public void TestTaxols()
{
var filename = "NCDK.Data.ASN.PubChem.taxols.xml";
Trace.TraceInformation("Testing: " + filename);
int modelCount = 0;
IChemSequence set;
using (var ins = ResourceLoader.GetAsStream(filename))
using (var sr = new StreamReader(ins))
using (var reader = new EnumerablePCSubstancesXMLReader(sr, ChemObjectBuilder.Instance))
{
set = ChemObjectBuilder.Instance.NewChemSequence();
foreach (var obj in reader)
{
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IChemModel);
set.Add((IChemModel)obj);
modelCount++;
}
}
Assert.AreEqual(77, modelCount);
IChemModel first = set[0];
Assert.AreEqual(63, ChemModelManipulator.GetAtomCount(first));
Assert.AreEqual(69, ChemModelManipulator.GetBondCount(first));
}
private static void CreateIDsForChemModel(IChemModel model, List <string> tabuList)
{
if (tabuList == null)
{
tabuList = ChemModelManipulator.GetAllIDs(model).ToList();
}
if (null == model.Id)
{
chemModelCount = SetId(CHEMMODEL_PREFIX, chemModelCount, model, tabuList);
}
var crystal = model.Crystal;
if (crystal != null)
{
if (policy == UniquePolicy.Object)
{
atomCount = 0;
bondCount = 0;
}
CreateIDsForAtomContainer(crystal, tabuList);
}
var moleculeSet = model.MoleculeSet;
if (moleculeSet != null)
{
if (policy == UniquePolicy.Object)
{
atomContainerSetCount = 0;
atomContainerCount = 0;
}
CreateIDsForAtomContainerSet(moleculeSet, tabuList);
}
var reactionSet = model.ReactionSet;
if (reactionSet != null)
{
if (policy == UniquePolicy.Object)
{
reactionSetCount = 0;
reactionCount = 0;
}
CreateIDsForReactionSet(reactionSet, tabuList);
}
}
public override void Write(IChemObject obj)
{
if (obj is ICrystal)
{
WriteCrystal((ICrystal)obj);
}
else if (obj is IAtomContainer)
{
WriteMolecule((IAtomContainer)obj);
}
else if (obj is IChemFile chemFile)
{
IChemSequence sequence = chemFile[0];
if (sequence != null)
{
IChemModel model = sequence[0];
if (model != null)
{
ICrystal crystal = model.Crystal;
if (crystal != null)
{
Write(crystal);
}
else
{
var containers = ChemModelManipulator.GetAllAtomContainers(model);
foreach (var container in containers)
{
WriteMolecule(model.Builder.NewAtomContainer(container));
}
}
}
}
}
else
{
throw new CDKException("Only supported is writing of Molecule, Crystal and ChemFile objects.");
}
}
void AssertBondCount(int expectedBondCount, IChemObject chemObject)
{
if (expectedBondCount != -1)
{
if (chemObject is IChemFile)
{
Assert.AreEqual(expectedBondCount, ChemFileManipulator.GetBondCount((IChemFile)chemObject));
}
else if (chemObject is IChemModel)
{
Assert.AreEqual(expectedBondCount, ChemModelManipulator.GetBondCount((IChemModel)chemObject));
}
else if (chemObject is IAtomContainer)
{
Assert.AreEqual(expectedBondCount, ((IAtomContainer)chemObject).Bonds.Count);
}
else if (chemObject is IReaction)
{
Assert.AreEqual(expectedBondCount, ReactionManipulator.GetBondCount((IReaction)chemObject));
}
}
}
/// <summary>
/// Reads NMR nuclear shieldings.
