/// <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 void TestPercieveAtomTypesAndConfigureAtoms()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(rawMolSmiles);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(atomContainer);
Assert.IsNotNull(atomContainer);
}
/// <summary>
/// Fixes Aromaticity of the molecule
/// i.e. need to find rings and aromaticity again since added H's
/// <param name="mol"></param>
/// </summary>
public static void Configure(IAtomContainer mol)
{
// need to find rings and aromaticity again since added H's
IRingSet ringSet = null;
try
{
var arf = new AllRingsFinder();
ringSet = arf.FindAllRings(mol);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
try
{
// figure out which atoms are in aromatic rings:
var cdk = CDK.HydrogenAdder;
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
cdk.AddImplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
// figure out which rings are aromatic:
RingSetManipulator.MarkAromaticRings(ringSet);
// figure out which simple (non cycles) rings are aromatic:
// only atoms in 6 membered rings are aromatic
// determine largest ring that each atom is a part of
foreach (var atom in mol.Atoms)
{
atom.IsAromatic = false;
foreach (var ring in ringSet)
{
if (!ring.IsAromatic)
{
continue;
}
bool haveatom = ring.Contains(atom);
//Debug.WriteLine("haveatom="+haveatom);
if (haveatom && ring.Atoms.Count == 6)
{
atom.IsAromatic = true;
}
}
}
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
}
/// <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;
}
/// <summary>
/// This function finds rings and uses aromaticity detection code to
/// aromatize the molecule.
/// </summary>
/// <param name="mol">input molecule</param>
public static void AromatizeMolecule(IAtomContainer mol)
{
// need to find rings and aromaticity again since added H's
IRingSet ringSet = null;
try
{
AllRingsFinder arf = new AllRingsFinder();
ringSet = arf.FindAllRings(mol);
// SSSRFinder s = new SSSRFinder(atomContainer);
// srs = s.FindEssentialRings();
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
try
{
// figure out which atoms are in aromatic rings:
// PrintAtoms(atomContainer);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
// PrintAtoms(atomContainer);
Aromaticity.CDKLegacy.Apply(mol);
// PrintAtoms(atomContainer);
// figure out which rings are aromatic:
RingSetManipulator.MarkAromaticRings(ringSet);
// PrintAtoms(atomContainer);
// figure out which simple (non cycles) rings are aromatic:
// HueckelAromaticityDetector.DetectAromaticity(atomContainer, srs);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
// only atoms in 6 membered rings are aromatic
// determine largest ring that each atom is atom part of
for (int i = 0; i <= mol.Atoms.Count - 1; i++)
{
mol.Atoms[i].IsAromatic = false;
foreach (var ring in ringSet)
{
if (!ring.IsAromatic)
{
continue;
}
bool haveatom = ring.Contains(mol.Atoms[i]);
//Debug.WriteLine("haveatom="+haveatom);
if (haveatom && ring.Atoms.Count == 6)
{
mol.Atoms[i].IsAromatic = true;
}
}
}
}