/// <summary>
/// Remove the following features from a molecule
/// - Atom non-standard mass
/// - Stereo chemistry
/// - explicit hydrogens
/// </summary>
/// <param name="src"></param>
/// <returns>Modified mol</returns>
public static IAtomContainer RemoveIsotopesStereoExplicitHydrogens(
IAtomContainer src)
{
IAtom[] atoms = new IAtom[src.Atoms.Count];
IBond[] bonds = new IBond[src.Bonds.Count];
IChemObjectBuilder builder = src.Builder;
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = src.Atoms[i];
IAtom atom2 = builder.NewAtom(atom.Symbol);
SetImplicitHydrogenCount(atom2, GetImplicitHydrogenCount(atom));
atom2.Point2D = atom.Point2D;
atoms[i] = atom2;
}
for (int i = 0; i < bonds.Length; i++)
{
IBond bond = src.Bonds[i];
int u = bond.Atoms[0].Index;
int v = bond.Atoms[1].Index;
IBond bond2 = builder.NewBond(atoms[u], atoms[v]);
bond2.IsAromatic = bond.IsAromatic;
bond2.IsInRing = bond.IsInRing;
bond2.Order = bond.Order;
bond2.IsAromatic = bond.IsAromatic;
bond2.IsSingleOrDouble = bond.IsSingleOrDouble;
bonds[i] = bond2;
}
IAtomContainer dest = ChemObjectBuilder.Instance.NewAtomContainer();
dest.SetAtoms(atoms);
dest.SetBonds(bonds);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(dest);
dest = AtomContainerManipulator.SuppressHydrogens(dest);
GetHydrogenAdder().AddImplicitHydrogens(dest);
return(dest);
}
public void TestTraversal_Chain()
{
var builder = CDK.Builder;
IAtom[] atoms = new IAtom[] { builder.NewAtom("C"), builder.NewAtom("C"),
builder.NewAtom("C"), builder.NewAtom("C"),
builder.NewAtom("C"), builder.NewAtom("C") };
IBond[] bonds = new IBond[] { builder.NewBond(atoms[0], atoms[1]),
builder.NewBond(atoms[1], atoms[2]),
builder.NewBond(atoms[2], atoms[3]),
builder.NewBond(atoms[3], atoms[4]),
builder.NewBond(atoms[4], atoms[5]) };
IAtomContainer m = builder.NewAtomContainer();
m.SetAtoms(atoms);
m.SetBonds(bonds);
List <IBond> accumulator = new List <IBond>();
// traverse from one end
FragmentUtils.Traverse(m, atoms[0], accumulator);
Assert.AreEqual(5, accumulator.Count);
Assert.AreEqual(bonds[0], accumulator[0]);
Assert.AreEqual(bonds[1], accumulator[1]);
Assert.AreEqual(bonds[2], accumulator[2]);
Assert.AreEqual(bonds[3], accumulator[3]);
Assert.AreEqual(bonds[4], accumulator[4]);
// traverse from the middle
accumulator.Clear();
FragmentUtils.Traverse(m, atoms[3], accumulator);
Assert.AreEqual(5, accumulator.Count);
Assert.AreEqual(bonds[2], accumulator[0]);
Assert.AreEqual(bonds[1], accumulator[1]);
Assert.AreEqual(bonds[0], accumulator[2]);
Assert.AreEqual(bonds[3], accumulator[3]);
Assert.AreEqual(bonds[4], accumulator[4]);
}
/// <summary>
/// (Converted from Java to C# for possible later modification)
/// Suppress any explicit hydrogens in the provided container. Only hydrogens
/// that can be represented as a hydrogen count value on the atom are
/// suppressed. The container is updated and no elements are copied, please
/// use either <seealso cref="#copyAndSuppressedHydrogens"/> if you would to preserve
/// the old instance.
