new StringWriter();
Mol2Writer writer = new Mol2Writer(swriter);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(swriter.ToString().IndexOf("1 C1 0.000 0.000 0.000 C.3") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("1 1 2 1") > 0);
}
[TestMethod(), Ignore()] // moved to SMILES2Mol2WriterTest
public void TestWriter2()
{
IAtomContainer molecule = new Mock <IAtomContainer>().Object;
Aromaticity.CDKLegacy.Apply(molecule);
StringWriter swriter = new StringWriter();
Mol2Writer writer = new Mol2Writer(swriter);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(swriter.ToString().IndexOf("1 C1 0.000 0.000 0.000 C.ar") > 0, "Aromatic atom not properly reported");
Assert.IsTrue(swriter.ToString().IndexOf("8 O8 0.000 0.000 0.000 O.2") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("7 C7 0.000 0.000 0.000 C.2") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("1 2 1 ar") > 0, "Aromatic bond not properly reported");
Assert.IsTrue(swriter.ToString().IndexOf("8 8 7 2") > 0);
}
[TestMethod(), Ignore()] // moved to SMILES2Mol2WriterTest
public void TestWriterForAmide()
{
IAtomContainer molecule = new Mock <IAtomContainer>().Object;
Aromaticity.CDKLegacy.Apply(molecule);
StringWriter swriter = new StringWriter();
Mol2Writer writer = new Mol2Writer(swriter);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(swriter.ToString().IndexOf("1 C1 0.000 0.000 0.000 C.3") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("3 O3 0.000 0.000 0.000 O.") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("4 N4 0.000 0.000 0.000 N.a") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("1 2 1 1") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("3 4 2 am") > 0, "Amide bond not properly reported");
Assert.IsTrue(swriter.ToString().IndexOf("4 5 4 1") > 0);
}
public void TestWriterForAmide()
{
var sp = CDK.SmilesParser;
var molecule = sp.ParseSmiles("CC(=O)NC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
StringWriter swriter = new StringWriter();
Mol2Writer writer = new Mol2Writer(swriter);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(swriter.ToString().IndexOf("1 C1 0.000 0.000 0.000 C.3") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("3 O3 0.000 0.000 0.000 O.") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("4 N4 0.000 0.000 0.000 N.a") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("1 1 2 1") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("3 2 4 am") > 0, "Amide bond not properly reported");
Assert.IsTrue(swriter.ToString().IndexOf("4 4 5 1") > 0);
}
public void TestWriter2()
{
var sp = CDK.SmilesParser;
var molecule = sp.ParseSmiles("c1ccccc1C=O");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.CDKLegacy.Apply(molecule);
StringWriter swriter = new StringWriter();
Mol2Writer writer = new Mol2Writer(swriter);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(swriter.ToString().IndexOf("1 C1 0.000 0.000 0.000 C.ar") > 0, "Aromatic atom not properly reported");
Assert.IsTrue(swriter.ToString().IndexOf("8 O8 0.000 0.000 0.000 O.2") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("7 C7 0.000 0.000 0.000 C.2") > 0);
Assert.IsTrue(swriter.ToString().IndexOf("1 1 2 ar") > 0, "Aromatic bond not properly reported");
Assert.IsTrue(swriter.ToString().IndexOf("8 7 8 2") > 0);
}
public void TestMissingAtomType()
{
var filename = "NCDK.Data.MDL.ligand-1a0i.sdf";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
IChemFile fileContents = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
var molecules = ChemFileManipulator.GetAllAtomContainers(fileContents).ToReadOnlyList();
IAtomContainer mol = molecules[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
StringWriter writer = new StringWriter();
Mol2Writer molwriter = new Mol2Writer(writer);
molwriter.Write(mol);
molwriter.Close();
string mol2file = writer.ToString();
Assert.IsTrue(mol2file.Contains("-1.209 -18.043 49.44 X") || mol2file.Contains("-1.209 -18.043 49.440 X"));
}
public void TestAccepts()
{
Mol2Writer writer = new Mol2Writer(new StringWriter());
Assert.IsTrue(writer.Accepts(typeof(AtomContainer)));
}