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CDKAtomTypeMatcherTest.java
6582 lines (5816 loc) · 249 KB
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CDKAtomTypeMatcherTest.java
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/* Copyright (C) 2007-2011 Egon Willighagen <egonw@users.sf.net>
* 2007 Rajarshi Guha
* 2011 Nimish Gopal <nimishg@ebi.ac.uk>
* 2011 Syed Asad Rahman <asad@ebi.ac.uk>
* 2011 Gilleain Torrance <gilleain.torrance@gmail.com>
*
* 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.atomtype;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.Bond;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.PseudoAtom;
import org.openscience.cdk.Ring;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.config.Elements;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.silent.AtomType;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
import org.openscience.cdk.tools.periodictable.PeriodicTable;
/**
* This class tests the matching of atom types defined in the
* CDK atom type list. All tests in this class <b>must</b> use
* explicit {@link IAtomContainer}s; test using data files
* must be placed in {@link CDKAtomTypeMatcherFilesTest}.
*
* @cdk.module test-core
*/
public class CDKAtomTypeMatcherTest extends AbstractCDKAtomTypeTest {
private static Map<String, Integer> testedAtomTypes = new HashMap<String, Integer>();
@Test public void testGetInstance_IChemObjectBuilder() throws Exception {
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(matcher);
}
@Test public void testGetInstance_IChemObjectBuilder_int() throws Exception {
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
DefaultChemObjectBuilder.getInstance(),
CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS
);
Assert.assertNotNull(matcher);
}
@Test public void testFindMatchingAtomType_IAtomContainer_IAtom() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
final IAtomType.Hybridization thisHybridization = IAtomType.Hybridization.SP3;
atom.setHybridization(thisHybridization);
mol.addAtom(atom);
String[] expectedTypes = {"C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testFindMatchingAtomType_IAtomContainer() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
final IAtomType.Hybridization thisHybridization = IAtomType.Hybridization.SP3;
atom.setHybridization(thisHybridization);
mol.addAtom(atom);
// just check consistency; other methods do perception testing
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
DefaultChemObjectBuilder.getInstance());
IAtomType[] types = matcher.findMatchingAtomType(mol);
for (int i=0; i<types.length; i++) {
IAtomType type = matcher.findMatchingAtomType(mol, mol.getAtom(i));
Assert.assertEquals(type.getAtomTypeName(), types[i].getAtomTypeName());
}
}
@Test public void testDummy() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new PseudoAtom("R");
mol.addAtom(atom);
String[] expectedTypes = {"X"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
/**
* @cdk.bug 2445178
*/
@Test public void testNonExistingType() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("Error");
mol.addAtom(atom);
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
DefaultChemObjectBuilder.getInstance());
Assert.assertNull(matcher.findMatchingAtomType(mol, atom));
}
@Test public void testEthene() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"C.sp2", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testEthyneKation() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("C"); atom2.setFormalCharge(+1);
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_TRIPLE);
String[] expectedTypes = {"C.sp", "C.plus.sp1"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testEthyneRadical() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addSingleElectron(1);
mol.addBond(0,1,CDKConstants.BONDORDER_TRIPLE);
String[] expectedTypes = {"C.sp", "C.radical.sp1"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testImine() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("N");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"C.sp2", "N.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testImineRadical() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("N");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addSingleElectron(1);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"C.sp2", "N.sp2.radical"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testEtheneRadical() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addSingleElectron(1);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"C.sp2", "C.radical.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testGuanineMethyl() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom1 = new Atom("C");
IAtom atom2 = new Atom("N");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("N");
IAtom atom5 = new Atom("C");
IAtom atom6 = new Atom("C");
IAtom atom7 = new Atom("N");
IAtom atom8 = new Atom("C");
IAtom atom9 = new Atom("C");
IAtom atom10 = new Atom("N");
IAtom atom11 = new Atom("O");
IAtom atom12 = new Atom("N");
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addAtom(atom6);
mol.addAtom(atom7);
mol.addAtom(atom8);
mol.addAtom(atom9);
mol.addAtom(atom10);
mol.addAtom(atom11);
mol.addAtom(atom12);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(0,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(0,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(4,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,5,CDKConstants.BONDORDER_SINGLE);
mol.addBond(2,6,CDKConstants.BONDORDER_SINGLE);
mol.addBond(2,7,CDKConstants.BONDORDER_SINGLE);
mol.addBond(3,8,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(5,6,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(7,9,CDKConstants.BONDORDER_SINGLE);