/// </summary>
/// <param name="org"> the container from which to remove hydrogens </param>
/// <returns> the input for convenience </returns>
/// <seealso cref= #copyAndSuppressedHydrogens </seealso>
public IAtomContainer suppressHydrogens(IAtomContainer org)
{
bool anyHydrogenPresent = false;
for (int ai = 0; ai < org.Atoms.Count; ai++)
{
IAtom atom = org.Atoms[ai];
if ("H".Equals(atom.Symbol))
{
anyHydrogenPresent = true;
break;
}
}
if (!anyHydrogenPresent)
{
return(org);
}
// we need fast adjacency checks (to check for suppression and
// update hydrogen counts)
int[][] graph = GraphUtil.ToAdjList(org);
int nOrgAtoms = org.Atoms.Count;
int nOrgBonds = org.Bonds.Count;
int nCpyAtoms = 0;
int nCpyBonds = 0;
ISet <IAtom> hydrogens = new HashSet <IAtom>();
IAtom[] cpyAtoms = new IAtom[nOrgAtoms];
// filter the original container atoms for those that can/can't
// be suppressed
for (int v = 0; v < nOrgAtoms; v++)
{
IAtom atom = org.Atoms[v];
if (suppressibleHydrogen(org, graph, v))
{
hydrogens.Add(atom);
incrementImplHydrogenCount(org.Atoms[graph[v][0]]);
}
else
{
cpyAtoms[nCpyAtoms++] = atom;
}
}
// none of the hydrogens could be suppressed - no changes need to be made
if (hydrogens.Count == 0)
{
return(org);
}
org.SetAtoms(cpyAtoms);
// we now update the bonds - we have auxiliary variable remaining that
// bypasses the set membership checks if all suppressed bonds are found
IBond[] cpyBonds = new IBond[nOrgBonds - hydrogens.Count];
int remaining = hydrogens.Count;
for (int bi = 0; bi < org.Bonds.Count; bi++)
{
IBond bond = org.Bonds[bi];
if (remaining > 0 && (hydrogens.Contains(bond.Atoms[0]) || hydrogens.Contains(bond.Atoms[1])))
{
remaining--;
continue;
}
cpyBonds[nCpyBonds++] = bond;
}
// we know how many hydrogens we removed and we should have removed the
// same number of bonds otherwise the container is strange
if (nCpyBonds != cpyBonds.Length)
{
throw new System.ArgumentException("number of removed bonds was less than the number of removed hydrogens");
}
org.SetBonds(cpyBonds);
return(org);
}
/// <summary>
/// Remove explicit and implicit hydrogens bonded to positive nitrogens
/// </summary>
/// <param name="org"></param>
/// <returns></returns>
public int RemoveHydrogensBondedToPositiveNitrogens(IAtomContainer org)
{
int chg, impHydCnt;
int implicitHydRemoved = 0;
HashSet <IAtom> atomsToRemove = new HashSet <IAtom>();
HashSet <IBond> bondsToRemove = new HashSet <IBond>();
int nOrgAtoms = org.Atoms.Count;
int nOrgBonds = org.Bonds.Count;
// Get H atoms and their bonds to pos-charged Nitrogen, adjusting charge
for (int bi = 0; bi < org.Bonds.Count; bi++)
{
IBond bond = org.Bonds[bi];
if (bond.Atoms.Count != 2)
{
continue;
}
IAtom a1 = bond.Atoms[0];
IAtom a2 = bond.Atoms[1];
if (a1.Symbol == "H" && a2.Symbol == "N" && GetFormalCharge(a2) > 0)
{
chg = GetFormalCharge(a2) - 1;
SetFormalCharge(a2, chg);
atomsToRemove.Add(a1);
bondsToRemove.Add(bond);
}
else if (a2.Symbol == "H" && a1.Symbol == "N" && GetFormalCharge(a1) > 0)
{
chg = GetFormalCharge(a1) - 1;
SetFormalCharge(a1, chg);
atomsToRemove.Add(a2);
bondsToRemove.Add(bond);
}
}
// Check for implicit H attached to pos-charged N
for (int ai = 0; ai < nOrgAtoms; ai++)
{
IAtom a = org.Atoms[ai];
if (a.Symbol == "N" && GetFormalCharge(a) > 0 && GetImplicitHydrogenCount(a) > 0)
{
chg = GetFormalCharge(a) - 1;
SetFormalCharge(a, chg);
impHydCnt = GetImplicitHydrogenCount(a) - 1;
SetImplicitHydrogenCount(a, impHydCnt);
implicitHydRemoved++;
}
}
if (implicitHydRemoved > 0)
{
implicitHydRemoved = implicitHydRemoved; // debug
}
if (atomsToRemove.Count == 0)
{
return(implicitHydRemoved); // just return if no explicit H to remove
}
// Get list of atoms to keep
IAtom[] cpyAtoms = new IAtom[nOrgAtoms - atomsToRemove.Count];
int nCpyAtoms = 0;
for (int ai = 0; ai < nOrgAtoms; ai++)
{
IAtom atom = org.Atoms[ai];
if (!atomsToRemove.Contains(atom))
{
cpyAtoms[nCpyAtoms++] = atom;
}
}
org.SetAtoms(cpyAtoms);
// Get list of bonds to keep
IBond[] cpyBonds = new IBond[nOrgBonds - bondsToRemove.Count];
int nCpyBonds = 0;
for (int bi = 0; bi < org.Bonds.Count; bi++)
{
IBond bond = org.Bonds[bi];
if (!bondsToRemove.Contains(bond))
{
cpyBonds[nCpyBonds++] = bond;
}
}
org.SetBonds(cpyBonds);
return(atomsToRemove.Count + implicitHydRemoved);
}