/// </summary>
/// <param name="model"></param>
/// <param name="labelLine"></param>
private void ReadNMRData(IChemModel model, string labelLine)
{
var containers = ChemModelManipulator.GetAllAtomContainers(model).ToReadOnlyList();
if (containers.Count == 0)
{
// nothing to store the results into
return;
} // otherwise insert in the first AC
IAtomContainer ac = containers[0];
// Determine label for properties
string label;
if (labelLine.Contains("Diamagnetic"))
{
label = "Diamagnetic Magnetic shielding (Isotropic)";
}
else if (labelLine.Contains("Paramagnetic"))
{
label = "Paramagnetic Magnetic shielding (Isotropic)";
}
else
{
label = "Magnetic shielding (Isotropic)";
}
int atomIndex = 0;
for (int i = 0; i < atomCount; ++i)
{
try
{
string line = input.ReadLine().Trim();
while (!line.Contains("Isotropic"))
{
if (line == null)
{
return;
}
line = input.ReadLine().Trim();
}
var st1 = Strings.Tokenize(line).GetEnumerator();
// Find Isotropic label
while (st1.MoveNext())
{
if (string.Equals(st1.Current, "Isotropic", StringComparison.Ordinal))
{
break;
}
}
// Find Isotropic value
while (st1.MoveNext())
{
if (string.Equals(st1.Current, "=", StringComparison.Ordinal))
{
break;
}
}
st1.MoveNext();
double shielding = double.Parse(st1.Current, NumberFormatInfo.InvariantInfo);
Trace.TraceInformation("Type of shielding: " + label);
ac.Atoms[atomIndex].SetProperty(CDKPropertyName.IsotropicShielding, shielding);
++atomIndex;
}
catch (Exception exc)
{
if (!(exc is IOException || exc is FormatException))
{
throw;
}
Debug.WriteLine("failed to read line from gaussian98 file where I expected one.");
}
}
}
/// <summary> Reads a set of vibrations into ChemFrame.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <exception cref="IOException"> if an I/O error occurs
/// </exception>
// private void readFrequencies(IChemModel model) throws IOException
// {
/*
* FIXME: this is yet to be ported
* String line;
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* while ((line != null) && line.startsWith(" Frequencies --")) {
* Vector currentVibs = new Vector();
* StringReader vibValRead = new StringReader(line.substring(15));
* StreamTokenizer token = new StreamTokenizer(vibValRead);
* while (token.nextToken() != StreamTokenizer.TT_EOF) {
* Vibration vib = new Vibration(Double.toString(token.nval));
* currentVibs.addElement(vib);
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* for (int i = 0; i < frame.getAtomCount(); ++i) {
* line = input.readLine();
* StringReader vectorRead = new StringReader(line);
* token = new StreamTokenizer(vectorRead);
* token.nextToken();
* / ignore first token
* token.nextToken();
* / ignore second token
* for (int j = 0; j < currentVibs.size(); ++j) {
* double[] v = new double[3];
