/// <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 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 static string MolToMolBlock(IAtomContainer mol, bool forceV3000 = false)
{
using (var sr = new StringWriter())
{
IChemObjectWriter w;
if (forceV3000 ||
mol.Atoms.Count > 999 ||
mol.Bonds.Count > 999)
{
w = new MDLV3000Writer(sr);
}
else
{
w = new MDLV2000Writer(sr);
}
try
{
w.Write(mol);
}
finally
{
w.Close();
}
return(sr.ToString());
}
}
public void SkipDefaultProps()
{
var sw = new StringWriter();
using (var mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.tetrahedral-parity-withImplH.mol")))
using (var mdlw = new MDLV2000Writer(sw))
{
mdlw.IOSettings[MDLV2000Writer.OptWriteDefaultProperties].Setting = "false";
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
var output = sw.ToString();
Assert.IsTrue(output.Contains(
"\n"
+ " 5 4 0 0 1 0 0 0 0 0999 V2000\n"
+ " 0.0000 0.0000 0.0000 C 0 0 1 0 0 0\n"
+ " 0.0000 0.0000 0.0000 C 0 0\n"
+ " 0.0000 0.0000 0.0000 C 0 0\n"
+ " 0.0000 0.0000 0.0000 O 0 0\n"
+ " 0.0000 0.0000 0.0000 C 0 0\n"
+ " 1 2 1 0\n"
+ " 2 3 1 0\n"
+ " 1 4 1 0\n"
+ " 1 5 1 0\n"
+ "M END"));
}
}
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 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 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 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 TestAccepts()
{
MDLV2000Writer reader = new MDLV2000Writer();
Assert.IsTrue(reader.Accepts(typeof(IChemFile)));
Assert.IsTrue(reader.Accepts(typeof(IChemModel)));
Assert.IsTrue(reader.Accepts(typeof(IAtomContainer)));
}
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();
}
public void RoundtripAtomParityImplH()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.tetrahedral-parity-withImplH.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains(" 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0" + "\n"));
}
}
public void SgroupBracketStylesRoundTrip()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.sgroup-sru-bracketstyles.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains("M STY 2 1 SRU 2 SRU"));
Assert.IsTrue(output.Contains("M SBT 1 1 1"));
}
}
public void SgroupUnorderedMixtureRoundTrip()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.sgroup-unord-mixture.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains("M STY 3 1 COM 2 COM 3 MIX"));
Assert.IsTrue(output.Contains("M SPL 1 1 3"));
}
}
public void SgroupCopolymerRoundTrip()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.sgroup-ran-copolymer.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains("M SST 1 1 RAN"));
Assert.IsTrue(output.Contains("M STY 3 1 COP 2 SRU 3 SRU"));
}
}
public void SgroupExpandedAbbreviationRoundTrip()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.triphenyl-phosphate-expanded.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains("M STY 3 1 SUP 2 SUP 3 SUP" + "\n"));
Assert.IsTrue(output.Contains("M SDS EXP 1 1"));
}
}
public void SgroupParentAtomListRoundTrip()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.ChEBI_81539.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains("M STY 5 1 MUL 2 SRU"));
Assert.IsTrue(output.Contains("M SPA 1 12"));
}
}
/// <summary>
/// Convert mol to V2000 Molfile
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static string AtomContainerToMolfile(IAtomContainer mol)
{
java.io.StringWriter sw = new java.io.StringWriter();
MDLV2000Writer writer = new MDLV2000Writer(sw);
writer.write(mol);
writer.close();
sw.close();
string molFile = sw.toString();
return(molFile);
}
/// <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 SgroupRepeatUnitRoundTrip()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.sgroup-sru.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mdlr.Read(builder.NewAtomContainer()));
string output = sw.ToString();
Assert.IsTrue(output.Contains("M STY 1 1 SRU"));
Assert.IsTrue(output.Contains("M SMT 1 n"));
Assert.IsTrue(output.Contains("M SCN 1 1 HT"));
}
}
public void AromaticBondTypes()
{
var mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("C"));
var bond = builder.NewBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Unset);
bond.IsAromatic = true;
mol.Bonds.Add(bond);
using (MDLV2000Writer mdlw = new MDLV2000Writer(new StringWriter()))
{
mdlw.Write(mol);
}
}
public void RoundtripAtomParityImplModified()
{
StringWriter sw = new StringWriter();
using (MDLV2000Reader mdlr = new MDLV2000Reader(ResourceLoader.GetAsStream("NCDK.Data.MDL.tetrahedral-parity-withImplH.mol")))
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
var mol = mdlr.Read(builder.NewAtomContainer());
var tc = (ITetrahedralChirality)mol.StereoElements.First();
tc.Stereo = tc.Stereo.Invert();
mdlw.Write(mol);
string output = sw.ToString();
Assert.IsTrue(output.Contains(" 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0" + "\n"));
}
}
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 WriteCarbon13AtomProps()
{
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom();
atom.Symbol = "C";
atom.MassNumber = 13;
mol.Atoms.Add(atom);
var sw = new StringWriter();
using (var mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mol);
}
Assert.IsTrue(sw.ToString().Contains("C 1"));
}
public void WriteChargeAtomProps()
{
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom();
atom.Symbol = "C";
atom.FormalCharge = +1;
mol.Atoms.Add(atom);
var sw = new StringWriter();
using (var mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mol);
}
Assert.IsTrue(sw.ToString().Contains("C 0 3"));
}
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 WriteDimensionField3D()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom atom = builder.NewAtom();
atom.Symbol = "C";
atom.ImplicitHydrogenCount = 4;
atom.Point3D = new Vector3(0.5, 0.5, 0.1);
mol.Atoms.Add(atom);
StringWriter sw = new StringWriter();
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mol);
}
Assert.IsTrue(sw.ToString().Contains("3D"));
}
public void IgnoreCarbon12()
{
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom();
atom.Symbol = "C";
atom.MassNumber = 12;
mol.Atoms.Add(atom);
var sw = new StringWriter();
using (var mdlw = new MDLV2000Writer(sw))
{
mdlw.IOSettings[MDLV2000Writer.OptWriteMajorIsotopes].Setting = "false";
mdlw.Write(mol);
}
Assert.IsFalse(sw.ToString().Contains("M ISO 1 1 12"));
}
public void NonDefaultValenceFe3()
{
var container = builder.NewAtomContainer();
var fe1 = builder.NewAtom("Fe");
fe1.ImplicitHydrogenCount = 3;
container.Atoms.Add(fe1);
string output;
using (var writer = new StringWriter())
using (var mdlWriter = new MDLV2000Writer(writer))
{
mdlWriter.Write(container);
output = writer.ToString();
}
Assert.IsTrue(output.Contains("Fe 0 0 0 0 0 3 0 0 0 0 0 0"));
}
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);
}
