/// <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>
/// Places the atoms in a linear chain.
/// </summary>
/// <remarks>
/// Expects the first atom to be placed and
/// places the next atom according to initialBondVector. The rest of the chain
/// is placed such that it is as linear as possible (in the overall result, the
/// angles in the chain are set to 120 Deg.)
/// </remarks>
/// <param name="atomContainer">The IAtomContainer containing the chain atom to be placed</param>
/// <param name="initialBondVector">The Vector indicating the direction of the first bond</param>
/// <param name="bondLength">The factor used to scale the initialBondVector</param>
public void PlaceLinearChain(IAtomContainer atomContainer, Vector2 initialBondVector, double bondLength)
{
var withh = atomContainer.Builder.NewAtomContainer(atomContainer);
// BUGFIX - withh does not have cloned cloned atoms, so changes are
// reflected in our atom container. If we're using implicit hydrogens
// the correct counts need saving and restoring
var numh = new int[atomContainer.Atoms.Count];
for (int i = 0, n = atomContainer.Atoms.Count; i < n; i++)
{
numh[i] = atomContainer.Atoms[i].ImplicitHydrogenCount ?? 0;
}
Debug.WriteLine($"Placing linear chain of length {atomContainer.Atoms.Count}");
var bondVector = initialBondVector;
IBond prevBond = null;
for (int f = 0; f < atomContainer.Atoms.Count - 1; f++)
{
var atom = atomContainer.Atoms[f];
var nextAtom = atomContainer.Atoms[f + 1];
var currBond = atomContainer.GetBond(atom, nextAtom);
var atomPoint = atom.Point2D.Value;
bondVector = Vector2.Normalize(bondVector);
bondVector = bondVector * bondLength;
atomPoint += bondVector;
nextAtom.Point2D = atomPoint;
nextAtom.IsPlaced = true;
bool trans = false;
if (prevBond != null && IsColinear(atom, Molecule.GetConnectedBonds(atom)))
{
int atomicNumber = atom.AtomicNumber;
int charge = atom.FormalCharge.Value;
// double length of the last bond to determining next placement
var p = prevBond.GetOther(atom).Point2D.Value;
p = Vector2.Lerp(p, atom.Point2D.Value, 2);
nextAtom.Point2D = p;
}
if (GeometryUtil.Has2DCoordinates(atomContainer))
{
try
{
if (f > 2 && BondTools.IsValidDoubleBondConfiguration(withh, withh.GetBond(withh.Atoms[f - 2], withh.Atoms[f - 1])))
{
trans = BondTools.IsCisTrans(withh.Atoms[f - 3], withh.Atoms[f - 2], withh.Atoms[f - 1], withh.Atoms[f - 0], withh);
}
}
catch (Exception)
{
Debug.WriteLine("Exception in detecting E/Z. This could mean that cleanup does not respect E/Z");
}
bondVector = GetNextBondVector(nextAtom, atom, GeometryUtil.Get2DCenter(Molecule), trans);
}
else
{
bondVector = GetNextBondVector(nextAtom, atom, GeometryUtil.Get2DCenter(Molecule), true);
}
prevBond = currBond;
}
// BUGFIX part 2 - restore hydrogen counts
for (int i = 0, n = atomContainer.Atoms.Count; i < n; i++)
{
atomContainer.Atoms[i].ImplicitHydrogenCount = numh[i];
}
}
