/// <summary>
/// Applies the MDL valence model to atoms using the explicit valence (bond
/// order sum) and charge to determine the correct number of implicit
/// hydrogens. The model is not applied if the explicit valence is less than
/// 0 - this is the case when a query bond was read for an atom.
/// </summary>
/// <param name="atom">the atom to apply the model to</param>
/// <param name="explicitValence">the explicit valence (bond order sum)</param>
private static void ApplyMDLValenceModel(IAtom atom, int explicitValence, int unpaired)
{
if (atom.Valency != null)
{
if (atom.Valency >= explicitValence)
{
atom.ImplicitHydrogenCount = atom.Valency - (explicitValence - unpaired);
}
else
{
atom.ImplicitHydrogenCount = 0;
}
}
else
{
int element = atom.AtomicNumber;
int charge = atom.FormalCharge ?? 0;
int implicitValence = MDLValence.ImplicitValence(element, charge, explicitValence);
if (implicitValence < explicitValence)
{
atom.Valency = explicitValence;
atom.ImplicitHydrogenCount = 0;
}
else
{
atom.Valency = implicitValence;
atom.ImplicitHydrogenCount = implicitValence - explicitValence;
}
}
}
public void Nitrogen_anion()
{
Assert.AreEqual(2, MDLValence.ImplicitValence(7, -1, 0));
Assert.AreEqual(2, MDLValence.ImplicitValence(7, -1, 1));
Assert.AreEqual(2, MDLValence.ImplicitValence(7, -1, 2));
Assert.AreEqual(3, MDLValence.ImplicitValence(7, -1, 3));
Assert.AreEqual(4, MDLValence.ImplicitValence(7, -1, 4));
Assert.AreEqual(5, MDLValence.ImplicitValence(7, -1, 5));
Assert.AreEqual(6, MDLValence.ImplicitValence(7, -1, 6));
}
public void Sodium_implicit()
{
IAtomContainer container = new AtomContainer();
IAtom atom = new Atom("Na");
container.Atoms.Add(atom);
MDLValence.Apply(container);
Assert.AreEqual(1, atom.Valency);
Assert.AreEqual(1, atom.ImplicitHydrogenCount);
}
public void Nitrogen_neutral()
{
Assert.AreEqual(3, MDLValence.ImplicitValence(7, 0, 0));
Assert.AreEqual(3, MDLValence.ImplicitValence(7, 0, 1));
Assert.AreEqual(3, MDLValence.ImplicitValence(7, 0, 2));
Assert.AreEqual(3, MDLValence.ImplicitValence(7, 0, 3));
Assert.AreEqual(5, MDLValence.ImplicitValence(7, 0, 4));
Assert.AreEqual(5, MDLValence.ImplicitValence(7, 0, 5));
Assert.AreEqual(6, MDLValence.ImplicitValence(7, 0, 6));
}
public void Carbon_neutral()
{
IAtomContainer container = new AtomContainer();
IAtom atom = new Atom("C");
container.Atoms.Add(atom);
MDLValence.Apply(container);
Assert.AreEqual(4, atom.Valency);
Assert.AreEqual(4, atom.ImplicitHydrogenCount);
}
public void Tin_ii()
{
IAtomContainer container = new AtomContainer();
IAtom atom = new Atom("Sn");
atom.Valency = 2;
container.Atoms.Add(atom);
MDLValence.Apply(container);
Assert.AreEqual(2, atom.Valency);
Assert.AreEqual(2, atom.ImplicitHydrogenCount);
}
public void Carbon_anion()
{
IAtomContainer container = new AtomContainer();
IAtom atom = new Atom("C");
atom.FormalCharge = +1;
container.Atoms.Add(atom);
MDLValence.Apply(container);
Assert.AreEqual(3, atom.Valency);
Assert.AreEqual(3, atom.ImplicitHydrogenCount);
}
public void Tin_iv()
{
IAtomContainer container = new AtomContainer();
IAtom atom = new Atom("Sn");
atom.Valency = 4;
IAtom hydrogen = new Atom("H");
container.Atoms.Add(atom);
container.Atoms.Add(hydrogen);
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
MDLValence.Apply(container);
Assert.AreEqual(4, atom.Valency);
Assert.AreEqual(3, atom.ImplicitHydrogenCount); // 4 - explicit H
}
public void Bismuth()
{
IAtomContainer container = new AtomContainer();
IAtom bi1 = new Atom("Bi");
IAtom h2 = new Atom("H");
bi1.FormalCharge = +2;
container.Atoms.Add(bi1);
container.Atoms.Add(h2);
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
MDLValence.Apply(container);
Assert.AreEqual(3, bi1.Valency);
Assert.AreEqual(1, h2.Valency);
Assert.AreEqual(2, bi1.ImplicitHydrogenCount);
Assert.AreEqual(0, h2.ImplicitHydrogenCount);
}
public void Carbon_cation_DoubleBonded()
{
IAtomContainer container = new AtomContainer();
IAtom c1 = new Atom("C");
IAtom c2 = new Atom("C");
c1.FormalCharge = -1;
container.Atoms.Add(c1);
container.Atoms.Add(c2);
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Double);
MDLValence.Apply(container);
Assert.AreEqual(3, c1.Valency);
Assert.AreEqual(1, c1.ImplicitHydrogenCount);
Assert.AreEqual(4, c2.Valency);
Assert.AreEqual(2, c2.ImplicitHydrogenCount);
}
/// <summary>
/// Write the atoms of a molecule. We pass in the order of atoms since for compatibility we
/// have shifted all hydrogens to the back.
