asad

3292
  Marvin  07210922142D          

 52 57  0  0  0  0            999 V2000
    9.2616    1.9250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5472    1.5125    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.1347    2.2270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597    0.7980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8327    1.1000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1182    1.5125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

asad

3292
  Marvin  07240902122D          

 82 87  0  0  0  0            999 V2000
    7.0737   -0.4431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3592   -2.2845    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3176   -0.1272    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5429   -0.1272    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9077   -1.7174    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1032   -0.4133    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

asad

  EBI  11210921182D          

  3  3  0  0  0  0            999 V2000
    0.5048    2.1204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0923    1.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9173    1.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  3  1  0  0  0  0

asad

SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  // Benzene
  IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1");
  // Napthalene
  IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2");
  //Turbo mode search
  //Bond Sensitive is set true
  SMSD comparison = new SMSD(Algorithm.SubStructure, true);
  // set molecules and remove hydrogens
  comparison.init(A1, A2, true);

asad

SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  // Benzene
  IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1");
  // Napthalene
  IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2");
  //{ 0: Default SMSD Algorithm, 1: MCSPlus Algorithm, 2: VFLibMCS Algorithm, 3: CDKMCS Algorithm}
  //Bond Sensitive is set true
  SMSD comparison = new SMSD(Algorithm.DEFAULT, true);
  // set molecules and remove hydrogens
  comparison.init(A1, A2, true);

asad

KEGG	MSD
C02447	3257
C02668	37992
C02668	121250
C04054	1137
C04382	37992
C04480	3257
C04804	3257
C06185	121251
C06544	121745

asad

 OpenBabel03011112432D

  7  7  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 I   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0

asad

311
  CDK     0421111417

 21 20  0  0  0  0  0  0  0  0999 V2000
    4.7690   -1.0005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0010   -0.1345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350    1.3655    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5369   -2.1345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2690    1.5976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -2.1345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

asad

 rBLAST 02051100062D

 31 33  0  0  0  0            999 V2000
  -10.5253   -1.9067    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  -11.7515   -0.8026    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  -11.6905   -1.9677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1384   -1.3546    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5864   -0.7415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7794   -0.9131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

asad

package tools;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.junit.Test;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.Bond;
import org.openscience.cdk.DefaultChemObjectBuilder;