public void TestAtomValueLine()
{
IAtom carbon = builder.NewAtom("C");
carbon.SetProperty(CDKPropertyName.Comment, "Carbon comment");
IAtom oxygen = builder.NewAtom("O");
oxygen.SetProperty(CDKPropertyName.Comment, "Oxygen comment");
IBond bond = builder.NewBond(carbon, oxygen, BondOrder.Double);
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(oxygen);
molecule.Atoms.Add(carbon);
molecule.Bonds.Add(bond);
StringWriter writer = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("V 1 Oxygen comment") != -1);
Assert.IsTrue(writer.ToString().IndexOf("V 2 Carbon comment") != -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 TestRGPLine()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer();
IPseudoAtom atom1 = builder.NewPseudoAtom();
atom1.Symbol = "R";
atom1.Label = "R12";
IAtom atom2 = builder.NewAtom("C");
IBond bond = builder.NewBond(atom1, atom2);
IPseudoAtom atom3 = builder.NewPseudoAtom();
atom3.Symbol = "A";
atom3.Label = "A";
IBond bond2 = builder.NewBond(atom3, atom2);
molecule.Atoms.Add(atom1);
molecule.Atoms.Add(atom2);
molecule.Atoms.Add(atom3);
molecule.Bonds.Add(bond);
molecule.Bonds.Add(bond2);
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
Assert.IsTrue(-1 != output.IndexOf("R#"), "Test for R#");
Assert.IsTrue(-1 != output.IndexOf("M RGP 1 1 12"), "Test for RGP line");
}
public void TestBug1649526()
{
//Read the original
var filename = "NCDK.Data.MDL.bug-1649526.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins);
var mol = reader.Read(builder.NewAtomContainer());
reader.Close();
//Write it as cml
var writer = new StringWriter();
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(mol);
cmlWriter.Close();
//Read this again
var cmlreader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(writer.ToString())));
var file = (IChemFile)cmlreader.Read(builder.NewChemFile());
cmlreader.Close();
//And finally write as mol
var writermdl = new StringWriter();
var mdlWriter = new MDLV2000Writer(writermdl);
mdlWriter.Write(file);
mdlWriter.Close();
var output = writermdl.ToString().Replace("\r\n", "\n");
//if there would be 3 instances (as in the bug), the only instance wouldnt't be right at the end
Assert.AreEqual(2994, output.IndexOf("M END"));
//there would need some $$$$ to be in
Assert.AreEqual(-1, output.IndexOf("$$$$"));
//check atom/bond count
Assert.AreEqual(25, output.IndexOf(" 31 33 0 0 0 0"));
}
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);
}
/// <summary>
/// Writes a MoleculeSet to an Stream for the reaction.
/// </summary>
/// <param name="som">The MoleculeSet that is written to an Stream</param>
private void WriteAtomContainerSet(IChemObjectSet <IAtomContainer> som)
{
for (int i = 0; i < som.Count; i++)
{
IAtomContainer mol = som[i];
for (int j = 0; j < som.GetMultiplier(i); j++)
{
StringWriter sw = new StringWriter();
writer.Write("$MOL");
writer.Write('\n');
MDLV2000Writer mdlwriter = null;
try
{
mdlwriter = new MDLV2000Writer(sw);
}
catch (Exception ex)
{
Trace.TraceError(ex.Message);
Debug.WriteLine(ex);
throw new CDKException("Exception while creating MDLWriter: " + ex.Message, ex);
}
mdlwriter.Write(mol);
mdlwriter.Close();
writer.Write(sw.ToString());
}
}
}
public void TestUnsupportedBondOrder()
{
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Bonds.Add(builder.NewBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Quadruple));
MDLV2000Writer mdlWriter = new MDLV2000Writer(new StringWriter());
mdlWriter.Write(molecule);
mdlWriter.Close();
}
/// <summary>
/// Convert mol to V2000 Molfile
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static string AtomContainerToMolfile(IAtomContainer mol)
{
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(mol);
writer.Close();
sw.Close();
string molFile = sw.ToString();
return(molFile);
}
public void TestBug890456()
{
StringWriter writer = new StringWriter();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewPseudoAtom("*"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("M END") != -1);
}
public void TestWriteStringAtomAtomMapping()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = TestMoleculeFactory.MakeAlphaPinene();
molecule.Atoms[0].SetProperty(CDKPropertyName.AtomAtomMapping, "1");
molecule.Atoms[1].SetProperty(CDKPropertyName.AtomAtomMapping, "15");
