SMARTS search examples

Using ambit2.smarts.SmartsManager.java 

                SmartsManager man = new SmartsManager();
                IMolecule mol = MoleculeFactory.createAlkane(5);
                String smarts = "CCC";  
                man.setQuery(smarts); 
                if (!man.getErrors().equals(""))
                {
                        System.out.println(man.getErrors());
                        return;
                } else {                
                        boolean res = man.searchIn(mol);
                        System.out.println(String.format("SMARTS manager search example %s in %s  --> %s",smarts,smiles,res);
                }

Using ambit2.smarts.query.AbstractSmartsPattern.java descendants.

All of them implement ambit2.smarts.query.ISmartsPattern interface.

Use ambit2.smarts.FastSmartsMatcher.java

            IAtomContainer mol = (initialize)
                FastSmartsMatcher match = new FastSmartsMatcher();
                match.setSmarts("F[r5;r6]");
                if (match.hasSMARTSPattern(mol)>0) 
                        System.out.println("A hit");
                else    
                        System.out.println("Not a hit");

Use ambit2.smarts.FastSmartsMatcher.java. Uses ambit2.smarts.IsomorphismTester.java to match structures.

            IAtomContainer mol = (initialize)
                FastSmartsMatcher match = new FastSmartsMatcher();
                match.setSmarts("F[r5;r6]");
                if (match.hasSMARTSPattern(mol)>0) 
                        System.out.println("A hit");
                else    
                        System.out.println("Not a hit");

Use ambit2.smarts.SmartsPatternAmbit.java. Optionally uses ambit2.smarts.IsomorphismTester.java or CDK UIT to match structures.

            IAtomContainer mol = (initialize)
                SmartsPatternAmbit match = new SmartsPatternAmbit();
                //match.setUseCDKIsomorphism(true); //will use CDK UIT
                match.setUseCDKIsomorphism(false); //will use Ambit Isomorphism tester
                //match.useMOEvPrimitive(true); //will use MOE syntax
                match.setSmarts("F[r5;r6]");
                if (match.hasSMARTSPattern(mol)>0) 
                        System.out.println("A hit");
                else    
                        System.out.println("Not a hit");

Use ambit2.smarts.SmartsPatternCDK.java . A wrapper for CDK SMARTS and UIT, implements ambit2.smarts.query.ISmartsPattern interface.

            IAtomContainer mol = (initialize)
                SmartsPatternCDK match = new SmartsPatternCDK();
                match.setSmarts("F[r5;r6]");
                if (match.hasSMARTSPattern(mol)>0) 
                        System.out.println("A hit");
                else    
                        System.out.println("Not a hit");

SMIRKS examples

                IAtomContainer target = (initialize)
                SMIRKSManager smrkMan = new SMIRKSManager();
                SMIRKSReaction reaction = smrkMan.parse(smirks);
                if (!smrkMan.getErrors().equals(""))
                {
                        throw(new Exception("Smirks Parser errors:\n" + smrkMan.getErrors()));
                }
                
                if (smrkMan.applyTransformation(target, reaction)) 
                        return target; //all products inside the same atomcontainer, could be disconnected
                else return null;

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