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SmilesParserTest.java
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SmilesParserTest.java
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/* $Revision$ $Author$ $Date$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
* 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.
*
* 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 org.openscience.cdk.smiles;
import java.util.Iterator;
import java.util.List;
import org.junit.Assert;
import org.junit.Assume;
import org.junit.Ignore;
import org.junit.Test;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.isomorphism.IsomorphismTester;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* Please see the test.gui package for visual feedback on tests.
*
* @author steinbeck
* @cdk.module test-smiles
* @cdk.created 2003-09-19
*
* @see org.openscience.cdk.gui.smiles.SmilesParserTest
*/
public class SmilesParserTest extends CDKTestCase {
private static SmilesParser sp = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
/** @cdk.bug 1363882 */
@Test (timeout=1000)
public void testBug1363882() throws Exception {
String smiles = "[H]c2c([H])c(c1c(nc(n1([H]))C(F)(F)F)c2Cl)Cl";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(18, mol.getAtomCount());
Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol));
}
/** @cdk.bug 1535587 */
@Test (timeout=1000)
public void testBug1535587() throws Exception {
String smiles = "COC(=O)c2ccc3n([H])c1ccccc1c3(c2)";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(18, mol.getAtomCount());
Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol));
Assert.assertEquals("N", mol.getAtom(8).getSymbol());
Assert.assertTrue(mol.getAtom(8).getFlag(CDKConstants.ISAROMATIC));
}
/** @cdk.bug 1579235 */
@Test (timeout=1000)
public void testBug1579235() throws Exception {
String smiles = "c2cc1cccn1cc2";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(9, mol.getAtomCount());
Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol));
Assert.assertEquals("N", mol.getAtom(6).getSymbol());
for (IAtom atom : mol.atoms()) {
if (atom.getSymbol().equals("C")) {
Assert.assertEquals(IAtomType.Hybridization.SP2, atom.getHybridization());
} else {
Assert.assertEquals(IAtomType.Hybridization.PLANAR3, atom.getHybridization());
}
}
}
@Test (timeout=1000)
public void testBug1579229() throws Exception {
String smiles = "c1c(c23)ccc(c34)ccc4ccc2c1";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(14, mol.getAtomCount());
Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol));
for (IAtom atom : mol.atoms()) {
Assert.assertEquals(IAtomType.Hybridization.SP2, atom.getHybridization());
}
}
/** @cdk.bug 1579230 */
@Test (timeout=1000)
public void testBug1579230() throws Exception {
String smiles = "Cc1cccc2sc3nncn3c12";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(13, mol.getAtomCount());
Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol));
for (int i=1;i<13;i++) { // first atom is not aromatic
IAtom atom = mol.getAtom(i);
if (atom.getSymbol().equals("C"))
Assert.assertEquals(IAtomType.Hybridization.SP2, atom.getHybridization());
if (atom.getSymbol().equals("N") || atom.getSymbol().equals("S")) {
Assert.assertTrue(
IAtomType.Hybridization.SP2 == atom.getHybridization() ||
IAtomType.Hybridization.PLANAR3 == atom.getHybridization()
);
}
}
}
@org.junit.Test (timeout=1000)
public void testPyridine_N_oxideUncharged() throws Exception {
String smiles = "O=n1ccccc1";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(7, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testPyridine_N_oxideCharged() throws Exception {
String smiles = "[O-][n+]1ccccc1";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(7, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testPositivePhosphor() throws Exception {
String smiles = "[Cl+3]([O-])([O-])([O-])[O-].[P+]([O-])(c1ccccc1)(c1ccccc1)c1cc([nH0+](C)c(c1)c1ccccc1)c1ccccc1";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(0, mol.getAtom(22).getHydrogenCount().intValue());
assertAtomTypesPerceived(mol);
Assert.assertEquals(38, mol.getAtomCount());
Assert.assertEquals("P", mol.getAtom(5).getSymbol());
Assert.assertEquals(+1, mol.getAtom(5).getFormalCharge().intValue());
Assert.assertEquals("Cl", mol.getAtom(0).getSymbol());
Assert.assertEquals(+3, mol.getAtom(0).getFormalCharge().intValue());
}
/*
* The next methods tests compounds with several conjugated rings
* These compounds would not fail if the Aromaticity Detection was changed
* so that a ring is aromatic if all the atoms in a ring have already been flagged
* as aromatic from the testing of other rings in the system.
