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 TestBug1275()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol-malformedDictRef.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// we check here that the malformed dictRef doesn't throw an exception
Assert.AreEqual(BondStereo.None, container.Bonds[0].Stereo, "expected non-stereo bond");
Assert.AreEqual(BondStereo.Up, container.Bonds[1].Stereo, "expected Wedge (Up) Bond");
Assert.AreEqual(BondStereo.None, container.Bonds[2].Stereo, "expected non-stereo bond");
}
finally
{
reader.Close();
}
}
public void TestBug1248()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
IBond bond = container.Bonds[2];
Assert.IsNotNull(bond, "Null bond");
Assert.AreEqual(BondStereo.Up, bond.Stereo, "Expected Wedge (Up) Bond");
}
finally
{
reader.Close();
}
}
public void TestBug1274()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol-multipleBondStereo.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// we check here that the charContent is not used and also that more then
// one stereo isn't set
Assert.AreEqual(BondStereo.None, container.Bonds[0].Stereo, "expected non-stereo bond");
Assert.AreEqual(BondStereo.Down, container.Bonds[1].Stereo, "expected Hatch (Down) Bond");
Assert.AreEqual(BondStereo.None, container.Bonds[2].Stereo, "expected non-stereo bond");
}
finally
{
reader.Close();
}
}
public void TestBug1245()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
foreach (var atom in container.Atoms)
{
Assert.AreEqual(
PeriodicTable.GetAtomicNumber(atom.Symbol),
atom.AtomicNumber,
"Incorrect atomic number");
}
}
finally
{
reader.Close();
}
}
public void TestSFBug1085912_1()
{
string cmlContent = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>"
+ "<molecule convention=\"PDB\" dictRef=\"pdb:model\" xmlns=\"http://www.xml-cml.org/schema\">"
+ " <molecule dictRef=\"pdb:sequence\" id=\"ALAA116\">"
+ " <atomArray>"
+ " <atom id=\"a9794931\" elementType=\"N\" x3=\"-10.311\" y3=\"2.77\" z3=\"-9.837\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a5369354\" elementType=\"C\" x3=\"-9.75\" y3=\"4.026\" z3=\"-9.35\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a14877152\" elementType=\"C\" x3=\"-10.818\" y3=\"5.095\" z3=\"-9.151\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a26221736\" elementType=\"O\" x3=\"-11.558\" y3=\"5.433\" z3=\"-10.074\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a4811470\" elementType=\"C\" x3=\"-8.678\" y3=\"4.536\" z3=\"-10.304\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a211489\" elementType=\"H\" x3=\"-10.574\" y3=\"2.695\" z3=\"-10.778\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a31287617\" elementType=\"H\" x3=\"-9.279\" y3=\"3.829\" z3=\"-8.398\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a19487109\" elementType=\"H\" x3=\"-8.523\" y3=\"3.813\" z3=\"-11.09\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a28589522\" elementType=\"H\" x3=\"-8.994\" y3=\"5.477\" z3=\"-10.737\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>"
+ " <atom id=\"a4638116\" elementType=\"H\" x3=\"-7.754\" y3=\"4.682\" z3=\"-9.763\" formalCharge=\"0\">"
+ " <scalar dictRef=\"cdk:partialCharge\" dataType=\"xsd:double\">0.0</scalar>"
+ " </atom>" + " </atomArray>" + " </molecule>" + "</molecule>";
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlContent)));
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// OK, now test that the residue identifier is properly read
Assert.AreEqual("ALAA116", container.Id);
}
finally
{
reader.Close();
}
}
public void TestMixedNamespaces()
{
var ins = ResourceLoader.GetAsStream(this.GetType(), "US06358966-20020319-C00001-enr.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.AreEqual(34, ChemFileManipulator.GetAtomCount(cfile));
Assert.AreEqual(39, ChemFileManipulator.GetBondCount(cfile));
}
finally
{
reader.Close();
}
}
public void TestWedgeBondParsing()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.AZD5423.xml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
// we check here that the malformed dictRef doesn't throw an exception
for (int i = 0; i < 19; i++)
{
Assert.AreEqual(
BondStereo.None, container.Bonds[i].Stereo,
"found an unexpected wedge bond for " + i + ": " + container.Bonds[i].Stereo);
}
Assert.AreEqual(BondStereo.Down, container.Bonds[19].Stereo, "expected a wedge bond");
for (int i = 20; i < 30; i++)
{
Assert.AreEqual(
BondStereo.None, container.Bonds[i].Stereo,
"found an unexpected wedge bond for " + i + ": " + container.Bonds[i].Stereo);
}
Assert.AreEqual(BondStereo.Up, container.Bonds[30].Stereo, "expected a wedge bond");
for (int i = 31; i <= 37; i++)
{
Assert.AreEqual(
BondStereo.None, container.Bonds[i].Stereo,
"found an unexpected wedge bond for " + i + ": " + container.Bonds[i].Stereo);
}
}
finally
{
reader.Close();
}
}