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/*
* $Id: PicklingTests.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 PicklingTests extends GraphMolTest {
private ROMol mol1;
@Before
public void setUp() {
String smiles = "c1ccccc1";
mol1 = RWMol.MolFromSmiles(smiles);
}
@Test
public void testBasicPickling() {
Int_Vect pkl = mol1.ToBinary();
ROMol m1 = ROMol.MolFromBinary(pkl);
assertEquals(6, m1.getNumAtoms());
assertEquals(6, m1.getNumBonds());
}
@Test
public void testBasicReactionPickling() {
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());
Int_Vect pkl = rxn.ToBinary();
ChemicalReaction rxn2 = ChemicalReaction.RxnFromBinary(pkl);
assertEquals(2, rxn2.getNumReactantTemplates());
assertEquals(1, rxn2.getNumProductTemplates());
}
@Test
public void testIssue164() {
String smi = "NCCCCC(NC(C(C(C)C)NC(=O)C1CCCN1C(C(N)CCCNC(=N)N)=O)=O)C(NC(C(C)C)C(NC(Cc2ccc(O)cc2)C(=O)N6C(C(NC(CC(N)=O)C(NCC(NC(C)C(NC(CCC(O)=O)C(NC(CC(O)=O)C(NC(C(NC(CO)C(NC(C)C(NC(CCC(O)=O)C(NC(C)C(NC(Cc3ccccc3)C(=O)N5C(C(NC(CC(C)C)C(NC(C(NC(C(O)=O)Cc4ccccc4)=O)CCC(O)=O)=O)=O)CCC5)=O)=O)=O)=O)=O)CCC(O)=O)=O)=O)=O)=O)=O)=O)CCC6)=O)=O";
ROMol m1 = RWMol.MolFromSmiles(smi);
Int_Vect pickle;
ROMol m2;
pickle = m1.ToBinary();
m2 = ROMol.MolFromBinary(pickle);
assertEquals(m2.getNumAtoms(), m1.getNumAtoms());
// the issue had to do with number of atoms, so let's make an enormous
// molecule and try again:
RWMol m3 = RWMol.MolFromSmiles(smi);
m3.insertMol(m1);
m3.insertMol(m1);
m3.sanitizeMol();
pickle = m3.ToBinary();
ROMol m4 = ROMol.MolFromBinary(pickle);
assertEquals(m4.getNumAtoms(), m3.getNumAtoms());
assertEquals(m4.getNumBonds(), m3.getNumBonds());
}
@Test
public void testIssue219() {
String smi = "CC";
ROMol m1 = RWMol.MolFromSmiles(smi);
Int_Vect pickle = m1.ToBinary();
ROMol m2 = ROMol.MolFromBinary(pickle);
assertEquals(m2.getNumAtoms(),m1.getNumAtoms());
Conformer conf = new Conformer(2);
conf.setId(23);
m1.addConformer(conf);
pickle = m1.ToBinary();
m2 = ROMol.MolFromBinary(pickle);
assertEquals(m2.getNumAtoms(),m1.getNumAtoms());
assertEquals(23,m2.getConformer().getId());
}
@Test
public void testIssue220() {
String smi = "N/N=C/C";
ROMol m1 = RWMol.MolFromSmiles(smi);
assertEquals(m1.getBondWithIdx(1).getStereo(),Bond.BondStereo.STEREOE);
Int_Vect pickle = m1.ToBinary();
ROMol m2 = ROMol.MolFromBinary(pickle);
assertEquals(m2.getNumAtoms(), m1.getNumAtoms());
assertEquals(m2.getNumBonds(), m1.getNumBonds());
assertEquals(m2.getBondWithIdx(1).getStereo(), Bond.BondStereo.STEREOE);
for (int i = 0; i < m1.getNumBonds(); ++i) {
assertEquals(m1.getBondWithIdx(i).getStereo(), m2.getBondWithIdx(i).getStereo());
Int_Vect s1 = m1.getBondWithIdx(i).getStereoAtoms();
Int_Vect s2 = m2.getBondWithIdx(i).getStereoAtoms();
assertEquals(s2.size(), s1.size());
for (int j = 0; j < s1.size(); j++)
assertEquals(s2.get(j), s1.get(j));
}
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.PicklingTests");
}
}
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