*/
@org.junit.Test (timeout=1000)
public void testUnusualConjugatedRings() throws Exception {
//7090-41-7:
String smiles = "c1(Cl)cc2c3cc(Cl)c(Cl)cc3c2cc1Cl";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(16, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testUnusualConjugatedRings_2() throws Exception {
//206-44-0:
String smiles = "c(c(ccc1)ccc2)(c1c(c3ccc4)c4)c23";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(16, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testUnusualConjugatedRings_3() throws Exception {
Assume.assumeTrue(runSlowTests());
//207-08-9:
String smiles = "c2ccc1cc3c(cc1c2)c4cccc5cccc3c45";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(20, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testUnusualConjugatedRings_4() throws Exception {
//2693-46-1:
String smiles = "Nc1c(c23)cccc3c4ccccc4c2cc1";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(17, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testUnusualConjugatedRings_5() throws Exception {
//205-99-2:
String smiles = "c12ccccc1cc3c4ccccc4c5c3c2ccc5";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(20, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void test187_78_0 () throws Exception {
// are all 4 rings aromatic? Is smiles correct?
String smiles = "c1c(c23)ccc(c34)ccc4ccc2c1";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(14, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void test187_78_0_PubChem() throws Exception {
// are all 4 rings aromatic? Is smiles correct?
String smiles = "C1=CC2=C3C(=CC=C4C3=C1C=C4)C=C2";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(14, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void test41814_78_2 () throws Exception {
String smiles = "Cc1cccc2sc3nncn3c12";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(13, mol.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void test239_64_5 () throws Exception {
String smiles = "c1ccc4c(c1)ccc5c3ccc2ccccc2c3nc45";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(21, mol.getAtomCount());
}
/*
* Compounds like Indolizine (274-40-8) with a fused nitrogen as part of a 6 membered ring
* and another ring do not parse
*/
@org.junit.Test (timeout=1000)
public void testIndolizine () throws Exception {
String smiles = "c2cc1cccn1cc2";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(9, mol.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSmiles1() throws Exception {
String smiles = "C1c2c(c3c(c(O)cnc3)cc2)CC(=O)C1";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertEquals(16, molecule.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSmiles2() throws Exception {
String smiles = "O=C(O3)C1=COC(OC4OC(CO)C(O)C(O)C4O)C2C1C3C=C2COC(C)=O";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertEquals(29, molecule.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSmiles3() throws Exception
{
String smiles = "CN1C=NC2=C1C(N(C)C(N2C)=O)=O";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertEquals(14, molecule.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSmiles4() throws Exception {
String smiles = "CN(C)CCC2=CNC1=CC=CC(OP(O)(O)=O)=C12";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertEquals(19, molecule.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSmiles5() throws Exception {