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
Assert.IsTrue(output.Contains("0 0 0 0 0 0 0 0 0 1 0 0"));
Assert.IsTrue(output.Contains("0 0 0 0 0 0 0 0 0 15 0 0"));
}
public void TestUndefinedStereo()
{
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
mol.Bonds[0].Stereo = BondStereo.UpOrDown;
mol.Bonds[1].Stereo = BondStereo.EOrZ;
StringWriter writer = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(mol);
mdlWriter.Close();
string output = writer.ToString();
Assert.IsTrue(output.IndexOf("1 2 2 4 0 0 0") > -1);
Assert.IsTrue(output.IndexOf("2 3 1 3 0 0 0") > -1);
}
public void TestBug1212219()
{
StringWriter writer = new StringWriter();
var molecule = builder.NewAtomContainer();
var atom = builder.NewAtom("C");
atom.MassNumber = 14;
molecule.Atoms.Add(atom);
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
//Debug.WriteLine($"MDL output for testBug1212219: {output}");
Assert.IsTrue(output.IndexOf("M ISO 1 1 14") != -1);
}
public void TestAtomParity()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.mol_testAtomParity.mol");
var reader = new MDLV2000Reader(ins);
IAtomContainer molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(molecule);
writer.Close();
Assert.IsTrue(sw.ToString().Contains(
" -1.1749 0.1436 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0"));
}
public void TestWriteInvalidAtomAtomMapping()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = TestMoleculeFactory.MakeAlphaPinene();
molecule.Atoms[0].SetProperty(CDKPropertyName.AtomAtomMapping, "1a");
molecule.Atoms[1].SetProperty(CDKPropertyName.AtomAtomMapping, "15");
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
Regex p = new Regex(".*V2000.* 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 "
+ "0 0.* 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 15 0 0.*",
RegexOptions.Compiled | RegexOptions.Multiline | RegexOptions.Singleline);
var m = p.Match(output);
Assert.IsTrue(m.Success);
}
public void TestSingleTripletRadical()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.singleTripletRadical.mol");
var reader = new MDLV2000Reader(ins);
IAtomContainer molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(molecule);
writer.Close();
string[] lines = SplitLines(sw.ToString());
Assert.AreEqual(9, lines.Length, "incorrect file length");
Assert.AreEqual("M RAD 1 2 1", lines[7], "incorrect radical output");
}
public void TestAlias_TruncatedLabel()
{
IAtomContainer container = builder.NewAtomContainer();
string label = "This is a very long label - almost too long. it should be cut here -> and the rest is truncated";
container.Atoms.Add(builder.NewPseudoAtom(label));
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(container);
writer.Close();
string output = sw.ToString();
Assert.IsTrue(output.Contains("This is a very long label - almost too long. it should be cut here ->"));
// make sure the full label wasn't output
Assert.IsFalse(output.Contains(label));
}
public void TestWritePseudoAtoms()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.pseudoatoms.sdf");
var reader = new MDLV2000Reader(ins);
IAtomContainer molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
StringWriter writer = new StringWriter();
MDLV2000Writer mwriter = new MDLV2000Writer(writer);
mwriter.Write(molecule);
mwriter.Close();
string output = writer.ToString();
Assert.IsTrue(output.IndexOf("Gln") != -1);
Assert.IsTrue(output.IndexOf("Leu") != -1);
}
public void TestWriteValence()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = TestMoleculeFactory.MakeAlphaPinene();
molecule.Atoms[0].Valency = 1;
molecule.Atoms[1].Valency = 0;
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
var customSettings = new NameValueCollection
{
["WriteQueryFormatValencies"] = "true"
};
mdlWriter.Listeners.Add(new PropertiesListener(customSettings));
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
Assert.IsTrue(output.IndexOf("0 0 0 0 0 1 0 0 0 0 0 0") != -1);
Assert.IsTrue(output.IndexOf("0 0 0 0 0 15 0 0 0 0 0 0") != -1);
}
public void TestRGPLine_Multiline()
{
IAtomContainer container = builder.NewAtomContainer();
for (int i = 1; i < 20; i++)
{
container.Atoms.Add(builder.NewPseudoAtom("R" + i));
}
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(container);
writer.Close();
string output = sw.ToString();