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[0] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[1] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
* v[2] = token.nval;
* } else {
* throw new IOException("Error reading frequency");
* }
* ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
* }
* }
* for (int i = 0; i < currentVibs.size(); ++i) {
* frame.addVibration((Vibration) currentVibs.elementAt(i));
* }
* line = input.readLine();
* line = input.readLine();
* line = input.readLine();
* }
*/
// }
/// <summary> Reads NMR nuclear shieldings.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <param name="labelLine">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
private void readNMRData(IChemModel model, System.String labelLine)
{
IAtomContainer ac = ChemModelManipulator.getAllInOneContainer(model);
// Determine label for properties
System.String label;
if (labelLine.IndexOf("Diamagnetic") >= 0)
{
label = "Diamagnetic Magnetic shielding (Isotropic)";
}
else if (labelLine.IndexOf("Paramagnetic") >= 0)
{
label = "Paramagnetic Magnetic shielding (Isotropic)";
}
else
{
label = "Magnetic shielding (Isotropic)";
}
int atomIndex = 0;
for (int i = 0; i < atomCount; ++i)
{
try
{
System.String line = input.ReadLine().Trim();
while (line.IndexOf("Isotropic") < 0)
{
if (line == null)
{
return;
}
line = input.ReadLine().Trim();
}
SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(line);
// Find Isotropic label
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("Isotropic"))
{
break;
}
}
// Find Isotropic value
while (st1.HasMoreTokens())
{
if (st1.NextToken().Equals("="))
{
break;
}
}
double shielding = System.Double.Parse(st1.NextToken());
//logger.info("Type of shielding: " + label);
ac.getAtomAt(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, (System.Object)shielding);
++atomIndex;
}
catch (System.Exception exc)
{
//logger.debug("failed to read line from gaussian98 file where I expected one.");
}
}
}
private static void ProcessChemModel(IChemModel chemModel, ISettings settings, FileUsage usage,
MoleculeLoadingResults results, MoleculeProcessingProgress progress,
float sectionSz)
{
//if (ChemModelManipulator.getAllInOneContainer(chemModel).getBondCount() == 0)
//{
// return;
//}
// check for coordinates
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))//
{
results.Num2DCoords++;
}
// usage == FileUsage.TwoD)
//{
// throw new UserLevelException("File has no 2D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))// &&
{
results.Num3DCoords++;
}
// usage == FileUsage.ThreeD)
//{
// throw new UserLevelException("File has no 3D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
ElementPTFactory elements = ElementPTFactory.Instance;
// calc item sz
int numItems = 0;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
