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| /** | ||
| * Copyright (C) 2009-2013 Syed Asad Rahman <asad@ebi.ac.uk> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * 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., | ||
| * 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. | ||
| */ | ||
| package tools; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.Calendar; | ||
| import java.util.Collection; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.logging.Level; | ||
| import java.util.logging.Logger; | ||
| import org.junit.Assert; | ||
| import org.junit.Test; | ||
| import org.openscience.cdk.DefaultChemObjectBuilder; | ||
| import org.openscience.cdk.exception.CDKException; | ||
| import org.openscience.cdk.exception.InvalidSmilesException; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.smiles.SmilesGenerator; | ||
| import org.openscience.cdk.smiles.SmilesParser; | ||
| import org.openscience.smsd.mcss.MCSSJF; | ||
|
|
||
| /** | ||
| * | ||
| * @author Syed Asad Rahman <asad@ebi.ac.uk> | ||
| * | ||
| */ | ||
| public class TestMCSSJF { | ||
|
|
||
| @Test | ||
| public void case1() { | ||
| HashMap<String, String> map = new HashMap<>(); | ||
| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | ||
| //Data | ||
|
|
||
| map.put("30331701", "Cc1ccc(C2N(C(c3c(Cl)cccc3)=O)c(c4N=C(C2=C5O)CC(c6c(Cl)cccc6)C5)cccc4)cc1"); | ||
| map.put("4170207", "CCC(N1C(c2ccc(F)cc2)C(C3=Nc(c14)cccc4)=C(O)CC(c5ccc(C(C)(C)C)cc5)C3)=O"); | ||
| map.put("6368123", "CC(N1C(c2ccc(F)cc2)C(C3=Nc(c14)cccc4)=C(O)CC(c5ccc(Cl)cc5)C3)=O"); | ||
| map.put("MCS", "O=C(N4c5ccccc5(N=C2C(=C(O)CC(c1ccccc1)C2)C4(c3ccccc3)))C"); | ||
| map.put("MMV011436", "CC(c1ccc(C2CC(C3=C(O)C2)=Nc(c4N(C(c5c(Cl)cccc5)=O)C3c6ccc(F)cc6)cccc4)cc1)(C)C"); | ||
| map.put("4196500", "CC(c1ccc(C2CC(C3=C(O)C2)=Nc(c4N(C(c5c(Cl)cccc5)=O)C3c6ccc(F)cc6)cccc4)cc1)(C)C"); | ||
|
|
||
| List<IAtomContainer> jobs = new ArrayList<>(); | ||
| for (String s : map.values()) { | ||
| try { | ||
| jobs.add(sp.parseSmiles(s)); | ||
| } catch (InvalidSmilesException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| } | ||
| long startTime = Calendar.getInstance().getTimeInMillis(); | ||
| MCSSJF mcss = new MCSSJF(jobs, true, true, true); | ||
| for (IAtomContainer ac : mcss.getSolutions()) { | ||
| ////System.out.println("Result MCS " + getMCSSSmiles(ac)); | ||
| Assert.assertEquals(31, ac.getAtomCount()); | ||
| } | ||
| long endCalcTime = Calendar.getInstance().getTimeInMillis(); | ||
|
|
||
| ////System.out.println("Total time: " + (endCalcTime - startTime) + "ms"); | ||
| } | ||
|
|
||
| @Test | ||
| public void case2() { | ||
| HashMap<String, String> map = new HashMap<>(); | ||
| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | ||
| // Data | ||
|
|
||
| map.put("1", "CCCCC=NNN"); | ||
| map.put("2", "CCCC-NNN"); | ||
| map.put("3", "CCCSNNN"); | ||
| map.put("4", "CCCC=NNN"); | ||
|
|
||
| List<IAtomContainer> jobs = new ArrayList<>(); | ||
| for (String s : map.values()) { | ||
| try { | ||
| jobs.add(sp.parseSmiles(s)); | ||
| } catch (InvalidSmilesException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| } | ||
| long startTime = Calendar.getInstance().getTimeInMillis(); | ||
| MCSSJF mcss = new MCSSJF(jobs, true, true, true); | ||
| for (IAtomContainer ac : mcss.getSolutions()) { | ||
| ////System.out.println("Result MCS " + getMCSSSmiles(ac)); | ||
| Assert.assertEquals(3, ac.getAtomCount()); | ||
| } | ||
| long endCalcTime = Calendar.getInstance().getTimeInMillis(); | ||
|
|
||
| ////System.out.println("Total time: " + (endCalcTime - startTime) + "ms"); | ||
