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/*
* $Id: SmilesTests.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.Test;
public class SmilesTests extends GraphMolTest {
private void testSpellings(String smi, String[] spellings) {
ROMol m = RWMol.MolFromSmiles(smi);
String canSmi = m.MolToSmiles();
for (String spelling : spellings) {
m = RWMol.MolFromSmiles(spelling);
assertNotNull("Can't parse " + spelling, m);
String trySmi = m.MolToSmiles();
assertEquals("Non-canonical: mol " + spelling + " gave " + trySmi + "(should be "
+ canSmi + ")", canSmi, trySmi);
m = RWMol.MolFromSmiles(trySmi);
String trySmi2 = m.MolToSmiles();
assertEquals("Non-canonical: mol " + spelling + " gave " + trySmi2 + "(should be "
+ canSmi + ") on second pass", canSmi, trySmi2);
}
}
// testing first batch of linear mols
@Test
public void testLinear1() {
testSpellings("O=CCO", new String[] { "OCC=O", "C(O)C=O", "C(C=O)O", "C(CO)=O" });
testSpellings("OCC(C=C)CCC(C#N)CC", new String[] { "C=CC(CO)CCC(C#N)CC",
"C(CO)(C=C)CCC(CC)C#N", "C(CO)(C=C)CCC(C#N)CC", "C(C=C)(CO)CCC(C#N)CC",
"C(C=C)(CO)CCC(CC)C#N" });
testSpellings("[Se]=CCO", new String[] { "OCC=[Se]", "C(O)C=[Se]", "C(C=[Se])O","C(CO)=[Se]" });
}
// testing first batch of rings
@Test
public void testRings1() {
testSpellings("C1OCCCC1", new String[] { "O1CCCCC1", "C1COCCC1", "C1CCOCC1", "C1CCCOC1","C1CCCCO1"});
testSpellings("CC1=CCCCC1", new String[] { "C1=C(C)CCCC1", "C1CC=C(C)CC1"});
testSpellings("CC1C=CCCC1", new String[] { "C1=CC(C)CCC1", "C1CC=CC(C)C1"});
}
// testing second batch of rings
@Test
public void testRings2() {
testSpellings("c1c(cc2nc3cc(ccc3cc2c1))", new String[] { "c1ccc2cc3ccccc3nc2c1",
"c1ccc2nc3ccccc3cc2c1", "c1c2nc3ccccc3cc2ccc1"});
testSpellings("Cc1ccc2nc3ccccc3cc2c1", new String[] { "c1ccc2nc3ccc(C)cc3cc2c1"});
testSpellings("c1c(C)cc2nc3ccccc3cc2c1", new String[] { "c1ccc2nc3cc(C)ccc3cc2c1"});
}
// testing molecules which have been problematic
@Test
public void testProblems() {
testSpellings("[Al+3]CCC",
new String[] { "CCC[Al+3]", "C(C)(C[Al+3])"});
testSpellings("C(=O)(Cl)CC(=O)Cl",
new String[] { "ClC(CC(Cl)=O)=O", "C(Cl)(=O)CC(=O)Cl","C(Cl)(=O)CC(Cl)=O"});
testSpellings("C(=O)(Cl)c1ccc(C(=O)Cl)cc1",
new String[] { "O=C(Cl)c1ccc(cc1)C(Cl)=O","C(Cl)(=O)C1=CC=C(C=C1)C(Cl)=O", "ClC(=O)c1ccc(cc1)C(=O)Cl"});
testSpellings("[N+](=O)([O-])c1ccc([N+](=O)[O-])cc1",
new String[] { "[N+]([O-])(=O)C1=CC=C(C=C1)[N+](=O)[O-]","O=[N+1]([O-1])c1ccc(cc1)[N+1]([O-1])=O", "[O-1][N+1](=O)c1ccc(cc1)[N+1]([O-1])=O"});
testSpellings("Oc1c3c(cc(c1)S(=O)(=O)O)cc(NC(=O)c2ccccc2)cc3",
new String[] { "C1=C(C2=C(C=C1S(O)(=O)=O)C=C(C=C2)NC(C3=CC=CC=C3)=O)O", "O=S(=O)(O)c1cc(O)c2ccc(NC(=O)c3ccccc3)cc2c1", "OS(=O)(=O)c1cc(O)c2ccc(NC(=O)c3ccccc3)cc2c1"});
testSpellings("C",
new String[] { "C"});
testSpellings("C(Cl)(Br)(F)CC(Cl)(Br)(F)",
new String[] { "C(Cl)(F)(Br)CC(F)(Cl)(Br)","C(Cl)(Br)(F)CC(Cl)(F)(Br)", "C(F)(Br)(Cl)CC(Br)(Cl)(F)","C(C(Cl)(Br)(F))C(F)(Cl)Br"});
}
// testing tricky (high-symmetry) molecules
@Test
public void testHighSymmetry() {
testSpellings("CC(C)CC", new String[] { "CCC(C)C"});
testSpellings("C1CCCC1CCC", new String[] { "CCCC1CCCC1"});
testSpellings("C1(C)CC(C)CCC1", new String[] { "CC1CCCC(C)C1"});
testSpellings("CCC1CCCCC1CC", new String[] { "CCC1CCCCC1CC"});
testSpellings("CCC1CC(CC)CCC1", new String[] { "CCC1CCCC(CC)C1"});
testSpellings("C1CCCCC1CC(CC)CC", new String[] { "CCC(CC)CC1CCCCC1"});
testSpellings("C1CCCC2C1CC(CC)CC2", new String[] { "CCC1CCC2CCCCC2C1"});
testSpellings("CC1CCCC2C1C(C)CCC2", new String[] { "CC1CCCC2CCCC(C)C12"});
testSpellings("C2CCC1CCC(C)C12", new String[] { "CC1CCC2CCCC12"});
testSpellings("CC(C)CCCC(C)C", new String[] { "CC(CCCC(C)C)C"});
}
// EXPECT FAILURES -> testing molecules which are known to fail
@Test
public void testFailures() {
testSpellings("C13C6C1C2C4C2C3C5C4C56",
new String[] { "C45C1C6C3C6C5C4C2C3C12","C45C2C6C3C6C5C4C1C3C12"});
}
@Test
public void testReplacements() {
String_String_Map repls=new String_String_Map();
repls.set("{X}","OC1CC1");
RWMol nmol = RWMol.MolFromSmiles("c1ccccc1{X}",0,true,repls);
String nsmi = RDKFuncs.MolToSmiles(nmol, true);
String expected="c1ccc(OC2CC2)cc1";
assertEquals("bad smiles: "+nsmi+"!="+expected,nsmi,expected);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.SmilesTests");
}
}
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