public static void AmbitTest()
{
//string smirks = "[*:1][N:2](=[O:3])=[O:4]>>[*:1][N+:2](=[O:3])[O-:4]";
//string smirks = "[N:1]1[C:2][C:3]=[C:4][C:5]1>>[N:1]1[C:2]=[C:3][C:4]=[C:5]1";
string smirks = "[#16:1]>>[#16:1](=[O])";
//string targetSmiles = "O=S(c2nc1ccc(OC)cc1n2)Cc3ncc(c(OC)c3C)C";
string targetSmiles = "CC1=CN=C(C(=C1OC)C)CS(=O)C2=NC3=C(N2)C=C(C=C3)OC"; // Omeprazole
string productSmiles = "";
IAtomContainer target = new AtomContainer();
IChemObjectBuilder icob = org.openscience.cdk.silent.SilentChemObjectBuilder.getInstance();
SMIRKSManager smrkMan = new SMIRKSManager(icob);
//SMIRKSManager smrkMan = SMIRKSManager.getDefaultSMIRKSManager();
SMIRKSReaction reaction = smrkMan.parse(smirks);
if (!smrkMan.getErrors().Equals(""))
{
throw (new Exception("Smirks Parser errors:\n" + smrkMan.getErrors()));
}
target = CdkUtil.SmilesToAtomContainer(targetSmiles);
if (smrkMan.applyTransformation(target, reaction))
{
IAtomContainer product = target;
productSmiles = CdkUtil.AtomContainerToSmiles(product);
return; // all products inside the same atomcontainer (target), could be disconnected
}
else
{
return;
}
//Generate separate products for every possible reaction(used in Toxtree)
//SMIRKSManager smrkMan = new SMIRKSManager();
//SMIRKSReaction smr = smrkMan.parse(reaction.getSMIRKS());
//IAtomContainer product = reactant; //(IAtomContainer) reactant.clone();
//IAtomContainerSet rproducts = smrkMan.applyTransformationWithSingleCopyForEachPos(product, null, smr);
//products returned in a separate atom sontainer set
}
