mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
127 lines
3.9 KiB
Java
127 lines
3.9 KiB
Java
/*
|
|
* $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");
|
|
}
|
|
|
|
}
|