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357 lines
11 KiB
Java
357 lines
11 KiB
Java
/*
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* $Id: WrapperTests.java 131 2011-01-20 22:01:29Z ebakke $
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import java.io.*;
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import java.io.File;
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import java.util.ArrayList;
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import org.junit.*;
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public class WrapperTests extends GraphMolTest {
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private ArrayList<String> tmpFiles = new ArrayList<String>();
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@After
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public void tearDown() {
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for (String fn : tmpFiles) {
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new File(fn).delete();
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}
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}
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@Test
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public void testBasicInstantiation_Conformer() {
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Conformer conformer = new Conformer();
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assertNotNull(conformer);
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}
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@Test
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public void testBasicInstantiation_QueryAtom() {
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QueryAtom queryAtom = new QueryAtom();
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assertNotNull(queryAtom);
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}
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@Test
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public void testBasicInstantiation_QueryBond() {
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QueryBond queryBond = new QueryBond();
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assertNotNull(queryBond);
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}
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@Test
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public void testBasicInstantiation_QueryOps() {
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// Comes from QueryOps.cpp
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RecursiveStructureQuery rsQuery = new RecursiveStructureQuery();
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assertNotNull(rsQuery);
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AtomRingQuery arQuery = new AtomRingQuery();
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assertNotNull(arQuery);
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}
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@Test
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public void testBasicInstantiation_Atom() {
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Atom atom = new Atom();
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assertNotNull(atom);
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}
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@Test
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public void testBasicInstantiation_ROMol() {
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ROMol roMol = new ROMol();
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assertNotNull(roMol);
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}
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@Test
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public void testBasicInstantiation_Bond() {
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Bond bond = new Bond();
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assertNotNull(bond);
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}
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@Test
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public void testBasicInstantiation_MolStackElem() {
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// Came from Canon.cpp
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MolStackElem molStack = new MolStackElem(1);
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assertNotNull(molStack);
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}
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@Test
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public void testBasicInstantiation_RWMol() {
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RWMol rwMol = new RWMol();
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assertNotNull(rwMol);
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}
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@Test
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public void testBasicInstantiation_PeriodicTable() {
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assertNotNull(PeriodicTable.getTable());
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}
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@Test
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public void testBasicInstantiation_MolSanitizeException() {
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MolSanitizeException sanit = new MolSanitizeException("some error message");
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assertNotNull(sanit);
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}
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@Test
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public void testBasicInstantiation_SmilesParseException() {
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SmilesParseException parse = new SmilesParseException("some error message");
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assertNotNull(parse);
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}
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@Test
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public void testBasicInstantiation_RingInfo() {
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RingInfo rInfo = new RingInfo();
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assertNotNull(rInfo);
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}
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@Test
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public void testBasicInstantiation_ChemicalReaction() {
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ChemicalReaction reaction = new ChemicalReaction();
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assertNotNull(reaction);
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}
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@Test
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public void testBasicInstantiation_BondIterator() {
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ROMol m = RWMol.MolFromSmiles("CS");
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BondIterator bonditer = new BondIterator(m);
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assertNotNull(bonditer);
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}
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@Test
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public void testBasicInstantiation_ConstBondIterator() {
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ROMol m = RWMol.MolFromSmiles("CS");
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ConstBondIterator bonditer = new ConstBondIterator(m);
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assertNotNull(bonditer);
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}
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@Test
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public void testBasicInstantiation_AtomIterator() {
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ROMol m = RWMol.MolFromSmiles("CS");
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AtomIterator atomiter = new AtomIterator(m);
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assertNotNull(atomiter);
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}
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@Test
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public void testBasicInstantiation_HeteroatomIterator() {
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ROMol m = RWMol.MolFromSmiles("CS");
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HeteroatomIterator atomiter = new HeteroatomIterator(m);
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assertNotNull(atomiter);
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}
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@Test
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public void testBasicInstantiation_QueryAtomIterator() {
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ROMol m = RWMol.MolFromSmiles("CS");
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QueryAtomIterator atomiter = new QueryAtomIterator(m, new QueryAtom(6));
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assertNotNull(atomiter);
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}
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@Test
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public void testBasicInstantiation_AromaticAtomIterator() {
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ROMol m = RWMol.MolFromSmiles("Cc1ccccc1");
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AromaticAtomIterator atomiter = new AromaticAtomIterator(m);
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assertNotNull(atomiter);
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}
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@Test
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public void testBasicInstantiation_SDMolSupplier() {
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SDMolSupplier sup = new SDMolSupplier();
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assertNotNull(sup);
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}
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@Test
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public void testBasicInstantiation_ForwardSDMolSupplier() {
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ForwardSDMolSupplier sup = new ForwardSDMolSupplier();
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assertNotNull(sup);
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}
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@Test