String smiles = "O=C(O)C1C(OC(C3=CC=CC=C3)=O)CC2N(C)C1CC2";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertEquals(21, molecule.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSmiles6() throws Exception {
String smiles = "C1(C2(C)(C))C(C)=CCC2C1";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertEquals(10, molecule.getAtomCount());
}
@org.junit.Test (timeout=1000)
public void testSmiles7() throws Exception {
String smiles = "C1(C=C(C=C(C=C(C=C(C=CC%35=C%36)C%31=C%35C%32=C%33C%36=C%34)C%22=C%31C%23=C%32C%24=C%25C%33=C%26C%34=CC%27=CC%28=CC=C%29)C%14=C%22C%15=C%23C%16=C%24C%17=C%18C%25=C%19C%26=C%27C%20=C%28C%29=C%21)C6=C%14C7=C%15C8=C%16C9=C%17C%12=C%11C%18=C%10C%19=C%20C%21=CC%10=CC%11=CC(C=C%30)=C%12%13)=C(C6=C(C7=C(C8=C(C9=C%13C%30=C5)C5=C4)C4=C3)C3=C2)C2=CC=C1";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertNotNull(molecule);
}
@org.junit.Test (timeout=1000)
public void testSmiles8() throws Exception {
String smiles = "CC1(C(=C(CC(C1)O)C)C=CC(=CC=CC(=CC=CC=C(C=CC=C(C=CC1=C(CC(CC1(C)C)O)C)C)C)C)C)C";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertNotNull(molecule);
}
@org.junit.Test (timeout=1000)
public void testSmiles9() throws Exception {
String smiles = "NC(C(C)C)C(NC(C(C)O)C(NC(C(C)C)C(NC(CCC(N)=O)C(NC(CC([O-])[O-])C(NCC(NC(CC(N)=O)C(NC(Cc1ccccc1)C(NC(CO)C(NC(Cc2ccccc2)C(NC(CO)C(NC(CC(C)C)C(NC(CCC([O-])[O-])C(NC(CO)C(NC(C(C)C)C(NC(CCCC[N+])C(NC(CCCC[N+])C(NC(CC(C)C)C(NC(CCCC[N+])C(NC(CC([O-])[O-])C(NC(CC(C)C)C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(N3CCCC3C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(N4CCCC4C(NC(CCCNC([N+])[N+])C(NC(C(C)C)C(NCC(NC(CCCC[N+])C(NC(CC(C)C)C(NC(CCCNC([N+])[N+])C(NC(CC(N)=O)C(NC(Cc5ccccc5)C(NC(C)C(N6CCCC6C(NC(C(C)CC)C(N7CCCC7C(NCC(NC(CCC([O-])[O-])C(N8CCCC8C(NC(C(C)C)C(NC(C(C)C)C(N9CCCC9C(NC(C(C)CC)C(NC(CC(C)C)C(NC%19C[S][S]CC(C(NC(CCCC[N+])C(NC(CCC([O-])[O-])C(N%10CCCC%10C(NC(CC(N)=O)C(NC(C)C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(NC(C(C)CC)C(NC(CC(C)C)C(NC(CCC(N)=O)C(NC(CCCNC([N+])[N+])C(NC(CC(C)C)C(NC(CCC([O-])[O-])C(NC(CCC([O-])[O-])C(NC(C(C)CC)C(NC(C)C(NC(CCC([O-])[O-])C(NC(CC([O-])[O-])C(N%11CCCC%11C(NCC(NC(C(C)O)C(NC%14C[S][S]CC%13C(NC(C(C)O)C(NCC(NC(C[S][S]CC(C(NC(C)C(NC(Cc%12ccc(O)cc%12)C(NC(C)C(NC(C)C(N%13)=O)=O)=O)=O)=O)NC(=O)C(C(C)CC)NC(=O)C(CCC([O-])[O-])NC%14=O)C(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)NC(=O)C(CC(C)C)NC(=O)C%15CCCN%15C(=O)C(CCCC[N+])NC(=O)C(CC(C)C)NC(=O)C(CCC([O-])[O-])NC(=O)C(CCC([O-])[O-])NC(=O)C%16CCCN%16C(=O)C(Cc%17ccccc%17)NC(=O)C(CC(N)=O)NC(=O)C%18CCCN%18C(=O)C(CC(N)=O)NC(=O)C(CO)NC%19=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertNotNull(molecule);
}
/**
* @cdk.bug 1296113
*/
@org.junit.Test (timeout=1000)
public void testSFBug1296113() throws Exception {
String smiles = "S(=O)(=O)(-O)-c1c2c(c(ccc2-N-c2ccccc2)-N=N-c2c3c(c(cc2)-N=N-c2c4c(c(ccc4)-S(=O)(=O)-O)ccc2)cccc3)ccc1";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertNotNull(molecule);
}
/**
* @cdk.bug 1324105
*/
@org.junit.Test (timeout=1000)
public void testAromaticSmiles2() throws Exception {
String smiles = "n12:n:n:n:c:2:c:c:c:c:1";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Iterator bonds = molecule.bonds().iterator();
while (bonds.hasNext()) Assert.assertTrue(((IBond)bonds.next()).getFlag(CDKConstants.ISAROMATIC));
}
/**
* A unit test for JUnit. It is currently ignored because the SMILES
* given is invalid: the negative has an implied zero hydrogen count,
* making it have an unfilled valency.
