/// <summary>
/// Constructor
/// </summary>
public DefaultBondMatcher()
{
this.queryBond = null;
this.smartQueryBond = null;
this.unsaturation = -1;
IsBondMatchFlag = false;
}
/// <summary>
/// Determine if a bond from the molecule exists and if it is matched
/// by the query bond. If the match is feasible the current query bond index
/// is increment and stored on the stack.
/// </summary>
/// /// <param name="qbond">bond from the query</param>
/// <param name="bond">bond from the molecule</param>
/// <returns>the match was feasible and the state was stored</returns>
private bool Feasible(IQueryBond qbond, IBond bond)
{
if (bond == null || !qbond.Matches(bond))
{
return(false);
}
Store(CurrBondIdx() + 1, null);
return(true);
}
public void QueryMatch()
{
BondMatcher matcher = BondMatcher.CreateQueryMatcher();
var m_bond1 = new Mock <IQueryBond>(); IQueryBond bond1 = m_bond1.Object;
var m_bond2 = new Mock <IBond>(); IBond bond2 = m_bond2.Object;
var m_bond3 = new Mock <IBond>(); IBond bond3 = m_bond3.Object;
m_bond1.Setup(n => n.Matches(bond2)).Returns(true);
m_bond1.Setup(n => n.Matches(bond3)).Returns(false);
Assert.IsTrue(matcher.Matches(bond1, bond2));
Assert.IsFalse(matcher.Matches(bond1, bond3));
}
/// <summary> Builds the nodes of the RGraph ( resolution graph ), from
/// two atom containers (description of the two molecules to compare)
///
/// </summary>
/// <param name="gr"> the target RGraph
/// </param>
/// <param name="ac1"> description of the first molecule
/// </param>
/// <param name="ac2"> description of the second molecule
/// </param>
private static void nodeConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2)
{
// resets the target graph.
gr.clear();
IBond[] bondsA1 = ac1.Bonds;
IBond[] bondsA2 = ac2.Bonds;
// compares each bond of G1 to each bond of G2
for (int i = 0; i < bondsA1.Length; i++)
{
for (int j = 0; j < bondsA2.Length; j++)
{
if (timeout > -1 && ((System.DateTime.Now.Ticks - 621355968000000000) / 10000 - start) > timeout)
{
throw new CDKException("Timeout exceeded in getOverlaps");
}
IBond bondA2 = bondsA2[j];
if (bondA2 is IQueryBond)
{
IQueryBond queryBond = (IQueryBond)bondA2;
IQueryAtom atom1 = (IQueryAtom)(bondA2.getAtomAt(0));
IQueryAtom atom2 = (IQueryAtom)(bondA2.getAtomAt(1));
IBond bond = bondsA1[i];
if (queryBond.matches(bond))
{
// ok, bonds match
if (atom1.matches(bond.getAtomAt(0)) && atom2.matches(bond.getAtomAt(1)) || atom1.matches(bond.getAtomAt(1)) && atom2.matches(bond.getAtomAt(0)))
{
// ok, atoms match in either order
gr.addNode(new RNode(i, j));
}
}
}
else
{
// if both bonds are compatible then create an association node
// in the resolution graph
if (((bondsA1[i].Order == bondsA2[j].Order && bondsA1[i].getFlag(CDKConstants.ISAROMATIC) == bondsA2[j].getFlag(CDKConstants.ISAROMATIC)) || (bondsA1[i].getFlag(CDKConstants.ISAROMATIC) && bondsA2[j].getFlag(CDKConstants.ISAROMATIC))) && ((bondsA1[i].getAtomAt(0).Symbol.Equals(bondsA2[j].getAtomAt(0).Symbol) && bondsA1[i].getAtomAt(1).Symbol.Equals(bondsA2[j].getAtomAt(1).Symbol)) || (bondsA1[i].getAtomAt(0).Symbol.Equals(bondsA2[j].getAtomAt(1).Symbol) && bondsA1[i].getAtomAt(1).Symbol.Equals(bondsA2[j].getAtomAt(0).Symbol))))
{
gr.addNode(new RNode(i, j));
}
}
}
}
}
public object Visit(ASTExplicitHighAndBond node, object data)
{
object left = node.JjtGetChild(0).JjtAccept(this, data);
if (node.JjtGetNumChildren() == 1)
{
return(left);
}
LogicalOperatorBond bond = new LogicalOperatorBond(builder)
{
Operator = "and",
Left = (IQueryBond)left
};
IQueryBond right = (IQueryBond)node.JjtGetChild(1).JjtAccept(this, data);
bond.Right = right;
return(bond);
}
/// <summary>
/// Constructor
/// <param name="queryBond">query Molecule</param>
/// </summary>
public DefaultVFBondMatcher(IQueryBond queryBond)
: base()
{
this.smartQueryBond = queryBond;
}
private static double GetBondTypeMatches(IBond queryBond, IBond targetBond)
{
double score = 0;
if (targetBond is IQueryBond && queryBond is IBond)
{
IQueryBond bond = (IQueryBond)targetBond;
IQueryAtom atom1 = (IQueryAtom)(targetBond.Atoms[0]);
IQueryAtom atom2 = (IQueryAtom)(targetBond.Atoms[1]);
if (bond.Matches(queryBond))
{
// ok, bonds match
if (atom1.Matches(queryBond.Atoms[0]) && atom2.Matches(queryBond.Atoms[1]) ||
atom1.Matches(queryBond.Atoms[1]) && atom2.Matches(queryBond.Atoms[0]))
{
// ok, atoms match in either order
score += 4;
}
}
else
{
score -= 4;
}
}
else if (queryBond is IQueryBond && targetBond is IBond)
{
IQueryBond bond = (IQueryBond)queryBond;
IQueryAtom atom1 = (IQueryAtom)(queryBond.Atoms[0]);
IQueryAtom atom2 = (IQueryAtom)(queryBond.Atoms[1]);
if (bond.Matches(targetBond))
{
// ok, bonds match
if (atom1.Matches(targetBond.Atoms[0]) && atom2.Matches(targetBond.Atoms[1]) ||
atom1.Matches(targetBond.Atoms[1]) && atom2.Matches(targetBond.Atoms[0]))
{
// ok, atoms match in either order
score += 4;
}
}
else
{
score -= 4;
}
}
else
{
int reactantBondType = ConvertBondOrder(queryBond);
int productBondType = ConvertBondOrder(targetBond);
int rStereo = ConvertBondStereo(queryBond);
int pStereo = ConvertBondStereo(targetBond);
if ((queryBond.IsAromatic == targetBond.IsAromatic) &&
(reactantBondType == productBondType))
{
score += 8;
}
else if (queryBond.IsAromatic && targetBond.IsAromatic)
{
score += 4;
}
if (reactantBondType == productBondType)
{
score += productBondType;
}
else
{
score -= 4 * Math.Abs(reactantBondType - productBondType);
}
if (rStereo != 4 || pStereo != 4 || rStereo != 3 || pStereo != 3)
{
if (rStereo == pStereo)
{
score += 1;
}
else
{
score -= 1;
}
}
}
return(score);
}
private static IVFBondMatcher CreateBondMatcher(IQueryBond bond)
{
return(new DefaultVFBondMatcher(bond));
}