numItems += chemModel.SetOfMolecules.Molecules[mol].Atoms.Length;
//numItems += chemModel.SetOfMolecules.Molecules[mol].Bonds.Length;
}
}
float itemSz = sectionSz / (float)numItems;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
IMolecule molecule = chemModel.SetOfMolecules.Molecules[mol];
results.NumAtoms += molecule.Atoms.Length;
results.NumBonds += molecule.Bonds.Length;
foreach (IAtom atom in molecule.Atoms)
{
PeriodicTableElement pe = elements.getElement(atom.Symbol);
if (pe != null)
{
atom.AtomicNumber = pe.AtomicNumber;
atom.Properties["PeriodicTableElement"] = pe;
atom.Properties["Period"] = int.Parse(pe.Period);
}
else
{
progress.Log(string.Format("Failed to find periodic element: {0}", atom.Symbol), LogItem.ItemLevel.Failure);
}
progress.UpdateProgress(itemSz);
}
progress.Log(string.Format("Processed {0} atoms", molecule.Atoms.Length), LogItem.ItemLevel.Info);
}
}
progress.Log("Processed Model", LogItem.ItemLevel.Success);
}
public void TestBug1714794()
{
var problematicMol2 = "@<TRIPOS>MOLECULE\n" + "mol_197219.smi\n" + " 129 135 0 0 0\n" + "SMALL\n"
+ "GASTEIGER\n" + "Energy = 0\n" + "\n" + "@<TRIPOS>ATOM\n"
+ " 1 N1 0.0000 0.0000 0.0000 N.am 1 <1> -0.2782\n"
+ " 2 H1 0.0000 0.0000 0.0000 H 1 <1> 0.1552\n"
+ " 3 C1 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0886\n"
+ " 4 C2 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1500\n"
+ " 5 C3 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0714\n"
+ " 6 C4 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0456\n"
+ " 7 C5 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0788\n"
+ " 8 C6 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1435\n"
+ " 9 C7 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0342\n"
+ " 10 C8 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1346\n"
+ " 11 O1 0.0000 0.0000 0.0000 O.3 1 <1> -0.5057\n"
+ " 12 H2 0.0000 0.0000 0.0000 H 1 <1> 0.2922\n"
+ " 13 C9 0.0000 0.0000 0.0000 C.3 1 <1> -0.0327\n"
+ " 14 H3 0.0000 0.0000 0.0000 H 1 <1> 0.0280\n"
+ " 15 H4 0.0000 0.0000 0.0000 H 1 <1> 0.0280\n"
+ " 16 H5 0.0000 0.0000 0.0000 H 1 <1> 0.0280\n"
+ " 17 O2 0.0000 0.0000 0.0000 O.3 1 <1> -0.4436\n"
+ " 18 C10 0.0000 0.0000 0.0000 C.3 1 <1> 0.3143\n"
+ " 19 O3 0.0000 0.0000 0.0000 O.2 1 <1> -0.4528\n"
+ " 20 C11 0.0000 0.0000 0.0000 C.2 1 <1> 0.0882\n"
+ " 21 H6 0.0000 0.0000 0.0000 H 1 <1> 0.1022\n"
+ " 22 C12 0.0000 0.0000 0.0000 C.2 1 <1> -0.0208\n"
+ " 23 H7 0.0000 0.0000 0.0000 H 1 <1> 0.0628\n"
+ " 24 C13 0.0000 0.0000 0.0000 C.3 1 <1> 0.0854\n"
+ " 25 H8 0.0000 0.0000 0.0000 H 1 <1> 0.0645\n"
+ " 26 C14 0.0000 0.0000 0.0000 C.3 1 <1> 0.0236\n"
+ " 27 H9 0.0000 0.0000 0.0000 H 1 <1> 0.0362\n"
+ " 28 C15 0.0000 0.0000 0.0000 C.3 1 <1> 0.1131\n"
+ " 29 H10 0.0000 0.0000 0.0000 H 1 <1> 0.0741\n"
+ " 30 C16 0.0000 0.0000 0.0000 C.3 1 <1> 0.0200\n"