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public void testBasicInstantiation_SmilesMolSupplier() {
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SmilesMolSupplier sup = new SmilesMolSupplier();
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assertNotNull(sup);
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}
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@Test
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public void testBasicInstantiation_TDTMolSupplier() {
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TDTMolSupplier sup = new TDTMolSupplier();
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assertNotNull(sup);
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}
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@Test
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public void testBasicInstantiation_ResonanceMolSupplier() {
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ROMol m = RWMol.MolFromSmiles("CC(=O)[O-]");
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ResonanceMolSupplier sup = new ResonanceMolSupplier(m);
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assertNotNull(sup);
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}
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@Test
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public void testBasicInstantiation_SDMWriter() {
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SDWriter mw = new SDWriter("tmp.sdf");
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mw.close();
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tmpFiles.add("tmp.sdf");
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assertNotNull(mw);
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}
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@Test
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public void testBasicInstantiation_TDTWriter() {
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TDTWriter mw = new TDTWriter("tmp.tdt");
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mw.close();
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tmpFiles.add("tmp.tdt");
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assertNotNull(mw);
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}
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@Test
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public void testBasicInstantiation_SmilesWriter() {
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SmilesWriter mw = new SmilesWriter("tmp.smi");
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mw.close();
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tmpFiles.add("tmp.smi");
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assertNotNull(mw);
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}
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@Test
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public void testBasicInstantiation_Transform2D() {
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Transform2D tr = new Transform2D();
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assertNotNull(tr);
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}
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@Test
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public void testBasicInstantiation_Transform3D() {
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Transform3D tr = new Transform3D();
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assertNotNull(tr);
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}
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//Tests for Exception#getMessage() wrapping
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private static final String TEST_MESSAGE = "test message";
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@Test
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public void testChemicalReactionException() {
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final ChemicalReactionException e =
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new ChemicalReactionException(TEST_MESSAGE);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testChemicalReactionParserException() {
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final ChemicalReactionParserException e =
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new ChemicalReactionParserException(TEST_MESSAGE);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testConformerException() {
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ROMol mol = null;
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try {
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mol = RWMol.MolFromSmiles("c1ccccc1");
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mol.getConformer();
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} catch (ConformerException e) {
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assertEquals("No conformations available on the molecule",
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e.getMessage());
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} finally {
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if (mol != null) {
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mol.delete();
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}
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}
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}
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@Test
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public void testMolPicklerException() {
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final MolPicklerException e = new MolPicklerException(TEST_MESSAGE);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testMolSanitizeException() {
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RWMol mol = null;
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try {
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mol = RWMol.MolFromSmiles("c1cccc1");
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mol.sanitizeMol();
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} catch (MolSanitizeException e) {
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assertEquals("Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4",
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e.getMessage());
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} finally {
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if (mol != null) {
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mol.delete();
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}
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}
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}
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@Test
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public void testSmilesParseException() {
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SmilesParseException e = new SmilesParseException(TEST_MESSAGE);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testGenericRDKitException() {
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final GenericRDKitException e =
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new GenericRDKitException(TEST_MESSAGE);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testAtomSanitizeException() {
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final AtomSanitizeException e =
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new AtomSanitizeException(TEST_MESSAGE, 1L);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testAtomValenceException() {
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final AtomValenceException e =
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new AtomValenceException(TEST_MESSAGE, 1L);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testAtomKekulizeException() {
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final AtomKekulizeException e =
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new AtomKekulizeException(TEST_MESSAGE, 1L);
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assertEquals(TEST_MESSAGE, e.getMessage());
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}
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@Test
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public void testKekulizeException() {
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final UInt_Vect uInt_Vect = new UInt_Vect();
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uInt_Vect.add(1L);
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final KekulizeException e =
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new KekulizeException(TEST_MESSAGE, uInt_Vect);
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assertEquals(TEST_MESSAGE, e.getMessage());
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uInt_Vect.delete();
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e.delete();
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}
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@Test
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public void cdxmlReader() {
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String rdpath = System.getenv("RDBASE");
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if (rdpath == null)
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org.junit.Assert.fail("No definition for RDBASE");
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File base = new File(rdpath);
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File testFile = new File(base, "Code" + File.separator + "GraphMol"
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+ File.separator + "test_data" + File.separator +
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"CDXML" + File.separator + "beta-cypermethrin.cdxml");
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String fn = testFile.getAbsolutePath();
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RWMol_Vect prods = RWMol.MolsFromCDXMLFile(fn);
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assertEquals(prods.size(), 1);
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for(int idx = 0; idx < prods.size(); idx++) {
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if(idx == 0) {
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assertEquals(prods.get(idx).MolToSmiles(true), "CC1(C)[C@H](C=C(Cl)Cl)[C@H]1C(=O)O[C@@H](C#N)c1cccc(Oc2ccccc2)c1");
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}
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}
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.WrapperTests");
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}
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}
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