package com.founder.cdk;

import Java.io.File;
import Java.io.FileNotFoundException;
import Java.io.FileReader;
import Java.util.ArrayList;
import Java.util.List;

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

public class SMARTSQueryToolTest {

 static SMARTSQueryTool sqt;static {
        try {
            sqt = new SMARTSQueryTool("c2ccc1ccccc1c2");
        } catch (CDKException e) {           
        }
    }

 /**
  * @param args
  */
 public static void main(String[] args) {
  String filename = "H:\\molecules.sdf";
  try {
            MDLV2000Reader reader = new MDLV2000Reader(new FileReader(new File(filename)));
            ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
            List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
           
            List<IAtomContainer> substructureList = new ArrayList<IAtomContainer>();
            
            sqt.setSmarts("c1ccc3c(c1)ccc4c2ccccc2ccc34");  //重新设置匹配的smiles值
            boolean matched = false;
            for (IAtomContainer molecule : containersList) {
                matched = sqt.matches(molecule);
                if (matched){
                 substructureList.add(molecule);
                }
            }
            System.out.println(substructureList.size());
           
            for (IAtomContainer molecule : substructureList) {
                 System.out.println(molecule.getProperty("ID"));
            }
           
        } catch (CDKException e) {
            e.printStackTrace();
        } catch (FileNotFoundException e) {
           e.printStackTrace();
        }

 }

}

通过测试, matches方法速度很慢, 一般一个结构需要200ms-1000ms左右.