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|
/*
* $Id: ChemReactionTests.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 java.io.*;
import java.util.ArrayList;
import org.junit.*;
public class ChemReactionTests extends GraphMolTest {
private ArrayList<String> tmpFiles = new ArrayList<String>();
private File baseTestPath;
@Before
public void setUp() {
File base = getRdBase();
baseTestPath = new File(base, "Code" + File.separator + "GraphMol" + File.separator +
"ChemReactions" + File.separator + "testData");
}
@After
public void tearDown() throws Exception {
for (String fn : tmpFiles) {
new File(fn).delete();
}
}
@Test
public void test1Basics() {
ChemicalReaction rxn = new ChemicalReaction();
assertEquals( 0,rxn.getNumReactantTemplates() );
assertEquals( 0,rxn.getNumProductTemplates() );
ROMol r1 = RWMol.MolFromSmarts("[C:1](=[O:2])O");
rxn.addReactantTemplate(r1);
assertEquals( 1,rxn.getNumReactantTemplates() );
r1 = RWMol.MolFromSmarts("[N;!$(N-C=O):3]");
rxn.addReactantTemplate(r1);
assertEquals( 2,rxn.getNumReactantTemplates() );
r1 = RWMol.MolFromSmarts("[C:1](=[O:2])[N:3]");
rxn.addProductTemplate(r1);
assertEquals( 1,rxn.getNumProductTemplates() );
ROMol_Vect reacts = new ROMol_Vect();
for (String react : new String[] {"C(=O)O","N"})
reacts.add(RWMol.MolFromSmiles(react));
// Need this init call since the reaction has been built
// "manually"
rxn.initReactantMatchers();
ROMol_Vect_Vect prods = rxn.runReactants(reacts);;
assertEquals( 1,prods.size() );
assertEquals( 1,prods.get(0).size() );
assertEquals( 3,prods.get(0).get(0).getNumAtoms() );
assertEquals( true, RDKFuncs.isMoleculeReactantOfReaction(rxn,reacts.get(0)) );
assertEquals( false, RDKFuncs.isMoleculeReactantOfReaction(rxn,prods.get(0).get(0)) );
assertEquals( true, RDKFuncs.isMoleculeProductOfReaction(rxn,prods.get(0).get(0)) );
assertEquals( false, RDKFuncs.isMoleculeProductOfReaction(rxn,reacts.get(0)) );
}
@Test
public void test2DaylightParser() {
ChemicalReaction rxn =
ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn );;
assertEquals( 2,rxn.getNumReactantTemplates() );
assertEquals( 1,rxn.getNumProductTemplates() );
assertTrue(rxn.getImplicitPropertiesFlag());
ROMol_Vect reacts = new ROMol_Vect();
for (String react : new String[] {"C(=O)O","N"})
reacts.add(RWMol.MolFromSmiles(react));
// Do not need the initReactantMatchers call here
ROMol_Vect_Vect prods = rxn.runReactants(reacts);;
assertEquals( 1,prods.size() );
assertEquals( 1,prods.get(0).size() );
assertEquals( 3,prods.get(0).get(0).getNumAtoms() );
reacts.clear();
for (String react : new String[] {"CC(=O)OC","CN"})
reacts.add(RWMol.MolFromSmiles(react));
// Do not need the initReactantMatchers call here
prods = rxn.runReactants(reacts);;
assertEquals( 1,prods.size() );
assertEquals( 1,prods.get(0).size() );
assertEquals( 5,prods.get(0).get(0).getNumAtoms() );
}
@Test
public void test3MDLParsers() throws Exception {
File rxnFile = new File(baseTestPath, "AmideBond.rxn");
String fileN = rxnFile.getPath();
ChemicalReaction rxn = ChemicalReaction.ReactionFromRxnFile(fileN);
assertNotNull(rxn );;
assertEquals( 2,rxn.getNumReactantTemplates() );
assertEquals( 1,rxn.getNumProductTemplates() );
assertFalse(rxn.getImplicitPropertiesFlag());
ROMol_Vect reacts = new ROMol_Vect();
for (String react : new String[] {"C(=O)O","N"})
reacts.add(RWMol.MolFromSmiles(react));
// Do not need the initReactantMatchers call here
ROMol_Vect_Vect prods = rxn.runReactants(reacts);;
assertEquals( 1,prods.size() );
assertEquals( 1,prods.get(0).size() );
assertEquals( 3,prods.get(0).get(0).getNumAtoms() );
String rxnBlock = "";
BufferedReader f = new BufferedReader(new FileReader(rxnFile));
String line;
try{
while ((line = f.readLine()) != null)
rxnBlock += line + "\n"; // ok only for small numbers of lines
} finally {
f.close();
}
rxn = ChemicalReaction.ReactionFromRxnBlock(rxnBlock);
assertNotNull(rxn );;
assertEquals( 2,rxn.getNumReactantTemplates() );
assertEquals( 1,rxn.getNumProductTemplates() );
reacts.clear();
for (String react : new String[] {"C(=O)O","N"})
reacts.add(RWMol.MolFromSmiles(react));
// Do not need the initReactantMatchers call here
prods = rxn.runReactants(reacts);;
