/// <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);
}
}
}
}
public IReaction LabelReaction(IReaction reaction, ICanonicalMoleculeLabeller labeller)
{
Console.Out.WriteLine("labelling");
var canonReaction = new Reaction();
var permutationMap = new Dictionary <IAtomContainer, int[]>();
var canonicalProducts = ChemObjectBuilder.Instance.NewChemObjectSet <IAtomContainer>();
foreach (var product in reaction.Products)
{
var canonicalForm = labeller.GetCanonicalMolecule(product);
if (fixAtomMappingCastType)
{
FixAtomMapping(canonicalForm);
}
var canonicalMolecule = canonicalForm.Builder.NewAtomContainer(canonicalForm);
permutationMap[canonicalMolecule] = labeller.GetCanonicalPermutation(product);
canonicalProducts.Add(canonicalMolecule);
}
var canonicalReactants = ChemObjectBuilder.Instance.NewChemObjectSet <IAtomContainer>();
foreach (var reactant in reaction.Reactants)
{
var canonicalForm = labeller.GetCanonicalMolecule(reactant);
if (fixAtomMappingCastType)
{
FixAtomMapping(canonicalForm);
}
var canonicalMolecule = canonicalForm.Builder.NewAtomContainer(canonicalForm);
permutationMap[canonicalMolecule] = labeller.GetCanonicalPermutation(reactant);
canonicalReactants.Add(canonicalMolecule);
}
canonReaction.Products.AddRange(canonicalProducts);
canonReaction.Reactants.AddRange(canonicalReactants);
CloneAndSortMappings(reaction, canonReaction, permutationMap);
return(canonReaction);
}
