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High-level tests verifying the smarts queries matches stereo correctly.
Signed-off-by: Stephan Beisken <sbeisken@gmail.com> Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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src/test/org/openscience/cdk/smiles/smarts/parser/SmartsStereoTest.java
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| /* | ||
| * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI) | ||
| * John May <jwmay@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * This program is free software; you can redistribute it and/or modify it | ||
| * under the terms of the GNU Lesser General Public License as published by | ||
| * the Free Software Foundation; either version 2.1 of the License, or (at | ||
| * your option) any later version. All we ask is that proper credit is given | ||
| * for our work, which includes - but is not limited to - adding the above | ||
| * copyright notice to the beginning of your source code files, and to any | ||
| * copyright notice that you may distribute with programs based on this work. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | ||
| * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public | ||
| * License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public License | ||
| * along with this program; if not, write to the Free Software | ||
| * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U | ||
| */ | ||
|
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| package org.openscience.cdk.smiles.smarts.parser; | ||
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| import org.junit.Test; | ||
| import org.openscience.cdk.DefaultChemObjectBuilder; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.silent.SilentChemObjectBuilder; | ||
| import org.openscience.cdk.smiles.SmilesParser; | ||
| import org.openscience.cdk.smiles.smarts.SMARTSQueryTool; | ||
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| import static org.hamcrest.CoreMatchers.is; | ||
| import static org.hamcrest.MatcherAssert.assertThat; | ||
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| /** | ||
| * Verifies stereo matching. We check the counts to ensure that | ||
| * tetrahedral/geometric stereo isn't matching absolute values (i.e. R/S or | ||
| * odd/even // parity from MDL molfile) | ||
| * | ||
| * @author John May | ||
| * @cdk.module test-smarts | ||
| */ | ||
| public class SmartsStereoTest { | ||
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| @Test public void nonAbsoluteGeometric_trans() throws Exception { | ||
| assertMatch("C/C=C/C", "C/C(CC)=C(CC)/C", 4, 2); | ||
| } | ||
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| @Test public void nonAbsoluteGeometric_cis() throws Exception { | ||
| assertMatch("C(/C)=C/C", "C/C(CC)=C(CC)/C", 4, 2); | ||
| } | ||
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| @Test public void unspecifiedGeometric() throws Exception { | ||
| assertMatch("C/C=C/?Cl", "CC=CCl", 1, 1); | ||
| assertMatch("C/C=C/?Cl", "C/C=C/Cl", 1, 1); | ||
| assertMatch("C/?C=C/Cl", "CC=CCl", 1, 1); | ||
| assertMatch("C/?C=C/Cl", "C/C=C/Cl", 1, 1); | ||
| assertMatch("C/C=C/?Cl", "CC=CCl", 1, 1); | ||
| assertMatch("C/C=C/?Cl", "C/C=C/Cl", 1, 1); | ||
| } | ||
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| @Test public void nonAbsoluteTetrahedral() throws Exception { | ||
| assertMatch("C[C@](C)(C)C", "C[C@](CC)(CCC)CCCC", 12, 1); | ||
| assertMatch("C[C@](C)(C)C", "C[C@@](CC)(CCC)CCCC", 12, 1); | ||
| } | ||
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| @Test public void tetrahedralNegation_anticlockwise() throws Exception { | ||
| assertMatch("[!@](C)(N)(O)CC", "C(C)(N)(O)CC", 1, 1); | ||
| assertMatch("[!@](C)(N)(O)CC", "[C@@](C)(N)(O)CC", 1, 1); | ||
| assertMatch("[!@](C)(N)(O)CC", "[C@](C)(N)(O)CC", 0, 0); | ||
| } | ||
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| @Test public void tetrahedralNegation_clockwise() throws Exception { | ||
| assertMatch("[!@@](C)(N)(O)CC", "C(C)(N)(O)CC", 1, 1); | ||
| assertMatch("[!@@](C)(N)(O)CC", "[C@@](C)(N)(O)CC", 0, 0); | ||
| assertMatch("[!@@](C)(N)(O)CC", "[C@](C)(N)(O)CC", 1, 1); | ||
| } | ||
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| @Test public void tetrahedralUnspecified_clockwise() throws Exception { | ||
| assertMatch("[@@?](C)(N)(O)CC", "C(C)(N)(O)CC", 1, 1); | ||
| assertMatch("[@@?](C)(N)(O)CC", "[C@@](C)(N)(O)CC", 1, 1); | ||
| assertMatch("[@@?](C)(N)(O)CC", "[C@](C)(N)(O)CC", 0, 0); | ||
| } | ||