Assert.IsTrue(output.Contains("M RGP 8 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8"));
Assert.IsTrue(output.Contains("M RGP 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 16"));
Assert.IsTrue(output.Contains("M RGP 3 17 17 18 18 19 19"));
}
public void TestWritePseudoAtoms_LongLabel()
{
IAtomContainer container = builder.NewAtomContainer();
IAtom c1 = builder.NewAtom("C");
IAtom tRNA = builder.NewPseudoAtom("tRNA");
container.Atoms.Add(c1);
container.Atoms.Add(tRNA);
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(container);
writer.Close();
string output = sw.ToString();
Assert.IsTrue(output.Contains("A 2"));
Assert.IsTrue(output.Contains("tRNA"));
}
public void TestNullFormalCharge()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer();
IAtom atom = builder.NewAtom("C");
atom.FormalCharge = null;
molecule.Atoms.Add(atom);
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
// test ensures that the writer does not throw an exception on
// null formal charges, so a mere assert on output being non-zero
// length is enough
Assert.IsNotNull(output);
Assert.AreNotSame(0, output.Length);
}
public void TestTwoFragmentsWithTitle()
{
IAtomContainer mol1 = TestMoleculeFactory.MakeAlphaPinene();
mol1.Title = "title1";
IAtomContainer mol2 = TestMoleculeFactory.MakeAlphaPinene();
mol2.Title = "title2";
var model = mol1.Builder.NewChemModel();
model.MoleculeSet = mol1.Builder.NewAtomContainerSet();
model.MoleculeSet.Add(mol1);
model.MoleculeSet.Add(mol2);
StringWriter writer = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(model);
mdlWriter.Close();
string output = writer.ToString();
Assert.IsTrue(output.Contains("title1; title2"));
}
public void TestMultipleRadicals()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.MDL.multipleRadicals.mol");
var reader = new MDLV2000Reader(ins);
IAtomContainer molecule = builder.NewAtomContainer();
molecule = reader.Read(molecule);
reader.Close();
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(molecule);
writer.Close();
string[] lines = SplitLines(sw.ToString());
Assert.AreEqual(24, lines.Length, "incorrect file length");
Assert.AreEqual("M RAD 8 1 2 2 2 3 2 4 2 5 2 6 2 7 2 8 2",
lines[21], "incorrect radical output on line 22");
Assert.AreEqual("M RAD 1 9 2", lines[22], "incorrect radical output on line 23");
}
public void TestWritePseudoAtoms_nullLabel()
{
IAtomContainer container = builder.NewAtomContainer();
IAtom c1 = builder.NewAtom("C");
IPseudoAtom nullAtom = builder.NewPseudoAtom("");
nullAtom.Label = null;
container.Atoms.Add(c1);
container.Atoms.Add(nullAtom);
StringWriter sw = new StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.Write(container);
writer.Close();
string output = sw.ToString();
Assert.IsTrue(output.Contains("R"));
}
public void TestBug1778479()
{
StringWriter writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer();
IAtom atom1 = builder.NewPseudoAtom();
IAtom atom2 = builder.NewAtom("C");
IBond bond = builder.NewBond(atom1, atom2);
molecule.Atoms.Add(atom1);
molecule.Atoms.Add(atom2);
molecule.Bonds.Add(bond);
MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
mdlWriter.Write(molecule);
mdlWriter.Close();
string output = writer.ToString();
Assert.AreEqual(-1,
output.IndexOf("0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0 0 0 0"),
"Test for zero length pseudo atom label in MDL file");
}
public void TestPrefer3DCoordinateOutput()
{
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);
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("3.0"));
Assert.IsTrue(output.Contains("4.0"));
Assert.IsTrue(output.Contains("5.0"));
}
/// <summary>
/// Produces a CTAB block for an atomContainer, without the header lines.
/// </summary>
/// <param name="atomContainer"></param>
/// <returns>CTAB block</returns>
private static string GetCTAB(IAtomContainer atomContainer)
{
StringWriter strWriter = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(strWriter);
mdlWriter.Write(atomContainer);
try
{
mdlWriter.Close();
}
catch (IOException)
{
// FIXME
}
string ctab = strWriter.ToString();
//strip of the individual header, as we have one super header instead.
for (int line = 1; line <= 3; line++)
{
ctab = ctab.Substring(ctab.IndexOf(LSEP, StringComparison.Ordinal) + (LSEP.Length));
}
return(ctab);
}