mol.addBond(7,10,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(8,11,CDKConstants.BONDORDER_SINGLE);
mol.addBond(8,9,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"C.sp2", "N.planar3", "C.sp2", "N.sp2", "C.sp3",
"C.sp2", "N.sp2", "C.sp2", "C.sp2", "N.amide",
"O.sp2", "N.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testPropyne() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("C");
IAtom atom3 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,1,CDKConstants.BONDORDER_TRIPLE);
mol.addBond(2,1,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"C.sp", "C.sp", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testFormaldehyde() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"O.sp2", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testCarboxylate() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom1 = new Atom("C");
IAtom atom2 = new Atom("O"); atom2.setFormalCharge(-1);
IAtom atom3 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2.co2", "C.sp2", "O.minus.co2", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testFormaldehydeRadicalKation() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O"); atom.setFormalCharge(+1);
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addSingleElectron(0);
String[] expectedTypes = {"O.plus.sp2.radical", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
/**
* Aim of this test is to see if the atom type matcher is OK with
* partial filled implicit hydrogen counts.
*/
@Test public void testPartialMethane() throws Exception {
IAtomContainer methane = new AtomContainer();
IAtom carbon = new Atom("C");
methane.addAtom(carbon);
String[] expectedTypes = {"C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, methane);
carbon.setImplicitHydrogenCount(1);
assertAtomTypes(testedAtomTypes, expectedTypes, methane);
carbon.setImplicitHydrogenCount(2);
assertAtomTypes(testedAtomTypes, expectedTypes, methane);
carbon.setImplicitHydrogenCount(3);
assertAtomTypes(testedAtomTypes, expectedTypes, methane);
carbon.setImplicitHydrogenCount(4);
assertAtomTypes(testedAtomTypes, expectedTypes, methane);
}
@Test public void testMethanol() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testLithiumMethanoxide() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("C");
IAtom atom3 = new Atom("Li");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(0,2,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp3", "C.sp3", "Li"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testHCN() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("N");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_TRIPLE);
String[] expectedTypes = {"N.sp1", "C.sp"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testHNO2() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("N");
IAtom atom2 = new Atom("O");
IAtom atom3 = new Atom("O");
IAtom atom4 = new Atom("H");
mol.addAtom(atom); atom.setFormalCharge(+1);
mol.addAtom(atom2);
mol.addAtom(atom3); atom3.setFormalCharge(-1);
mol.addAtom(atom4);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(0,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(0,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"N.plus.sp2", "O.sp2", "O.minus", "H"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testNitromethane() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("N");
IAtom atom2 = new Atom("O");
IAtom atom3 = new Atom("O");
IAtom atom4 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(0,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(0,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"N.nitro", "O.sp2", "O.sp2", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testMethylAmine() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("N");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"N.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testMethylAmineRadical() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("N");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addSingleElectron(0);
atom.setFormalCharge(+1);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"N.plus.sp3.radical", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testMethyleneImine() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("N");
IAtom atom2 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"N.sp2", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testEthene_withHybridInfo() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("C");
IAtom atom2 = new Atom("C");
final IAtomType.Hybridization thisHybridization = IAtomType.Hybridization.SP2;
atom.setHybridization(thisHybridization);
atom2.setHybridization(thisHybridization);
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"C.sp2", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test
public void testPiperidine() throws Exception {
IAtomContainer molecule = MoleculeFactory.makePiperidine();
String[] expectedTypes = {"N.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "H"};
assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
}
@Test
public void testTetrahydropyran() throws Exception {
IAtomContainer molecule = MoleculeFactory.makeTetrahydropyran();
String[] expectedTypes = {"O.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
}
@Test public void testS3() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom s = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"S");
IAtom o1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"O");
IAtom o2 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"O");
IBond b1 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,s, o1, IBond.Order.DOUBLE);
IBond b2 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,s, o2, IBond.Order.DOUBLE);