*/
@Ignore @Test (timeout=1000)
public void testAromaticSmilesWithCharge() throws Exception {
String smiles = "c1cc[c-]c1";
IMolecule molecule = sp.parseSmiles(smiles);
assertAtomTypesPerceived(molecule);
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.ISAROMATIC));
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testAromaticSmiles() throws Exception {
String smiles = "c1ccccc1";
IMolecule molecule = sp.parseSmiles(smiles);
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.ISAROMATIC));
}
/**
* @cdk.bug 630475
*/
@org.junit.Test (timeout=1000)
public void testSFBug630475() throws Exception {
String smiles = "CC1(C(=C(CC(C1)O)C)C=CC(=CC=CC(=CC=CC=C(C=CC=C(C=CC1=C(CC(CC1(C)C)O)C)C)C)C)C)C";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertTrue(mol.getAtomCount() > 0);
}
/**
* @cdk.bug 585811
*/
@org.junit.Test (timeout=1000)
public void testSFBug585811() throws Exception {
String smiles = "CC(C(C8CCC(CC8)=O)C3C4C(CC5(CCC(C9=CC(C=CN%10)=C%10C=C9)CCCC5)C4)C2CCC1CCC7(CCC7)C6(CC6)C1C2C3)=O";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertTrue(mol.getAtomCount() > 0);
}
/**
* @cdk.bug 593648
*/
@org.junit.Test (timeout=1000)
public void testSFBug593648() throws Exception {
String smiles = "CC1=CCC2CC1C(C)2C";
IMolecule mol = sp.parseSmiles(smiles);
IMolecule apinene = mol.getBuilder().newMolecule();
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 1
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 2
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 3
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 4
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 5
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 6
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 7
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 8
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 9
apinene.addAtom(mol.getBuilder().newAtom("C"));
// 10
apinene.addBond(0, 1, IBond.Order.DOUBLE);
// 1
apinene.addBond(1, 2, IBond.Order.SINGLE);
// 2
apinene.addBond(2, 3, IBond.Order.SINGLE);
// 3
apinene.addBond(3, 4, IBond.Order.SINGLE);
// 4
apinene.addBond(4, 5, IBond.Order.SINGLE);
// 5
apinene.addBond(5, 0, IBond.Order.SINGLE);
// 6
apinene.addBond(0, 6, IBond.Order.SINGLE);
// 7
apinene.addBond(3, 7, IBond.Order.SINGLE);
// 8
apinene.addBond(5, 7, IBond.Order.SINGLE);
// 9
apinene.addBond(7, 8, IBond.Order.SINGLE);
// 10
apinene.addBond(7, 9, IBond.Order.SINGLE);
// 11
IsomorphismTester it = new IsomorphismTester(apinene);
Assert.assertTrue(it.isIsomorphic(mol));
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testReadingOfTwoCharElements() throws Exception {
String smiles = "[Na+]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals("Na", mol.getAtom(0).getSymbol());
}
@org.junit.Test (timeout=1000)
public void testReadingOfOneCharElements() throws Exception {
String smiles = "[K+]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals("K", mol.getAtom(0).getSymbol());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testOrganicSubsetUnderstanding() throws Exception {
String smiles = "[Ni+2]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals("Ni", mol.getAtom(0).getSymbol());
smiles = "Ni";
mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals("N", mol.getAtom(0).getSymbol());
Assert.assertEquals("I", mol.getAtom(1).getSymbol());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testMassNumberReading() throws Exception {
String smiles = "[13C]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals("C", mol.getAtom(0).getSymbol());
Assert.assertEquals(13, mol.getAtom(0).getMassNumber().intValue());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testFormalChargeReading() throws Exception {
String smiles = "[OH-]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals("O", mol.getAtom(0).getSymbol());
Assert.assertEquals(-1, mol.getAtom(0).getFormalCharge().intValue());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testReadingPartionedMolecules() throws Exception {
