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/*
* $Id: BasicMolecule2Tests.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 BasicMolecule2Tests extends GraphMolTest {
private ROMol mol1;
@Before public void setUp() {
String smiles="c1ccccc1";
mol1 = (ROMol) RWMol.MolFromSmiles(smiles);
}
@Test public void testBasics() {
assertEquals(mol1.getNumAtoms(),6);
assertEquals(mol1.getNumBonds(),6);
}
@Test public void testAtoms() {
assertEquals(mol1.getAtomWithIdx(0).getAtomicNum(),6);
assertFalse(mol1.hasAtomBookmark(1));
mol1.setAtomBookmark(mol1.getAtomWithIdx(0),1);
assertTrue(mol1.hasAtomBookmark(1));
}
@Test public void testBonds() {
assertEquals(mol1.getBondWithIdx(0).getBondType(),Bond.BondType.AROMATIC);
}
@Test public void testSmilesWrite() {
String smi=((RWMol) mol1).MolToSmiles();
assertEquals(smi,smi,"c1ccccc1");
}
@Test public void testReactionBasics() {
ChemicalReaction rxn;
rxn=ChemicalReaction.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
assertEquals(2,rxn.getNumReactantTemplates());
assertEquals(1,rxn.getNumProductTemplates());
ROMol r1,r2;
r1=RWMol.MolFromSmiles("CC(=O)O");
r2=RWMol.MolFromSmiles("ClCN");
assertEquals(4,r1.getNumAtoms());
assertEquals(3,r2.getNumAtoms());
ROMol_Vect rs= new ROMol_Vect(2);
rs.set(0,r1);
rs.set(1,r2);
ROMol_Vect_Vect ps;
ps=rxn.runReactants(rs);
assertFalse(ps.isEmpty());
assertEquals(1,ps.size());
assertFalse(ps.get(0).isEmpty());
assertEquals(1,ps.get(0).size());
assertEquals(4,r1.getNumAtoms());
assertEquals(3,r2.getNumAtoms());
assertEquals(6,ps.get(0).get(0).getNumAtoms());
}
@Test public void testSubstruct1() {
ROMol p;
Match_Vect mv;
p = RWMol.MolFromSmarts("c");
assertTrue(mol1.hasSubstructMatch(p));
mv=mol1.getSubstructMatch(p);
assertEquals(1,mv.size());
assertEquals(0,mv.get(0).getFirst());
assertEquals(0,mv.get(0).getSecond());
}
@Test public void testSubstruct2() {
ROMol p;
Match_Vect mv;
p = RWMol.MolFromSmarts("C");
assertFalse(mol1.hasSubstructMatch(p));
mv=mol1.getSubstructMatch(p);
assertEquals(0,mv.size());
}
@Test public void testSubstruct3() {
ROMol p;
Match_Vect mv;
ROMol m2;
m2 = RWMol.MolFromSmiles("NC(=O)CC");
p = RWMol.MolFromSmarts("CN");
mv=m2.getSubstructMatch(p);
assertEquals(2,mv.size());
assertEquals(0,mv.get(0).getFirst());
assertEquals(1,mv.get(0).getSecond());
assertEquals(1,mv.get(1).getFirst());
assertEquals(0,mv.get(1).getSecond());
}
@Test public void testSubstruct4() {
ROMol p;
Match_Vect_Vect mvv;
ROMol m2;
m2 = RWMol.MolFromSmiles("NC(=O)CC");
p = RWMol.MolFromSmarts("CN");
mvv=m2.getSubstructMatches(p);
assertEquals(1,mvv.size());
assertEquals(2,mvv.get(0).size());
assertEquals(0,mvv.get(0).get(0).getFirst());
assertEquals(1,mvv.get(0).get(0).getSecond());
assertEquals(1,mvv.get(0).get(1).getFirst());
assertEquals(0,mvv.get(0).get(1).getSecond());
}
@Test public void testSubstruct5() {
ROMol p;
Match_Vect_Vect mvv;
ROMol m2;
m2 = RWMol.MolFromSmiles("NC(=O)NCC");
p = RWMol.MolFromSmarts("[$(C=O)]N");
mvv=m2.getSubstructMatches(p);
assertEquals(2,mvv.size());
assertEquals(2,mvv.get(0).size());
assertEquals(0,mvv.get(0).get(0).getFirst());
assertEquals(1,mvv.get(0).get(0).getSecond());
assertEquals(1,mvv.get(0).get(1).getFirst());
assertEquals(0,mvv.get(0).get(1).getSecond());
assertEquals(2,mvv.get(1).size());
assertEquals(0,mvv.get(1).get(0).getFirst());
assertEquals(1,mvv.get(1).get(0).getSecond());
assertEquals(1,mvv.get(1).get(1).getFirst());
assertEquals(3,mvv.get(1).get(1).getSecond());
}
@Test public void testSubstruct6() {
ROMol p;
Match_Vect_Vect mvv;
ROMol m2;
m2 = RWMol.MolFromSmiles("CC(=O)[O-]");
ResonanceMolSupplier rs = new ResonanceMolSupplier(m2);
assertEquals(2,rs.length());
p = RWMol.MolFromSmarts("C(=O)[O-]");
mvv=m2.getSubstructMatches(p);
assertEquals(1,mvv.size());
assertEquals(3,mvv.get(0).size());
mvv=rs.getSubstructMatches(p);
assertEquals(2,mvv.size());
assertEquals(3,mvv.get(0).size());
assertEquals(3,mvv.get(1).size());
mvv=rs.getSubstructMatches(p, true);
assertEquals(1,mvv.size());
assertEquals(3,mvv.get(0).size());
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.BasicMolecule2Tests");
}
}
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