Dear All, I am facing problem with SMARTSQueryTool class.My moleules are stored i vector .i am accessing those molecule by get method of vector and stored it in Molecule object.my smarts are stored in XML file. i access each smarts pattern one by one and searched againt my molecule.but it gives performance issue.it takes long time to search my smarts on molecule.but if i clone the molecule for each smart pattern it gives results very fast and if instead of using Molecule object if i use AtomContainer class it gives result fast.so i am not getting why this is happening.Previousely we had used JOELIB for smart search.it performs faster than CDK without cloning of molecule.I have attached my source code with this post please go through it .and please help me out for better performance of smarts search http://www.nabble.com/file/p25488758/FindPattern_cdk.txt FindPattern_cdk.txt
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