+ " 31 H11 0.0000 0.0000 0.0000 H 1 <1> 0.0359\n"
+ " 32 C17 0.0000 0.0000 0.0000 C.3 1 <1> 0.0661\n"
+ " 33 H12 0.0000 0.0000 0.0000 H 1 <1> 0.0600\n"
+ " 34 C18 0.0000 0.0000 0.0000 C.3 1 <1> 0.0091\n"
+ " 35 H13 0.0000 0.0000 0.0000 H 1 <1> 0.0348\n"
+ " 36 C19 0.0000 0.0000 0.0000 C.3 1 <1> 0.0661\n"
+ " 37 H14 0.0000 0.0000 0.0000 H 1 <1> 0.0602\n"
+ " 38 C20 0.0000 0.0000 0.0000 C.3 1 <1> 0.0009\n"
+ " 39 H15 0.0000 0.0000 0.0000 H 1 <1> 0.0365\n"
+ " 40 C21 0.0000 0.0000 0.0000 C.2 1 <1> -0.0787\n"
+ " 41 H16 0.0000 0.0000 0.0000 H 1 <1> 0.0576\n"
+ " 42 C22 0.0000 0.0000 0.0000 C.2 1 <1> -0.0649\n"
+ " 43 H17 0.0000 0.0000 0.0000 H 1 <1> 0.0615\n"
+ " 44 C23 0.0000 0.0000 0.0000 C.2 1 <1> -0.0542\n"
+ " 45 H18 0.0000 0.0000 0.0000 H 1 <1> 0.0622\n"
+ " 46 C24 0.0000 0.0000 0.0000 C.2 1 <1> 0.0115\n"
+ " 47 C25 0.0000 0.0000 0.0000 C.2 1 <1> 0.2441\n"
+ " 48 O4 0.0000 0.0000 0.0000 O.2 1 <1> -0.2702\n"
+ " 49 C26 0.0000 0.0000 0.0000 C.3 1 <1> -0.0348\n"
+ " 50 H19 0.0000 0.0000 0.0000 H 1 <1> 0.0279\n"
+ " 51 H20 0.0000 0.0000 0.0000 H 1 <1> 0.0279\n"
+ " 52 H21 0.0000 0.0000 0.0000 H 1 <1> 0.0279\n"
+ " 53 C27 0.0000 0.0000 0.0000 C.3 1 <1> -0.0566\n"
+ " 54 H22 0.0000 0.0000 0.0000 H 1 <1> 0.0236\n"
+ " 55 H23 0.0000 0.0000 0.0000 H 1 <1> 0.0236\n"
+ " 56 H24 0.0000 0.0000 0.0000 H 1 <1> 0.0236\n"
+ " 57 O5 0.0000 0.0000 0.0000 O.3 1 <1> -0.3909\n"
+ " 58 H25 0.0000 0.0000 0.0000 H 1 <1> 0.2098\n"
+ " 59 C28 0.0000 0.0000 0.0000 C.3 1 <1> -0.0577\n"
+ " 60 H26 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 61 H27 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 62 H28 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 63 O6 0.0000 0.0000 0.0000 O.3 1 <1> -0.3910\n"
+ " 64 H29 0.0000 0.0000 0.0000 H 1 <1> 0.2098\n"
+ " 65 C29 0.0000 0.0000 0.0000 C.3 1 <1> -0.0567\n"
+ " 66 H30 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 67 H31 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 68 H32 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 69 O7 0.0000 0.0000 0.0000 O.3 1 <1> -0.4608\n"
+ " 70 C30 0.0000 0.0000 0.0000 C.2 1 <1> 0.3042\n"
+ " 71 O8 0.0000 0.0000 0.0000 O.2 1 <1> -0.2512\n"
+ " 72 C31 0.0000 0.0000 0.0000 C.3 1 <1> 0.0332\n"
+ " 73 H33 0.0000 0.0000 0.0000 H 1 <1> 0.0342\n"
+ " 74 H34 0.0000 0.0000 0.0000 H 1 <1> 0.0342\n"
+ " 75 H35 0.0000 0.0000 0.0000 H 1 <1> 0.0342\n"
+ " 76 C32 0.0000 0.0000 0.0000 C.3 1 <1> -0.0564\n"
+ " 77 H36 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 78 H37 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 79 H38 0.0000 0.0000 0.0000 H 1 <1> 0.0234\n"
+ " 80 O9 0.0000 0.0000 0.0000 O.3 1 <1> -0.3753\n"
+ " 81 C33 0.0000 0.0000 0.0000 C.3 1 <1> 0.0372\n"
+ " 82 H39 0.0000 0.0000 0.0000 H 1 <1> 0.0524\n"