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| @Test public void tetrahedralUnspecified_anticlockwise() throws Exception { | ||
| assertMatch("[@?](C)(N)(O)CC", "C(C)(N)(O)CC", 1, 1); | ||
| assertMatch("[@?](C)(N)(O)CC", "[C@@](C)(N)(O)CC", 0, 0); | ||
| assertMatch("[@?](C)(N)(O)CC", "[C@](C)(N)(O)CC", 1, 1); | ||
| } | ||
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| @Test public void tetrahedral_or() throws Exception { | ||
| assertMatch("C[@,@@](C)(C)C", "CC(CC)(CCC)CCCC", 0, 0); | ||
| assertMatch("C[@,@@](C)(C)C", "C[C@](CC)(CCC)CCCC", 24, 1); | ||
| assertMatch("C[@,@@](C)(C)C", "C[C@](CC)(CCC)CCCC", 24, 1); | ||
| } | ||
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| @Test public void tetrahedral_and() throws Exception { | ||
| assertMatch("C[@&@@](C)(C)C", "CC(CC)(CCC)CCCC", 0, 0); | ||
| assertMatch("C[@&@@](C)(C)C", "C[C@](CC)(CCC)CCCC", 0, 0); | ||
| assertMatch("C[@&@@](C)(C)C", "C[C@@](CC)(CCC)CCCC", 0, 0); | ||
| } | ||
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| @Test public void tetrahedralAndSymbol_or() throws Exception { | ||
| assertMatch("C[C@,Si@@](CC)(CCC)CCCC", "CC(CC)(CCC)CCCCC", 0, 0); | ||
| assertMatch("C[C@,Si@@](CC)(CCC)CCCC", "C[Si](CC)(CCC)CCCCC", 0, 0); | ||
| assertMatch("C[C@,Si@@](CC)(CCC)CCCC", "C[C@](CC)(CCC)CCCC", 1, 1); | ||
| assertMatch("C[C@,Si@@](CC)(CCC)CCCC", "C[C@@](CC)(CCC)CCCC", 0, 0); | ||
| assertMatch("C[C@,Si@@](CC)(CCC)CCCC", "C[Si@](CC)(CCC)CCCC", 0, 0); | ||
| assertMatch("C[C@,Si@@](CC)(CCC)CCCC", "C[Si@@](CC)(CCC)CCCC", 1, 1); | ||
| } | ||
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| @Test public void recursiveGeometric_trans() throws Exception { | ||
| assertMatch("[$(*/C=C/*)]", "C/C=C/C", 2, 2); | ||
| assertMatch("[$(*/C=C/*)]", "F/C=C/Cl", 2, 2); | ||
| assertMatch("[$(*/C=C/*)]", "CC=CC", 0, 0); | ||
| assertMatch("[$(*/C=C/*)]", "FC=CCl", 0, 0); | ||
| assertMatch("[$(*/C=C/*)]", "C/C=C\\C", 0, 0); | ||
| assertMatch("[$(*/C=C/*)]", "F/C=C\\Cl", 0, 0); | ||
| } | ||
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| @Test public void recursiveGeometric_cis() throws Exception { | ||
| assertMatch("[$(C(/*)=C/*)]", "C/C=C/C", 0, 0); | ||
| assertMatch("[$(C(/*)=C/*)]", "F/C=C/Cl", 0, 0); | ||
| assertMatch("[$(C(/*)=C/*)]", "CC=CC", 0, 0); | ||
| assertMatch("[$(C(/*)=C/*)]", "FC=CCl", 0, 0); | ||
| assertMatch("[$(C(/*)=C/*)]", "C/C=C\\C", 2, 2); | ||
| assertMatch("[$(C(/*)=C/*)]", "F/C=C\\Cl", 2, 2); | ||
| } | ||
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| @Test public void recursiveTetrahedral() throws Exception { | ||
| assertMatch("[$([C@](C)(CC)(N)O)]", "C[C@@](N)(CC)O", 1, 1); | ||
| assertMatch("[$([C@](C)(CC)(N)O)]", "C[C@](N)(CC)O", 0, 0); | ||
| assertMatch("[$([C@](C)(CC)(N)O)]", "CC(N)(CC)O", 0, 0); | ||
| } | ||
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| @Test public void tetrahedralImplicitH() throws Exception { | ||
| assertMatch("[C@H](C)(N)O", "[C@@H](N)(C)O", 1, 1); | ||
| assertMatch("[C@H](C)(N)O", "[C@H](N)(C)O", 0, 0); | ||
| assertMatch("[C@H](C)(N)O", "C(N)(C)O", 0, 0); | ||
| } | ||
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| @Test public void tetrahedralImplicitH_unspec() throws Exception { | ||
| assertMatch("[C@?H](C)(N)O", "[C@@H](N)(C)O", 1, 1); | ||
| assertMatch("[C@?H](C)(N)O", "[C@H](N)(C)O", 0, 0); | ||
| assertMatch("[C@?H](C)(N)O", "C(N)(C)O", 1, 1); | ||
| } | ||
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| static void assertMatch(SMARTSQueryTool sqt, IAtomContainer m, int hits, int usaHits) throws Exception { | ||
| sqt.matches(m); | ||
| assertThat(sqt.getMatchingAtoms().size(), is(hits)); | ||
| assertThat(sqt.getUniqueMatchingAtoms().size(), is(usaHits)); | ||
| } | ||
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| static void assertMatch(String smarts, String smiles, int hits, int usaHits) throws Exception { | ||
| assertMatch(smarts(smarts), smiles(smiles), hits, usaHits); | ||
| } | ||
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| static IAtomContainer smiles(String smiles) throws Exception { | ||
| return sp.parseSmiles(smiles); | ||
| } | ||
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| static SMARTSQueryTool smarts(String smarts) { | ||
| return new SMARTSQueryTool(smarts, DefaultChemObjectBuilder.getInstance()); | ||
| } | ||
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| private static final SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance()); | ||
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| } |