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/*
* $Id: ChemAtomTests.java 131 2011-01-20 22:01:29Z ebakke $
*
* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package org.RDKit;
import static org.junit.Assert.*;
import org.junit.*;
public class ChemAtomTests extends GraphMolTest {
private ROMol m;
@Before
public void setUp() {
String smiles = "CC(=O)CCSC";
m = RWMol.MolFromSmiles(smiles);
}
// A new method introduced in the ROMol.i wrapper
@Test
public void testGetAtoms() {
Atom_Vect atoms = m.getAtoms();
assertEquals(7L, atoms.size());
}
@Test
public void test1Implicit() {
// Test implicit valence
Atom a = m.getAtoms().get(0);
int iV = a.getImplicitValence();
assertEquals(3, iV);
assertEquals(0, m.getAtomWithIdx(1).getImplicitValence());
assertEquals(0, m.getAtomWithIdx(2).getImplicitValence());
assertEquals(2, m.getAtomWithIdx(3).getImplicitValence());
}
// Test getBonds
@Test
public void testGetBonds() {
Bond_Vect bonds = m.getAtomWithIdx(1).getBonds();
assertEquals(3, bonds.size());
assertEquals(1, m.getAtomWithIdx(2).getBonds().size());
}
// Testing iteration over an atom's bonds
@Test
public void test2BondIter() {
Atom a = m.getAtomWithIdx(1);
Bond_Vect bonds = a.getBonds();
assertEquals(3, bonds.size());
for (int bond_num = 0; bond_num < bonds.size(); bond_num++) {
assertNotNull(bonds.get(bond_num));
}
}
// testing GetBondBetweenAtoms(idx,idx)
@Test
public void test3GetBond() {
Bond b = m.getBondBetweenAtoms(1, 2);
assertEquals("GetBondBetweenAtoms failed", Bond.BondType.DOUBLE, b.getBondType());
}
// Testing atomic props
@Test
public void test4Props() {
Atom a = m.getAtomWithIdx(1);
assertEquals("C",a.getSymbol());
assertEquals(6, a.getAtomicNum());
assertEquals(0, a.getFormalCharge());
assertEquals(3, a.getDegree());
assertEquals(0, a.getImplicitValence());
assertEquals(4, a.getExplicitValence());
}
// Testing setting atomic props and generic exception handler
@Test
public void test5Setters() {
Atom a = new Atom(6);
assertEquals("C",a.getSymbol());
assertEquals( 6,a.getAtomicNum() );
a.setFormalCharge(1);
assertEquals( 1,a.getFormalCharge() );
}
@Test(expected=GenericRDKitException.class)
public void testExceptionHandler() {
Atom a = new Atom(6);
a.getImplicitValence();
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.ChemAtomTests");
}
}
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