public void MatchRoot()
{
var mol = Smi("OC(=O)C(=O)O");
var qry = Sma("O=*");
var ptrn = DfPattern.CreateSubstructureFinder(qry);
Assert.IsFalse(ptrn.MatchesRoot(mol.Atoms[0]));
Assert.IsTrue(ptrn.MatchesRoot(mol.Atoms[2]));
Assert.IsTrue(ptrn.MatchesRoot(mol.Atoms[4]));
Assert.IsFalse(ptrn.MatchesRoot(mol.Atoms[5]));
}
/// <summary>
/// Internal match methods - does not null check.
/// </summary>
/// <param name="type">the type</param>
/// <param name="atom">the atom</param>
/// <returns>the expression matches</returns>
private bool Matches(ExprType type, IAtom atom, int stereo)
{
switch (type)
{
// predicates
case ExprType.True:
return(true);
case ExprType.False:
return(false);
case ExprType.IsAromatic:
return(atom.IsAromatic);
case ExprType.IsAliphatic:
return(!atom.IsAromatic);
case ExprType.IsInRing:
return(atom.IsInRing);
case ExprType.IsInChain:
return(!atom.IsInRing);
case ExprType.IsHetero:
return(!Eq(atom.AtomicNumber, 6) &&
!Eq(atom.AtomicNumber, 1));
case ExprType.HasImplicitHydrogen:
return(atom.ImplicitHydrogenCount != null &&
atom.ImplicitHydrogenCount > 0);
case ExprType.HasIsotope:
return(atom.MassNumber != null);
case ExprType.HasUnspecifiedIsotope:
return(atom.MassNumber == null);
case ExprType.Unsaturated:
foreach (var bond in atom.Bonds)
{
if (bond.Order == BondOrder.Double)
{
return(true);
}
}
return(false);
// value primitives
case ExprType.Element:
return(Eq(atom.AtomicNumber, value));
case ExprType.AliphaticElement:
return(!atom.IsAromatic &&
Eq(atom.AtomicNumber, value));
case ExprType.AromaticElement:
return(atom.IsAromatic &&
Eq(atom.AtomicNumber, value));
case ExprType.ImplicitHCount:
return(Eq(atom.ImplicitHydrogenCount, value));
case ExprType.TotalHCount:
if (atom.ImplicitHydrogenCount != null &&
atom.ImplicitHydrogenCount > value)
{
return(false);
}
return(GetTotalHCount(atom) == value);
case ExprType.Degree:
return(atom.Bonds.Count == value);
case ExprType.HeavyDegree: // XXX: CDK quirk
return(atom.Bonds.Count - (GetTotalHCount(atom) - atom.ImplicitHydrogenCount) == value);
case ExprType.TotalDegree:
int x = atom.Bonds.Count + Unbox(atom.ImplicitHydrogenCount);
return(x == value);
case ExprType.Valence:
int v = Unbox(atom.ImplicitHydrogenCount);
if (v > value)
{
return(false);
}
foreach (var bond in atom.Bonds)
{
if (!bond.Order.IsUnset())
{
v += bond.Order.Numeric();
}
}
return(v == value);
case ExprType.Isotope:
return(Eq(atom.MassNumber, value));
case ExprType.FormalCharge:
return(Eq(atom.FormalCharge, value));
case ExprType.RingBondCount:
if (!atom.IsInRing || atom.Bonds.Count < value)
{
return(false);
}
int rbonds = 0;
foreach (var bond in atom.Bonds)
{
rbonds += bond.IsInRing ? 1 : 0;
}
return(rbonds == value);
case ExprType.RingCount:
return(atom.IsInRing && GetRingCount(atom) == value);
case ExprType.RingSmallest:
return(atom.IsInRing && IsInSmallRingSize(atom, value));
case ExprType.RingSize:
return(atom.IsInRing && IsInRingSize(atom, value));
case ExprType.HeteroSubstituentCount:
if (atom.Bonds.Count < value)
{
return(false);
}
int q = 0;
foreach (var bond in atom.Bonds)
{
q += Matches(ExprType.IsHetero, bond.GetOther(atom), stereo) ? 1 : 0;
}
return(q == value);
case ExprType.Insaturation:
int db = 0;
foreach (var bond in atom.Bonds)
{
if (bond.Order == BondOrder.Double)
{
db++;
}
}
return(db == value);
case ExprType.HybridisationNumber:
var hyb = atom.Hybridization;
if (hyb.IsUnset())
{
return(false);
}
switch (value)
{
case 1:
return(hyb == Hybridization.SP1);
case 2:
return(hyb == Hybridization.SP2);
case 3:
return(hyb == Hybridization.SP3);
case 4:
return(hyb == Hybridization.SP3D1);
case 5:
return(hyb == Hybridization.SP3D2);
case 6:
return(hyb == Hybridization.SP3D3);
case 7:
return(hyb == Hybridization.SP3D4);
case 8:
return(hyb == Hybridization.SP3D5);
default:
return(false);
}
case ExprType.PeriodicGroup:
return(Tools.PeriodicTable.GetGroup(atom.AtomicNumber) == value);
case ExprType.Stereochemistry:
return(stereo == UnknownStereo || stereo == value);
case ExprType.ReactionRole:
var role = atom.GetProperty <ReactionRole>(CDKPropertyName.ReactionRole);
return(!role.IsUnset() && role.Ordinal() == value);
case ExprType.And:
return(left.Matches(left.type, atom, stereo) &&
right.Matches(right.type, atom, stereo));
case ExprType.Or:
return(left.Matches(left.type, atom, stereo) ||
right.Matches(right.type, atom, stereo));
case ExprType.Not:
return(!left.Matches(left.type, atom, stereo)
// XXX: ugly but needed, when matching stereo
|| (stereo == UnknownStereo &&
(left.type == ExprType.Stereochemistry ||
left.type == ExprType.Or &&
left.left.type == ExprType.Stereochemistry)));
case ExprType.Recursive:
if (ptrn == null)
{
ptrn = DfPattern.CreateSubstructureFinder(query);
}
return(ptrn.MatchesRoot(atom));
default:
throw new ArgumentException($"Cannot match AtomExpr, type={type}", nameof(type));
}
}
public override Pattern Create(IAtomContainer container)
{
return(DfPattern.CreateSubstructureFinder(container));
}