public void TestRemoveHydrogensAndPreserveAtomID()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(rawMolSmiles);
IAtom beforeAtom = null;
IAtom afterAtom = null;
foreach (var a in atomContainer.Atoms)
{
if (string.Equals(a.Symbol, "P", StringComparison.OrdinalIgnoreCase))
{
beforeAtom = a;
a.Id = "TEST";
break;
}
}
IAtomContainer result = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(atomContainer);
foreach (var a in result.Atoms)
{
if (string.Equals(a.Symbol, "P", StringComparison.OrdinalIgnoreCase))
{
afterAtom = a;
break;
}
}
Assert.AreEqual(afterAtom.Id, beforeAtom.Id);
}
/// <summary>
/// Creates a new instance of MolHandler
/// </summary>
/// <param name="molFile">atomContainer file name</param>
public MolHandler(string molFile, bool removeHydrogen, bool cleanMolecule)
{
MDLReader molRead = null;
this.removeHydrogen = removeHydrogen;
try
{
Stream readMolecule = null;
readMolecule = new FileStream(molFile, FileMode.Open, FileAccess.Read);
molRead = new MDLReader(new StreamReader(readMolecule));
this.atomContainer = (IAtomContainer)molRead.Read(new AtomContainer());
molRead.Close();
readMolecule.Close();
/* Remove Hydrogen by Asad */
if (removeHydrogen)
{
atomContainer = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(atomContainer);
}
if (cleanMolecule)
{
if (!IsPseudoAtoms())
{
atomContainer = canonLabeler.GetCanonicalMolecule(atomContainer);
}
// percieve atoms, set valency etc
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(atomContainer);
//Add implicit Hydrogens
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(atomContainer);
// figure out which atoms are in aromatic rings:
Aromaticity.CDKLegacy.Apply(atomContainer);
BondTools.MakeUpDownBonds(atomContainer);
}
}
catch (IOException ex)
{
Debug.WriteLine(ex);
}
catch (CDKException e)
{
Console.Error.WriteLine(e);
}
finally
{
if (molRead != null)
{
try
{
molRead.Close();
}
catch (IOException ioe)
{
Trace.TraceWarning("Couldn't close molReader: ", ioe.Message);
Debug.WriteLine(ioe);
}
}
}
}
/// <summary>
/// Creates a new instance of MolHandler
/// <param name="container">Molecule AtomContainer</param>
/// </summary>
public MolHandler(IAtomContainer container, bool removeHydrogen, bool cleanMolecule)
{
string molID = container.Id;
this.removeHydrogen = removeHydrogen;
this.atomContainer = container;
if (removeHydrogen)
{
try
{
this.atomContainer = ExtAtomContainerManipulator
.RemoveHydrogensExceptSingleAndPreserveAtomID(atomContainer);
}
catch (Exception ex)
{
Trace.TraceError(ex.Message);
}
}
else
{
this.atomContainer = container.Builder.NewAtomContainer(atomContainer);
}
if (cleanMolecule)
{
try
{
if (!IsPseudoAtoms())
{
atomContainer = canonLabeler.GetCanonicalMolecule(atomContainer);
}
// percieve atoms, set valency etc
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(atomContainer);
//Add implicit Hydrogens
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(atomContainer);
// figure out which atoms are in aromatic rings:
Aromaticity.CDKLegacy.Apply(atomContainer);
}
catch (CDKException ex)
{
Trace.TraceError(ex.Message);
}
}
atomContainer.Id = molID;
}