| } | ||
|
|
||
| @Test | ||
| public void case3() { | ||
| HashMap<String, String> map = new HashMap<>(); | ||
| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | ||
| // Data | ||
|
|
||
| map.put("1", "CCC=NNN"); | ||
| map.put("2", "CCC-NNN"); | ||
| map.put("3", "CCCSNNN"); | ||
|
|
||
| List<IAtomContainer> jobs = new ArrayList<>(); | ||
| for (String s : map.values()) { | ||
| try { | ||
| jobs.add(sp.parseSmiles(s)); | ||
| } catch (InvalidSmilesException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| } | ||
| long startTime = Calendar.getInstance().getTimeInMillis(); | ||
| MCSSJF mcss = new MCSSJF(jobs, true, true, false); | ||
| for (IAtomContainer ac : mcss.getSolutions()) { | ||
| //System.out.println("Result MCS " + getMCSSSmiles(ac)); | ||
| Assert.assertEquals(3, ac.getAtomCount()); | ||
| } | ||
| long endCalcTime = Calendar.getInstance().getTimeInMillis(); | ||
| ////System.out.println("Total time: " + (endCalcTime - startTime) + "ms"); | ||
| } | ||
|
|
||
| @Test | ||
| public void case4() { | ||
| HashMap<String, String> map = new HashMap<>(); | ||
| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | ||
| // Data | ||
|
|
||
| map.put("1", "CCC=NNN"); | ||
| map.put("2", "CCC-NNN"); | ||
| map.put("3", "CCCSNNN"); | ||
| map.put("4", "SSSCCC"); | ||
| map.put("5", "CSSSCSNNN"); | ||
|
|
||
| List<IAtomContainer> jobs = new ArrayList<>(); | ||
| for (String s : map.values()) { | ||
| try { | ||
| jobs.add(sp.parseSmiles(s)); | ||
| } catch (InvalidSmilesException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| } | ||
| long startTime = Calendar.getInstance().getTimeInMillis(); | ||
| MCSSJF mcss = new MCSSJF(jobs, true, true, true); | ||
| Collection<IAtomContainer> solutions = mcss.getSolutions(); | ||
| System.out.println("Number of Solutions: " + solutions.size()); | ||
| for (IAtomContainer ac : solutions) { | ||
| try { | ||
| System.out.println("Result MCS " + new SmilesGenerator().create(ac)); | ||
| } catch (CDKException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| Assert.assertEquals(1, ac.getAtomCount()); | ||
| } | ||
| long endCalcTime = Calendar.getInstance().getTimeInMillis(); | ||
|
|
||
| ////System.out.println("Total time: " + (endCalcTime - startTime) + "ms"); | ||
| } | ||
|
|
||
| @Test | ||
| public void case5() { | ||
| HashMap<String, String> map = new HashMap<>(); | ||
| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | ||
| // Data | ||
|
|
||
| map.put("1", "O=C(OC1OC(CO)C(O)C(O)C1(O))Cc3c[nH]c2ccccc23"); | ||
| map.put("2", "O=C(OC1C(O)C(O)C(O)C(O)C1(O))Cc3c[nH]c2ccccc23"); | ||
|
|
||
| List<IAtomContainer> jobs = new ArrayList<>(); | ||
| for (String s : map.values()) { | ||
| try { | ||
| IAtomContainer parseSmiles = sp.parseSmiles(s); | ||
| System.out.println(s + ", size:" + parseSmiles.getAtomCount()); | ||
| jobs.add(parseSmiles); | ||
| } catch (InvalidSmilesException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| } | ||
| long startTime = Calendar.getInstance().getTimeInMillis(); | ||
| MCSSJF mcss = new MCSSJF(jobs, true, true, false); | ||
| for (IAtomContainer ac : mcss.getSolutions()) { | ||
| try { | ||
| System.out.println("Result MCS " + new SmilesGenerator().create(ac)); | ||
| } catch (CDKException ex) { | ||
| Logger.getLogger(TestMCSSJF.class.getName()).log(Level.SEVERE, null, ex); | ||
| } | ||
| Assert.assertEquals(21, ac.getAtomCount()); | ||
| } | ||
| long endCalcTime = Calendar.getInstance().getTimeInMillis(); | ||
|
|
||
| ////System.out.println("Total time: " + (endCalcTime - startTime) + "ms"); | ||
| } | ||
| } |