String smiles = "[Na+].[OH-]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(0, mol.getBondCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testExplicitSingleBond() throws Exception {
String smiles = "C-C";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
Assert.assertEquals(IBond.Order.SINGLE, mol.getBond(0).getOrder());
}
/**
* @cdk.bug 1175478
*/
@org.junit.Test (timeout=1000)
public void testSFBug1175478() throws Exception {
String smiles = "c1cc-2c(cc1)C(c3c4c2onc4c(cc3N5CCCC5)N6CCCC6)=O";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(27, mol.getAtomCount());
Assert.assertEquals(32, mol.getBondCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testUnkownAtomType() throws Exception {
String smiles = "*C";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
Assert.assertTrue(mol.getAtom(0) instanceof IPseudoAtom);
Assert.assertFalse(mol.getAtom(1) instanceof IPseudoAtom);
smiles = "[*]C";
mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
Assert.assertTrue(mol.getAtom(0) instanceof IPseudoAtom);
Assert.assertFalse(mol.getAtom(1) instanceof IPseudoAtom);
}
/**
* @cdk.bug 2596061
* @throws InvalidSmilesException
*/
@org.junit.Test
public void testUnknownAtomType2() throws InvalidSmilesException {
String smiles = "[12*H2-]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals(0, mol.getBondCount());
Assert.assertTrue(mol.getAtom(0) instanceof IPseudoAtom);
Assert.assertEquals(12, mol.getAtom(0).getMassNumber().intValue());
Assert.assertEquals(2, mol.getAtom(0).getHydrogenCount().intValue());
Assert.assertEquals(-1, mol.getAtom(0).getFormalCharge().intValue());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testBondCreation() throws Exception {
String smiles = "CC";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
smiles = "cc";
mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
}
/**
* @cdk.bug 784433
*/
@org.junit.Test (timeout=1000)
public void testSFBug784433() throws Exception {
String smiles = "c1cScc1";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(5, mol.getAtomCount());
Assert.assertEquals(5, mol.getBondCount());
}
/**
* @cdk.bug 873783.
*/
@org.junit.Test (timeout=1000)
public void testProton() throws Exception {
String smiles = "[H+]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals(1, mol.getAtom(0).getFormalCharge().intValue());
}
/**
* @cdk.bug 881330.
*/
@org.junit.Test (timeout=1000)
public void testSMILESFromXYZ() throws Exception {
String smiles = "C.C.N.[Co].C.C.C.[H].[He].[H].[H].[H].[H].C.C.[H].[H].[H].[H].[H]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(20, mol.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSingleBracketH() throws Exception {
String smiles = "[H]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testSingleH() {
try {
String smiles = "H";
sp.parseSmiles(smiles);
Assert.fail("The SMILES string 'H' is not valid: H is not in the organic element subset");
} catch (Exception e) {
// yes! it should fail
}
}
/**
* @cdk.bug 862930.
*/
@org.junit.Test (timeout=1000)
public void testHydroxonium() throws Exception {
String smiles = "[H][O+]([H])[H]";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(4, mol.getAtomCount());
}
/**
* @cdk.bug 809412
*/
@org.junit.Test (timeout=1000)
public void testSFBug809412() throws Exception {
String smiles = "Nc4cc3[n+](c2c(c1c(cccc1)cc2)nc3c5c4cccc5)c6c7c(ccc6)cccc7";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(33, mol.getAtomCount());
}
/**
* A bug found with JCP.
*
* @cdk.bug 956926
*/
@org.junit.Test (timeout=1000)
public void testSFBug956926() throws Exception {
String smiles = "[c+]1ccccc1";
// C6H5+, phenyl cation
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(6, mol.getAtomCount());
Assert.assertEquals(1, mol.getAtom(0).getFormalCharge().intValue());
// I can also check whether all carbons have exact two neighbors
for (int i = 0; i < mol.getAtomCount(); i++)
{
Assert.assertEquals(2, mol.getConnectedAtomsCount(mol.getAtom(i)));
}
// and the number of implicit hydrogens
int hCount = 0;
for (int i = 0; i < mol.getAtomCount(); i++)
{
hCount += mol.getAtom(i).getHydrogenCount();
}
Assert.assertEquals(5, hCount);
}
/**
* A bug found with JCP.