mol.addAtom(s);
mol.addAtom(o1);
mol.addAtom(o2);
mol.addBond(b1);
mol.addBond(b2);
String[] expectedTypes = {"S.oxide", "O.sp2", "O.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testH2S() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom s = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"S");
IAtom h1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"H");
IAtom h2 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"H");
IBond b1 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,s, h1, IBond.Order.SINGLE);
IBond b2 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,s, h2, IBond.Order.SINGLE);
mol.addAtom(s);
mol.addAtom(h1);
mol.addAtom(h2);
mol.addBond(b1);
mol.addBond(b2);
String[] expectedTypes = {"S.3", "H", "H"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
/**
* @cdk.inchi InChI=1/H2Se/h1H2
*/
@Test public void testH2Se() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom se = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"Se");
IAtom h1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"H");
IAtom h2 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"H");
IBond b1 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,se, h1, IBond.Order.SINGLE);
IBond b2 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,se, h2, IBond.Order.SINGLE);
mol.addAtom(se);
mol.addAtom(h1);
mol.addAtom(h2);
mol.addBond(b1);
mol.addBond(b2);
String[] expectedTypes = {"Se.3", "H", "H"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
/**
* @cdk.inchi InChI=1/H2Se/h1H2
*/
@Test public void testH2Se_oneImplH() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom se = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"Se");
se.setImplicitHydrogenCount(1);
IAtom h1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"H");
IBond b1 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,se, h1, IBond.Order.SINGLE);
mol.addAtom(se);
mol.addAtom(h1);
mol.addBond(b1);
String[] expectedTypes = {"Se.3", "H"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
/**
* @cdk.inchi InChI=1/H2Se/h1H2
*/
@Test public void testH2Se_twoImplH() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom se = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"Se");
se.setImplicitHydrogenCount(2);
mol.addAtom(se);
String[] expectedTypes = {"Se.3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testSelenide() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom se = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"Se");
se.setImplicitHydrogenCount(0);
se.setFormalCharge(-2);
mol.addAtom(se);
String[] expectedTypes = {"Se.2minus"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testH2S_Hybridization() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom s = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"S");
s.setHybridization(Hybridization.SP3);
mol.addAtom(s);
String[] expectedTypes = {"S.3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testHS() throws Exception {
IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
IAtom s = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"S");
s.setFormalCharge(-1);
IAtom h1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class,"H");
IBond b1 = DefaultChemObjectBuilder.getInstance().newInstance(IBond.class,s, h1, IBond.Order.SINGLE);
mol.addAtom(s);
mol.addAtom(h1);
mol.addBond(b1);
String[] expectedTypes = {"S.minus", "H"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testDMSOCharged() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O"); atom.setFormalCharge(-1);
IAtom atom2 = new Atom("S"); atom2.setFormalCharge(1);
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.minus", "S.inyl.charged", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testDMSO() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("S");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "S.inyl", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testDMSOO() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom1 = new Atom("O");
IAtom atom2 = new Atom("S");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addBond(0,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(2,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(2,4,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "O.sp2", "S.onyl", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testStrioxide() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom1 = new Atom("O");
IAtom atom2 = new Atom("S");
IAtom atom3 = new Atom("O");
mol.addAtom(atom);
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(2,3,CDKConstants.BONDORDER_DOUBLE);
String[] expectedTypes = {"O.sp2", "O.sp2", "S.trioxide", "O.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testAmide() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("C");
IAtom atom3 = new Atom("N");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "C.sp2", "N.amide"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testAmineOxide() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("N");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
IAtom atom5 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "N.oxide", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testThioAmide() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("S");
IAtom atom2 = new Atom("C");
IAtom atom3 = new Atom("N");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"S.2", "C.sp2", "N.thioamide"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testAdenine() throws Exception {
IAtomContainer mol = MoleculeFactory.makeAdenine();
String[] expectedTypes = {"C.sp2", "C.sp2", "C.sp2", "N.sp2", "N.sp2", "N.planar3",
"N.sp2", "N.sp3", "C.sp2", "C.sp2"