+ " 83 H40 0.0000 0.0000 0.0000 H 1 <1> 0.0524\n"
+ " 84 H41 0.0000 0.0000 0.0000 H 1 <1> 0.0524\n"
+ " 85 C34 0.0000 0.0000 0.0000 C.2 1 <1> 0.2505\n"
+ " 86 O10 0.0000 0.0000 0.0000 O.2 1 <1> -0.2836\n"
+ " 87 C35 0.0000 0.0000 0.0000 C.3 1 <1> 0.0210\n"
+ " 88 H42 0.0000 0.0000 0.0000 H 1 <1> 0.0309\n"
+ " 89 H43 0.0000 0.0000 0.0000 H 1 <1> 0.0309\n"
+ " 90 H44 0.0000 0.0000 0.0000 H 1 <1> 0.0309\n"
+ " 91 C36 0.0000 0.0000 0.0000 C.ar 1 <1> 0.1361\n"
+ " 92 C37 0.0000 0.0000 0.0000 C.ar 1 <1> 0.0613\n"
+ " 93 C38 0.0000 0.0000 0.0000 C.2 1 <1> 0.0580\n"
+ " 94 H45 0.0000 0.0000 0.0000 H 1 <1> 0.0853\n"
+ " 95 N2 0.0000 0.0000 0.0000 N.2 1 <1> -0.1915\n"
+ " 96 N3 0.0000 0.0000 0.0000 N.pl3 1 <1> -0.2525\n"
+ " 97 C39 0.0000 0.0000 0.0000 C.3 1 <1> 0.0525\n"
+ " 98 C40 0.0000 0.0000 0.0000 C.3 1 <1> -0.0271\n"
+ " 99 H46 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 100 H47 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 101 C41 0.0000 0.0000 0.0000 C.3 1 <1> -0.0385\n"
+ " 102 H48 0.0000 0.0000 0.0000 H 1 <1> 0.0302\n"
+ " 103 C42 0.0000 0.0000 0.0000 C.3 1 <1> -0.0472\n"
+ " 104 H49 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 105 H50 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 106 C43 0.0000 0.0000 0.0000 C.3 1 <1> -0.0385\n"
+ " 107 H51 0.0000 0.0000 0.0000 H 1 <1> 0.0302\n"
+ " 108 C44 0.0000 0.0000 0.0000 C.3 1 <1> -0.0271\n"
+ " 109 H52 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 110 H53 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 111 C45 0.0000 0.0000 0.0000 C.3 1 <1> -0.0472\n"
+ " 112 H54 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 113 H55 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 114 C46 0.0000 0.0000 0.0000 C.3 1 <1> -0.0385\n"
+ " 115 H56 0.0000 0.0000 0.0000 H 1 <1> 0.0302\n"
+ " 116 C47 0.0000 0.0000 0.0000 C.3 1 <1> -0.0271\n"
+ " 117 H57 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 118 H58 0.0000 0.0000 0.0000 H 1 <1> 0.0289\n"
+ " 119 C48 0.0000 0.0000 0.0000 C.3 1 <1> -0.0472\n"
+ " 120 H59 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 121 H60 0.0000 0.0000 0.0000 H 1 <1> 0.0271\n"
+ " 122 C49 0.0000 0.0000 0.0000 C.3 1 <1> 0.0189\n"
+ " 123 H61 0.0000 0.0000 0.0000 H 1 <1> 0.0444\n"
+ " 124 H62 0.0000 0.0000 0.0000 H 1 <1> 0.0444\n"
+ " 125 H63 0.0000 0.0000 0.0000 H 1 <1> 0.0444\n"
+ " 126 O11 0.0000 0.0000 0.0000 O.3 1 <1> -0.5054\n"
+ " 127 H64 0.0000 0.0000 0.0000 H 1 <1> 0.2922\n"
+ " 128 O12 0.0000 0.0000 0.0000 O.3 1 <1> -0.5042\n"
+ " 129 H65 0.0000 0.0000 0.0000 H 1 <1> 0.2923\n" + "@<TRIPOS>BOND\n"
+ " 1 1 2 1\n" + " 2 1 3 1\n" + " 3 3 4 ar\n"
+ " 4 4 5 ar\n" + " 5 5 6 ar\n" + " 6 6 7 ar\n"
+ " 7 7 8 ar\n" + " 8 8 9 ar\n" + " 9 9 10 ar\n"
+ " 10 5 10 ar\n" + " 11 10 11 1\n" + " 12 11 12 1\n"
+ " 13 9 13 1\n" + " 14 13 14 1\n" + " 15 13 15 1\n"