*
* @cdk.bug 956929
* @cdk.inchi InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H
*
* @see #testPyrolle()
*/
@org.junit.Test (timeout=1000)
public void testPyrole() throws Exception {
String smiles = "c1ccc[NH]1";
IMolecule mol = sp.parseSmiles(smiles);
StructureDiagramGenerator sdg=new StructureDiagramGenerator(mol);
sdg.generateCoordinates();
/*MoleculeViewer2D v2d=new MoleculeViewer2D(mol);
v2d.display();
Thread.sleep(100000);*/
for(int i=0;i<mol.getAtomCount();i++){
if(mol.getAtom(i).getSymbol().equals("N")){
Assert.assertEquals(IBond.Order.SINGLE,((IBond)mol.getConnectedBondsList(mol.getAtom(i)).get(0)).getOrder());
Assert.assertEquals(IBond.Order.SINGLE,((IBond)mol.getConnectedBondsList(mol.getAtom(i)).get(1)).getOrder());
}
}
}
/**
* @cdk.bug 2679607
* @throws Exception
*/
@org.junit.Test (timeout=1000)
public void testHardCodedHydrogenCount() throws Exception {
String smiles = "c1ccc[NH]1";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtom(4).getHydrogenCount().intValue());
smiles = "[n]1cc[nH]c1";
mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtom(4).getHydrogenCount().intValue());
Assert.assertEquals(0, mol.getAtom(0).getHydrogenCount().intValue());
smiles = "[nH]1cc[n]c1";
mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtom(0).getHydrogenCount().intValue());
Assert.assertEquals(0, mol.getAtom(3).getHydrogenCount().intValue());
}
/**
* @throws Exception
* @cdk.bug 2679607
*/
@org.junit.Test
public void testHardCodedHydrogenCount2() throws Exception {
String smiles = "[CH2]CNC";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(2, mol.getAtom(0).getHydrogenCount().intValue());
}
/**
* A bug found with JCP.
*
* @cdk.bug 956929
*/
@org.junit.Test (timeout=1000)
public void testSFBug956929() throws Exception {
String smiles = "Cn1cccc1";
IMolecule mol = sp.parseSmiles(smiles);
StructureDiagramGenerator sdg=new StructureDiagramGenerator(mol);
sdg.generateCoordinates();
Assert.assertEquals(6, mol.getAtomCount());
// I can also check whether the total neighbor count around the
// nitrogen is 3, all single bonded
org.openscience.cdk.interfaces.IAtom nitrogen = mol.getAtom(1);
// the second atom
Assert.assertEquals("N", nitrogen.getSymbol());
List<IBond> bondsList = mol.getConnectedBondsList(nitrogen);
Assert.assertEquals(3, bondsList.size());
int totalBondOrder = BondManipulator.getSingleBondEquivalentSum(bondsList);
Assert.assertEquals(3.0, totalBondOrder, 0.001);
}
/**
* A bug found with JCP.
*
* @cdk.bug 956921
*/
@org.junit.Test (timeout=1000)
public void testSFBug956921() throws Exception {
String smiles = "[cH-]1cccc1";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(5, mol.getAtomCount());
// each atom should have 1 implicit hydrogen, and two neighbors
java.util.Iterator atoms = mol.atoms().iterator();
while (atoms.hasNext())
{
IAtom atomi = (IAtom)atoms.next();
Assert.assertEquals(1, atomi.getHydrogenCount().intValue());
Assert.assertEquals(2, mol.getConnectedAtomsCount(atomi));
}
// and the first atom should have a negative charge
Assert.assertEquals(-1, mol.getAtom(0).getFormalCharge().intValue());
}
/**
* @cdk.bug 1274464
*/
@org.junit.Test (timeout=1000)
public void testSFBug1274464() throws Exception {
IAtomContainer fromSmiles = new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("C1=CC=CC=C1");
AtomContainer fromFactory = MoleculeFactory.makeBenzene();
CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(fromFactory.getBuilder());
Iterator<IAtom> atoms = fromFactory.atoms().iterator();
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(fromFactory.getBuilder());
while (atoms.hasNext()) {
IAtom nextAtom = atoms.next();
IAtomType type = matcher.findMatchingAtomType(fromFactory, nextAtom);
AtomTypeManipulator.configure(nextAtom, type);
hAdder.addImplicitHydrogens(fromFactory, nextAtom);
}
CDKHueckelAromaticityDetector.detectAromaticity(fromFactory);
boolean result = UniversalIsomorphismTester.isIsomorph(fromFactory,
fromSmiles);
Assert.assertTrue(result);
}
/**
* @cdk.bug 1095696
*/
@org.junit.Test (timeout=1000)
public void testSFBug1095696() throws Exception {
String smiles = "Nc1ncnc2[nH]cnc12";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(10, mol.getAtomCount());
Assert.assertEquals("N", mol.getAtom(6).getSymbol());
Assert.assertEquals(1, mol.getAtom(6).getHydrogenCount().intValue());
}
/**
* Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 89
* (Part I).
