Hello all,
Trying to reply to this thread,
https://sourceforge.net/mailarchive/message.php?msg_name=49C96659.2090401%40ebi.ac.uk
,I have to say SmilesGenerator generates different smiles, depending on
how the molecule was created (e.g. read from a file or by SmilesParser).
Test attached.
Best regards,
Nina
/* SmilesTest.java
* Author: nina
* Date: Apr 7, 2009
* Revision: 0.1
*
* Copyright (C) 2005-2009
*
* Contact: nina
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may
distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package ambit2.core.test;
import java.io.StringReader;
import junit.framework.Assert;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.smiles.SmilesParser;
public class SmilesTest {
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
//String[] smiles = {"NCCO","OCCN"};
@Test
public void testCanonicalSmiles() throws Exception {
String[] smiles = {"c1cc(ccc1C(c2ccc(cc2)Cl)=C(Cl)Cl)Cl",
"Clc1ccc(cc1)C(=C(Cl)Cl)c2ccc(Cl)cc2",
"C(=C(Cl)Cl)(C1C=CC(=CC=1)Cl)C2=CC=C(C=C2)Cl"
};
String[] newSmiles = {"","",""};
SmilesGenerator gen = new SmilesGenerator();
gen.setUseAromaticityFlag(true);
IMolecule m = getMolecule();
String m_smiles = gen.createSMILES(m);
Assert.assertFalse("".equals(m_smiles));
SmilesParser parser = new
SmilesParser(NoNotificationChemObjectBuilder.getInstance());
int count_differences = 0;
for (int i=0; i < smiles.length;i++) {
IMolecule mol = parser.parseSmiles(smiles[i]);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(m,mol));
newSmiles[i] = gen.createSMILES(mol);
if (!newSmiles[i].equals(m_smiles)) {
count_differences++;
System.out.print(m_smiles);
System.out.print('\t');
System.out.println(newSmiles[i]);
}
}
Assert.assertEquals(0,count_differences);
}
public IMolecule getMolecule() {
String sdf =
"\n\n\n"+
"18 19 0 0 0 0 0 0 0 0 1 V2000\n"+
" 4.6054 -1.9895 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 4.6054 -0.6632 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 3.4540 -0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 5.7567 -0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 5.7567 -2.6527 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 6.9080 -1.9895 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 8.0594 -2.6527 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 8.0594 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 6.9080 -4.6514 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 5.7567 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 9.2107 -4.6514 0.0000 Cl 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 3.4540 -2.6527 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 3.4540 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 2.3027 -4.6514 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 1.1513 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 1.1513 -2.6527 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 2.3027 -1.9895 0.0000 C 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 0.0000 -4.6514 0.0000 Cl 0 0 0 0 0 0 0 0 0
0 0 0\n"+
" 1 2 2 0 0 0 0\n"+
" 1 5 1 0 0 0 0\n"+
" 1 12 1 0 0 0 0\n"+
" 2 3 1 0 0 0 0\n"+
" 2 4 1 0 0 0 0\n"+
" 5 6 1 0 0 0 0\n"+
" 5 10 2 0 0 0 0\n"+
" 6 7 2 0 0 0 0\n"+
" 7 8 1 0 0 0 0\n"+
" 8 9 2 0 0 0 0\n"+
" 8 11 1 0 0 0 0\n"+
" 9 10 1 0 0 0 0\n"+
" 12 13 2 0 0 0 0\n"+
" 12 17 1 0 0 0 0\n"+
" 13 14 1 0 0 0 0\n"+
" 14 15 2 0 0 0 0\n"+
" 15 16 1 0 0 0 0\n"+
" 15 18 1 0 0 0 0\n"+
" 16 17 2 0 0 0 0\n"+
"M END\n" +
"\n" +
"$$$$";
MDLReader r = new MDLReader(new StringReader(sdf));
IMolecule m = DefaultChemObjectBuilder.getInstance().newMolecule();
try {
m = (IMolecule)r.read(m);
} catch (CDKException x) {
x.printStackTrace();
}
return m;
}
}
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