assertEquals( 1,prods.size() );
assertEquals( 1,prods.get(0).size() );
assertEquals( 3,prods.get(0).get(0).getNumAtoms() );
}
@Test (expected=ChemicalReactionParserException.class)
public void test4ErrorHandling_1() {
ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])Q.[N:3]>>[C:1](=[O:2])[N:3]");
}
@Test (expected=ChemicalReactionParserException.class)
public void test4ErrorHandling_2() {
ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]Q");
}
@Test (expected=ChemicalReactionParserException.class)
public void test4ErrorHandling_3() {
ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]>>CC");
}
@Test (expected=ChemicalReactionParserException.class)
public void test4ErrorHandling_4() {
String rxnBlock =
"$RXN" + "\n" +
"" + "\n" +
" ISIS 082120061354" + "\n" +
"" + "\n" +
" 3 1" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 3 2 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0" + "\n" +
" -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0" + "\n" +
" -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0" + "\n" +
" 1 2 1 0 0 0 0" + "\n" +
" 1 3 2 0 0 0 0" + "\n" +
"M END" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 1 0 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0" + "\n" +
"M END" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 3 2 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0" + "\n" +
" 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0" + "\n" +
" 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0" + "\n" +
" 1 2 1 0 0 0 0" + "\n" +
" 2 3 2 0 0 0 0" + "\n" +
"M END";
ChemicalReaction.ReactionFromRxnBlock(rxnBlock);
}
@Test (expected=ChemicalReactionParserException.class)
public void test4ErrorHandling_5() {
String rxnBlock =
"$RXN" + "\n" +
"" + "\n" +
" ISIS 082120061354" + "\n" +
"" + "\n" +
" 2 1" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 4 2 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0" + "\n" +
" -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0" + "\n" +
" -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0" + "\n" +
" 1 2 1 0 0 0 0" + "\n" +
" 1 3 2 0 0 0 0" + "\n" +
"M END" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 1 0 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0" + "\n" +
"M END" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 3 2 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0" + "\n" +
" 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0" + "\n" +
" 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0" + "\n" +
" 1 2 1 0 0 0 0" + "\n" +
" 2 3 2 0 0 0 0" + "\n" +
"M END" + "\n" ;
ChemicalReaction.ReactionFromRxnBlock(rxnBlock);
}
@Test (expected=ChemicalReactionParserException.class)
public void test4ErrorHandling_6() {
String rxnBlock =
"$RXN" + "\n" +
"" + "\n" +
" ISIS 082120061354" + "\n" +
"" + "\n" +
" 2 1" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 3 2 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0" + "\n" +
" -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0" + "\n" +
" -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0" + "\n" +
" 1 2 1 0 0 0 0" + "\n" +
" 1 3 2 0 0 0 0" + "\n" +
"M END" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 1 0 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0" + "\n" +
"M END" + "\n" +
"$MOL" + "\n" +
"" + "\n" +
" -ISIS- 08210613542D" + "\n" +
"" + "\n" +
" 3 1 0 0 0 0 0 0 0 0999 V2000" + "\n" +
" 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0" + "\n" +
" 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0" + "\n" +
" 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0" + "\n" +
" 1 2 1 0 0 0 0" + "\n" +
" 2 3 2 0 0 0 0" + "\n" +
"M END" + "\n";
ChemicalReaction.ReactionFromRxnBlock(rxnBlock);
}
@Test
public void test5Validation() {
ChemicalReaction rxn = ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn);
Int_Pair validationResults = rxn.validateReaction();
assertEquals(0, validationResults.getFirst());
assertEquals(0, validationResults.getSecond());
rxn = ChemicalReaction.ReactionFromSmarts("[C:1](=[O:1])O.[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn);
validationResults = rxn.validateReaction();
assertEquals(1, validationResults.getFirst());