*/
@org.junit.Test (timeout=1000)
public void testNonBond() throws Exception {
String sodiumPhenoxide = "c1cc([O-].[Na+])ccc1";
IMolecule mol = sp.parseSmiles(sodiumPhenoxide);
Assert.assertEquals(8, mol.getAtomCount());
Assert.assertEquals(7, mol.getBondCount());
IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(mol);
int fragmentCount = fragments.getMoleculeCount();
Assert.assertEquals(2, fragmentCount);
org.openscience.cdk.interfaces.IMolecule mol1 = fragments.getMolecule(0);
org.openscience.cdk.interfaces.IMolecule mol2 = fragments.getMolecule(1);
// one should have one atom, the other seven atoms
// in any order, so just test the difference
Assert.assertEquals(6, Math.abs(mol1.getAtomCount() - mol2.getAtomCount()));
}
/**
* Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 89
* (Part I).
*/
@org.junit.Test (timeout=1000)
public void testConnectedByRingClosure() throws Exception {
String sodiumPhenoxide = "C1.O2.C12";
IMolecule mol = sp.parseSmiles(sodiumPhenoxide);
Assert.assertEquals(3, mol.getAtomCount());
Assert.assertEquals(2, mol.getBondCount());
IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(mol);
int fragmentCount = fragments.getMoleculeCount();
Assert.assertEquals(1, fragmentCount);
org.openscience.cdk.interfaces.IMolecule mol1 = fragments.getMolecule(0);
Assert.assertEquals(3, mol1.getAtomCount());
}
/**
* Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 89
* (Part I).
*/
@org.junit.Test (timeout=1000)
public void testReaction() throws Exception {
String reactionSmiles = "O>>[H+].[OH-]";
IReaction reaction = sp.parseReactionSmiles(reactionSmiles);
Assert.assertEquals(1, reaction.getReactantCount());
Assert.assertEquals(2, reaction.getProductCount());
}
/**
* Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 90
* (Part I).
*/
@org.junit.Test (timeout=1000)
public void testReactionWithAgents() throws Exception {
String reactionSmiles = "CCO.CC(=O)O>[H+]>CC(=O)OCC.O";
IReaction reaction = sp.parseReactionSmiles(reactionSmiles);
Assert.assertEquals(2, reaction.getReactantCount());
Assert.assertEquals(2, reaction.getProductCount());
Assert.assertEquals(1, reaction.getAgents().getMoleculeCount());
Assert.assertEquals(1, reaction.getAgents().getMolecule(0).getAtomCount());
}
/**
* A unit test for JUnit
*/
@org.junit.Test (timeout=1000)
public void testImplicitHydrogenCount() throws Exception {
String smiles = "C";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals(4, mol.getAtom(0).getHydrogenCount().intValue());
}
/**
* @cdk.bug 2028780
*/
@Test(timeout=1000)
public void testTungsten() throws Exception {
String smiles = "[W]";
IMolecule mol = sp.parseSmiles(smiles);
assertAtomTypesPerceived(mol);
Assert.assertEquals(1, mol.getAtomCount());
Assert.assertEquals("W", mol.getAtom(0).getSymbol());
}
/**