public static StereoConfigurations ToConfiguration(this DoubleBondConformation conformation)
{
switch (conformation)
{
case DoubleBondConformation.Unset:
return(StereoConfigurations.Unset);
case DoubleBondConformation.Together:
return(StereoConfigurations.Together);
case DoubleBondConformation.Opposite:
return(StereoConfigurations.Opposite);
default:
throw new ArgumentException($"Cannot map enum to config: {conformation}");
}
}
/// <summary>
/// Get the parity (-1,+1) of the geometric (double bond) configuration.
/// </summary>
/// <param name="conformation">configuration</param>
/// <returns>the parity</returns>
private static int Parity(DoubleBondConformation conformation)
{
return(conformation == DoubleBondConformation.Together ? 1 : -1);
}
/// <summary>
/// Invert this conformation.
/// <see cref="DoubleBondConformation.Together"/>.Invert() = <see cref="DoubleBondConformation.Opposite"/>, <see cref="DoubleBondConformation.Opposite"/>.Invert() = <see cref="DoubleBondConformation.Together"/>.
/// </summary>
/// <returns>the inverse conformation</returns>
public static DoubleBondConformation Invert(this DoubleBondConformation value)
=> value == DoubleBondConformation.Together
? DoubleBondConformation.Opposite
: DoubleBondConformation.Together;
public static bool IsUnset(this DoubleBondConformation value)
{
return(value == DoubleBondConformation.Unset);
}
public object Visit(ASTGroup node, object data)
{
IAtomContainer fullQuery = (IAtomContainer)data;
if (fullQuery == null)
{
fullQuery = new QueryAtomContainer(builder);
}
// keeps track of component grouping
var components = fullQuery.GetProperty <int[]>("COMPONENT.GROUPING", Array.Empty <int>());
int maxId = 0;
if (components.Length > 0)
{
foreach (int id in components)
{
if (id > maxId)
{
maxId = id;
}
}
}
for (int i = 0; i < node.JjtGetNumChildren(); i++)
{
ASTSmarts smarts = (ASTSmarts)node.JjtGetChild(i);
ringAtoms = new RingIdentifierAtom[10];
query = new QueryAtomContainer(builder);
smarts.JjtAccept(this, null);
// update component info
if (components.Length > 0 || smarts.ComponentId > 0)
{
components = Arrays.CopyOf(components, 1 + fullQuery.Atoms.Count + query.Atoms.Count);
int id = smarts.ComponentId;
Arrays.Fill(components, fullQuery.Atoms.Count, components.Length, id);
if (id > maxId)
{
maxId = id;
}
}
fullQuery.Add(query);
}
// only store if there was a component grouping
if (maxId > 0)
{
components[components.Length - 1] = maxId; // we left space to store how many groups there were
fullQuery.SetProperty("COMPONENT.GROUPING", components);
}
// create tetrahedral elements
foreach (var atom in neighbors.Keys)
{
IList <IAtom> localNeighbors = neighbors[atom];
if (localNeighbors.Count == 4)
{
fullQuery.StereoElements.Add(new TetrahedralChirality(atom, localNeighbors.ToArray(),
TetrahedralStereo.Clockwise)); // <- to be modified later
}
else if (localNeighbors.Count == 5)
{
localNeighbors.Remove(atom); // remove central atom (which represented implicit part)
fullQuery.StereoElements.Add(new TetrahedralChirality(atom, localNeighbors.ToArray(),
TetrahedralStereo.Clockwise)); // <- to be modified later
}
}
// for each double bond, find the stereo bonds. Currently doesn't
// handle logical bonds i.e. C/C-,=C/C
foreach (var bond in doubleBonds)
{
IAtom left = bond.Begin;
IAtom right = bond.End;
StereoBond leftBond = FindStereoBond(left);
StereoBond rightBond = FindStereoBond(right);
if (leftBond == null || rightBond == null)
{
continue;
}
DoubleBondConformation conformation = leftBond.GetDirection(left) == rightBond.GetDirection(right) ? DoubleBondConformation.Together
: DoubleBondConformation.Opposite;
fullQuery.StereoElements.Add(new DoubleBondStereochemistry(bond, new IBond[] { leftBond, rightBond },
conformation));
}
return(fullQuery);
}
/// <summary>
/// Creates a new double bond stereo chemistry. The path of length three is defined by
/// <paramref name="ligandBonds"/>[0], <paramref name="stereoBond"/>, and <paramref name="ligandBonds"/>[1].
/// </summary>
public DoubleBondStereochemistry(IBond stereoBond, IEnumerable <IBond> ligandBonds, DoubleBondConformation stereo)
: this(stereoBond, ligandBonds, stereo.ToConfiguration())
{
}
