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710bdfa60b
* Added AtomComparator.AtomCompareAnyHeavyAtom and test cases to FMCS code * Added AtomComparator.AtomCompareAnyHeavyAtom * Added AtomComparator.AtomCompareAnyHeavyAtom - fixed test typo * Added AtomComparator.AtomCompareAnyHeavyAtom and test cases to FMCS code (2) * Added AtomComparator.AtomCompareAnyHeavyAtom - fixed test cases * Added AtomComparator.AtomCompareAnyHeavyAtom and test cases * Update Code/GraphMol/FMCS/FMCS.cpp Co-Authored-By: Greg Landrum <greg.landrum@gmail.com> * Reverted tabs to 4 spaces * Update FMCS.cpp
126 lines
5.2 KiB
Java
126 lines
5.2 KiB
Java
/*
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*
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* Copyright (c) 2014, 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 org.junit.*;
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public class FMCSTests extends GraphMolTest {
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private ROMol m;
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@Before public void setUp() {
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}
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@Test
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public void test1Basics() {
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ROMol_Vect mols = new ROMol_Vect();
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mols.add(RWMol.MolFromSmiles("c1ccccc1OC"));
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mols.add(RWMol.MolFromSmiles("c1ccccc1C"));
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mols.add(RWMol.MolFromSmiles("c1c(C)cccc1OC"));
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MCSResult mcs=RDKFuncs.findMCS(mols);
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assertEquals(6,mcs.getNumAtoms());
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assertEquals(6,mcs.getNumBonds());
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assertEquals("[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1",mcs.getSmartsString());
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assertEquals(false,mcs.getCanceled());
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}
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@Test
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public void test2Basics() {
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ROMol_Vect mols = new ROMol_Vect();
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mols.add(RWMol.MolFromSmiles("c1ccccc1OC"));
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mols.add(RWMol.MolFromSmiles("c1ccccc1C"));
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mols.add(RWMol.MolFromSmiles("c1c(C)cccc1OC"));
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mols.add(RWMol.MolFromSmiles("C1CCCCC1C"));
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MCSResult mcs=RDKFuncs.findMCS(mols,true,1,60,false,false,false,false,false,
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AtomComparator.AtomCompareElements,
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BondComparator.BondCompareAny);
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assertEquals(6,mcs.getNumAtoms());
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assertEquals(6,mcs.getNumBonds());
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assertEquals("[#6]1:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-1",mcs.getSmartsString());
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assertEquals(false,mcs.getCanceled());
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}
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@Test
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public void test3Chirality() {
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ROMol_Vect mols = new ROMol_Vect();
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mols.add(RWMol.MolFromSmiles("C[C@H](F)CCl"));
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mols.add(RWMol.MolFromSmiles("C[C@H](F)C"));
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MCSResult mcs=RDKFuncs.findMCS_P(mols,"{\"MatchChiralTag\":true}");
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assertEquals(4,mcs.getNumAtoms());
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assertEquals(3,mcs.getNumBonds());
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//assertEquals("[#6]1:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-1",mcs.getSmartsString());
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assertEquals(false,mcs.getCanceled());
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}
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@Test
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public void testAtomCompareAnyHeavyAtom() {
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ROMol_Vect mols = new ROMol_Vect();
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mols.add(RWMol.MolFromSmiles("[H]c1ccccc1C",0, false));
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mols.add(RWMol.MolFromSmiles("[H]c1ccccc1O",0, false));
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// H matches H, O matches C
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MCSResult mcs=RDKFuncs.findMCS(mols,true,1,60,false,false,false,false,false,
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AtomComparator.AtomCompareAnyHeavyAtom,
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BondComparator.BondCompareAny);
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assertEquals(8,mcs.getNumAtoms());
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assertEquals(8,mcs.getNumBonds());
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//assertEquals("[#6]1:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-1",mcs.getSmartsString());
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assertEquals(false,mcs.getCanceled());
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}
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@Test
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public void testAtomCompareAnyHeavyAtom1() {
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ROMol_Vect mols = new ROMol_Vect();
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mols.add(RWMol.MolFromSmiles("[H]c1ccccc1C",0, false));
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mols.add(RWMol.MolFromSmiles("Oc1ccccc1O",0, false));
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// O matches C, H does not match O
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MCSResult mcs=RDKFuncs.findMCS(mols,true,1,60,false,false,false,false,false,
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AtomComparator.AtomCompareAnyHeavyAtom,
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BondComparator.BondCompareAny);
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assertEquals(7,mcs.getNumAtoms());
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assertEquals(7,mcs.getNumBonds());
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//assertEquals("[#6]1:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-1",mcs.getSmartsString());
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assertEquals(false,mcs.getCanceled());
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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.FMCSTests");
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}
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}
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