+ " 16 13 16 1\n" + " 17 8 17 1\n" + " 18 17 18 1\n"
+ " 19 18 19 1\n" + " 20 19 20 1\n" + " 21 20 21 1\n"
+ " 22 20 22 2\n" + " 23 22 23 1\n" + " 24 22 24 1\n"
+ " 25 24 25 1\n" + " 26 24 26 1\n" + " 27 26 27 1\n"
+ " 28 26 28 1\n" + " 29 28 29 1\n" + " 30 28 30 1\n"
+ " 31 30 31 1\n" + " 32 30 32 1\n" + " 33 32 33 1\n"
+ " 34 32 34 1\n" + " 35 34 35 1\n" + " 36 34 36 1\n"
+ " 37 36 37 1\n" + " 38 36 38 1\n" + " 39 38 39 1\n"
+ " 40 38 40 1\n" + " 41 40 41 1\n" + " 42 40 42 2\n"
+ " 43 42 43 1\n" + " 44 42 44 1\n" + " 45 44 45 1\n"
+ " 46 44 46 2\n" + " 47 46 47 1\n" + " 48 1 47 am\n"
+ " 49 47 48 2\n" + " 50 46 49 1\n" + " 51 49 50 1\n"
+ " 52 49 51 1\n" + " 53 49 52 1\n" + " 54 38 53 1\n"
+ " 55 53 54 1\n" + " 56 53 55 1\n" + " 57 53 56 1\n"
+ " 58 36 57 1\n" + " 59 57 58 1\n" + " 60 34 59 1\n"
+ " 61 59 60 1\n" + " 62 59 61 1\n" + " 63 59 62 1\n"
+ " 64 32 63 1\n" + " 65 63 64 1\n" + " 66 30 65 1\n"
+ " 67 65 66 1\n" + " 68 65 67 1\n" + " 69 65 68 1\n"
+ " 70 28 69 1\n" + " 71 69 70 1\n" + " 72 70 71 2\n"
+ " 73 70 72 1\n" + " 74 72 73 1\n" + " 75 72 74 1\n"
+ " 76 72 75 1\n" + " 77 26 76 1\n" + " 78 76 77 1\n"
+ " 79 76 78 1\n" + " 80 76 79 1\n" + " 81 24 80 1\n"
+ " 82 80 81 1\n" + " 83 81 82 1\n" + " 84 81 83 1\n"
+ " 85 81 84 1\n" + " 86 18 85 1\n" + " 87 7 85 1\n"
+ " 88 85 86 2\n" + " 89 18 87 1\n" + " 90 87 88 1\n"
+ " 91 87 89 1\n" + " 92 87 90 1\n" + " 93 6 91 ar\n"
+ " 94 91 92 ar\n" + " 95 3 92 ar\n" + " 96 92 93 1\n"
+ " 97 93 94 1\n" + " 98 93 95 2\n" + " 99 95 96 1\n"
+ " 100 96 97 1\n" + " 101 97 98 1\n" + " 102 98 99 1\n"
+ " 103 98 100 1\n" + " 104 98 101 1\n" + " 105 101 102 1\n"
+ " 106 101 103 1\n" + " 107 103 104 1\n" + " 108 103 105 1\n"
+ " 109 103 106 1\n" + " 110 106 107 1\n" + " 111 106 108 1\n"
+ " 112 108 109 1\n" + " 113 108 110 1\n" + " 114 97 108 1\n"
+ " 115 106 111 1\n" + " 116 111 112 1\n" + " 117 111 113 1\n"
+ " 118 111 114 1\n" + " 119 114 115 1\n" + " 120 114 116 1\n"
+ " 121 116 117 1\n" + " 122 116 118 1\n" + " 123 97 116 1\n"
+ " 124 114 119 1\n" + " 125 119 120 1\n" + " 126 119 121 1\n"
+ " 127 101 119 1\n" + " 128 96 122 1\n" + " 129 122 123 1\n"
+ " 130 122 124 1\n" + " 131 122 125 1\n" + " 132 91 126 1\n"
+ " 133 126 127 1\n" + " 134 4 128 1\n" + " 135 128 129 1\n";
IChemModel model;
using (var r = new Mol2Reader(new StringReader(problematicMol2)))
{
model = (IChemModel)r.Read(CDK.Builder.NewChemModel());
}
Assert.IsNotNull(model);
var containers = ChemModelManipulator.GetAllAtomContainers(model);
Assert.AreEqual(1, containers.Count());
var molecule = containers.FirstOrDefault();
Assert.IsNotNull(molecule);
Assert.AreEqual(129, molecule.Atoms.Count);
Assert.AreEqual(135, molecule.Bonds.Count);
foreach (var atom in molecule.Atoms)
{
Assert.IsNotNull(atom.AtomTypeName);
}
}