};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testAmide2() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom1 = new Atom("C");
IAtom atom2 = new Atom("N");
IAtom atom3 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(2,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "C.sp2", "N.amide", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testAmide3() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom1 = new Atom("C");
IAtom atom2 = new Atom("N");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(2,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(3,4,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "C.sp2", "N.amide", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testLactam() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom1 = new Atom("C");
IAtom atom2 = new Atom("N");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
IAtom atom5 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom1);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(2,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(3,4,CDKConstants.BONDORDER_SINGLE);
mol.addBond(4,5,CDKConstants.BONDORDER_SINGLE);
mol.addBond(5,1,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "C.sp2", "N.amide", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testThioAcetone() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("S");
IAtom atom2 = new Atom("C");
IAtom atom3 = new Atom("C");
IAtom atom4 = new Atom("C");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"S.2", "C.sp2", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testSulphuricAcid() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("S");
IAtom atom3 = new Atom("O");
IAtom atom4 = new Atom("O");
IAtom atom5 = new Atom("O");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.sp2", "S.onyl", "O.sp2", "O.sp3", "O.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
/**
* @cdk.inchi InChI=1S/CH4O2S2/c1-5(2,3)4/h1H3,(H,2,3,4)
*/
@Test public void testThioSulphonate() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
IAtom a1 = builder.newInstance(IAtom.class,"S");
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class,"S");
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class,"O");
mol.addAtom(a3);
IAtom a4 = builder.newInstance(IAtom.class,"O");
mol.addAtom(a4);
IAtom a5 = builder.newInstance(IAtom.class,"C");
mol.addAtom(a5);
IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.DOUBLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class,a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class,a1, a4, IBond.Order.DOUBLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class,a1, a5, IBond.Order.SINGLE);
mol.addBond(b4);
String[] expectedTypes = {"S.thionyl", "S.2", "O.sp3", "O.sp2", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testSulphuricAcid_Charged() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("S");
IAtom atom3 = new Atom("O");
IAtom atom4 = new Atom("O");
IAtom atom5 = new Atom("O");
mol.addAtom(atom); atom.setFormalCharge(-1);
mol.addAtom(atom2); atom2.setFormalCharge(+2);
mol.addAtom(atom3); atom3.setFormalCharge(-1);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"O.minus", "S.onyl.charged", "O.minus", "O.sp3", "O.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testSF6() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("F");
IAtom atom2 = new Atom("S");
IAtom atom3 = new Atom("F");
IAtom atom4 = new Atom("F");
IAtom atom5 = new Atom("F");
IAtom atom6 = new Atom("F");
IAtom atom7 = new Atom("F");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addAtom(atom6);
mol.addAtom(atom7);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,5,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,6,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"F", "S.octahedral", "F", "F", "F", "F", "F"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testMnF4() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("F");
IAtom atom2 = new Atom("Mn");
IAtom atom3 = new Atom("F");
IAtom atom4 = new Atom("F");
IAtom atom5 = new Atom("F");
mol.addAtom(atom); atom.setFormalCharge(-1);
mol.addAtom(atom2); atom2.setFormalCharge(+2);
mol.addAtom(atom3); atom3.setFormalCharge(-1);
mol.addAtom(atom4); atom4.setFormalCharge(-1);
mol.addAtom(atom5); atom5.setFormalCharge(-1);
String[] expectedTypes = {"F.minus", "Mn.2plus", "F.minus", "F.minus", "F.minus"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testCrF6() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("F");
IAtom atom2 = new Atom("Cr");
IAtom atom3 = new Atom("F");
IAtom atom4 = new Atom("F");
IAtom atom5 = new Atom("F");
IAtom atom6 = new Atom("F");
IAtom atom7 = new Atom("F");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addAtom(atom6);
mol.addAtom(atom7);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,5,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,6,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"F", "Cr", "F", "F", "F", "F", "F"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testXeF4() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("F");
IAtom atom2 = new Atom("Xe");
IAtom atom3 = new Atom("F");
IAtom atom4 = new Atom("F");
IAtom atom5 = new Atom("F");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
String[] expectedTypes = {"F", "Xe.3", "F", "F", "F"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
@Test public void testPhosphate() throws Exception {
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom("O");
IAtom atom2 = new Atom("P");
IAtom atom3 = new Atom("O");
IAtom atom4 = new Atom("O");
IAtom atom5 = new Atom("O");
mol.addAtom(atom);
mol.addAtom(atom2);
mol.addAtom(atom3);
mol.addAtom(atom4);
mol.addAtom(atom5);
mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);