/// </summary>
/// <param name="mol">molecule</param>
/// <param name="atoms">the atoms of a molecule in desired output order</param>
/// <param name="idxs">index lookup</param>
/// <param name="atomToStereo">tetrahedral stereo lookup</param>
/// <exception cref="IOException">low-level IO error</exception>
/// <exception cref="CDKException">inconsistent state etc</exception>
private void WriteAtomBlock(IAtomContainer mol, IAtom[] atoms, Dictionary <IChemObject, int> idxs, Dictionary <IAtom, ITetrahedralChirality> atomToStereo)
{
if (mol.Atoms.Count == 0)
{
return;
}
var dim = GetNumberOfDimensions(mol);
writer.Write("BEGIN ATOM\n");
int atomIdx = 0;
foreach (var atom in atoms)
{
var elem = NullAsZero(atom.AtomicNumber);
var chg = NullAsZero(atom.FormalCharge);
var mass = NullAsZero(atom.MassNumber);
var hcnt = NullAsZero(atom.ImplicitHydrogenCount);
var elec = mol.GetConnectedSingleElectrons(atom).Count();
int rad = 0;
switch (elec)
{
case 1: // 2
rad = MDLV2000Writer.SpinMultiplicity.Monovalent.Value;
break;
case 2: // 1 or 3? Information loss as to which
rad = MDLV2000Writer.SpinMultiplicity.DivalentSinglet.Value;
break;
}
int expVal = 0;
foreach (var bond in mol.GetConnectedBonds(atom))
{
if (bond.Order == BondOrder.Unset)
{
throw new CDKException($"Unsupported bond order: {bond.Order}");
}
expVal += bond.Order.Numeric();
}
string symbol = GetSymbol(atom, elem);
int rnum = -1;
if (symbol[0] == 'R')
{
var matcher = R_GRP_NUM.Match(symbol);
if (matcher.Success)
{
symbol = "R#";
rnum = int.Parse(matcher.Groups[1].Value, NumberFormatInfo.InvariantInfo);
}
}
writer.Write(++atomIdx)
.Write(' ')
.Write(symbol)
.Write(' ');
var p2d = atom.Point2D;
var p3d = atom.Point3D;
switch (dim)
{
case 0:
writer.Write("0 0 0 ");
break;
case 2:
if (p2d != null)
{
writer.Write(p2d.Value.X).WriteDirect(' ')
.Write(p2d.Value.Y).WriteDirect(' ')
.Write("0 ");
}
else
{
writer.Write("0 0 0 ");
}
break;
case 3:
if (p3d != null)
{
writer.Write(p3d.Value.X).WriteDirect(' ')
.Write(p3d.Value.Y).WriteDirect(' ')
.Write(p3d.Value.Z).WriteDirect(' ');
}
else
{
writer.Write("0 0 0 ");
}
break;
}
writer.Write(NullAsZero(atom.GetProperty <int>(CDKPropertyName.AtomAtomMapping)));
if (chg != 0 && chg >= -15 && chg <= 15)
{
writer.Write(" CHG=").Write(chg);
}
if (mass != 0)
{
writer.Write(" MASS=").Write(mass);
}
if (rad > 0 && rad < 4)
{
writer.Write(" RAD=").Write(rad);
}
if (rnum >= 0)
{
writer.Write(" RGROUPS=(1 ").Write(rnum).Write(")");
}
// determine if we need to write the valence
if (MDLValence.ImplicitValence(elem, chg, expVal) - expVal != hcnt)
{
int val = expVal + hcnt;
if (val <= 0 || val > 14)
{
val = -1; // -1 is 0
}
writer.Write(" VAL=").Write(val);
}
if (atomToStereo.TryGetValue(atom, out ITetrahedralChirality stereo))
{
switch (GetLocalParity(idxs, stereo))
{
case TetrahedralStereo.Clockwise:
writer.Write(" CFG=1");
break;
case TetrahedralStereo.AntiClockwise:
writer.Write(" CFG=2");
break;
default:
break;
}
}
writer.Write('\n');
}
writer.Write("END ATOM\n");
}