assertEquals(1, validationResults.getSecond());
rxn = ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])[O:4].[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn);
}
@Test (expected=ChemicalReactionException.class)
public void test6Exceptions_1() {
ChemicalReaction rxn = ChemicalReaction.ReactionFromSmarts("[C:1]Cl>>[C:1]");
assertNotNull(rxn);
rxn.runReactants(new ROMol_Vect());
}
@Test (expected=ChemicalReactionException.class)
public void test6Exceptions_2() {
ChemicalReaction rxn = ChemicalReaction.ReactionFromSmarts("[C:1]Cl>>[C:1]");
assertNotNull(rxn);
ROMol_Vect reactants = new ROMol_Vect();
reactants.add(RWMol.MolFromSmiles("CC"));
reactants.add(RWMol.MolFromSmiles("C"));
rxn.runReactants(reactants);
}
@Test
public void test6Exceptions_3() {
ChemicalReaction rxn = ChemicalReaction.ReactionFromSmarts("[C:1]Cl>>[C:1]");
assertNotNull(rxn);
ROMol_Vect reactants = new ROMol_Vect();
reactants.add(RWMol.MolFromSmiles("CCCl"));
ROMol_Vect_Vect products = rxn.runReactants(reactants);
assertEquals( 1,products.size() );
assertEquals( 1,products.get(0).size() );
}
@Test
public void test8Properties() {
ChemicalReaction rxn = ChemicalReaction.ReactionFromSmarts("[O:1]>>[O:1][3#0]");
assertNotNull(rxn );;
ROMol_Vect reactants = new ROMol_Vect();
reactants.add(RWMol.MolFromSmiles("CO"));
ROMol_Vect_Vect ps = rxn.runReactants(reactants);
assertEquals( 1,ps.size() );
assertEquals( 1,ps.get(0).size() );
// Can sanitize only RWMol objects
RWMol p00 = new RWMol(ps.get(0).get(0));
RDKFuncs.sanitizeMol(p00);
assertEquals( 3,p00.getAtomWithIdx(1).getIsotope());
}
@Test
public void test9AromaticityTransfer () {
ROMol mol = RWMol.MolFromSmiles("c1ccc(C2C3(Cc4c(cccc4)C2)CCCC3)cc1");
ChemicalReaction rxn =
ChemicalReaction.ReactionFromSmarts("[A:1]1~[*:2]~[*:3]~[*:4]~[*:5]~[A:6]-;@1>>[*:1]~[*:2]~[*:3]~[*:4]~[*:5]~[*:6]");
ROMol_Vect reactants = new ROMol_Vect();
reactants.add(mol);
ROMol_Vect_Vect products = rxn.runReactants(reactants);
assertEquals( 6,products.size() );
for (int prodSet = 0; prodSet < products.size(); prodSet++) {
assertEquals( 1,products.get(prodSet).size() );
RWMol prod = new RWMol(products.get(prodSet).get(0));
prod.sanitizeMol();
}
}
@Test
public void test10DotSeparation() {
ROMol mol = RWMol.MolFromSmiles("C1ON1");
ChemicalReaction rxn =
ChemicalReaction.ReactionFromSmarts("[C:1]1[O:2][N:3]1>>([C:1]1[O:2].[N:3]1)");
ROMol_Vect reactants = new ROMol_Vect();
reactants.add(mol);
ROMol_Vect_Vect products = rxn.runReactants(reactants);
assertEquals( 1,products.size() );
for (int prodSet = 0; prodSet < products.size(); prodSet++) {
assertEquals( 1,products.get(prodSet).size() );
assertEquals( 3,products.get(prodSet).get(0).getNumAtoms() );
assertEquals( 2,products.get(prodSet).get(0).getNumBonds() );
}
}
@Test
public void test11ImplicitProperties() {
ROMol mol = RWMol.MolFromSmiles("CCO");
ROMol mol2 = RWMol.MolFromSmiles("C[CH-]O");
ChemicalReaction rxn =
ChemicalReaction.ReactionFromSmarts("[C:1]O>>[C:1]");
ROMol_Vect reactants = new ROMol_Vect();
reactants.add(mol);
ROMol_Vect_Vect products = rxn.runReactants(reactants);
assertEquals( 1,products.size() );
for (int prodSet = 0; prodSet < products.size(); prodSet++) {
assertEquals( 1,products.get(prodSet).size() );
assertEquals("CC",products.get(prodSet).get(0).MolToSmiles());
}
reactants.clear();
reactants.add(mol2);
products = rxn.runReactants(reactants);
assertEquals( 1,products.size() );
for (int prodSet = 0; prodSet < products.size(); prodSet++) {
assertEquals( 1,products.get(prodSet).size() );
assertEquals("[CH2-]C",products.get(prodSet).get(0).MolToSmiles());
}
rxn.setImplicitPropertiesFlag(false);
products = rxn.runReactants(reactants);
assertEquals( 1,products.size() );
for (int prodSet = 0; prodSet < products.size(); prodSet++) {
assertEquals( 1,products.get(prodSet).size() );
assertEquals("CC",products.get(prodSet).get(0).MolToSmiles());
}
reactants.clear();
reactants.add(mol2);
products = rxn.runReactants(reactants);
assertEquals( 1,products.size() );
for (int prodSet = 0; prodSet < products.size(); prodSet++) {
assertEquals( 1,products.get(prodSet).size() );
assertEquals("CC",products.get(prodSet).get(0).MolToSmiles());
}
}
// @Test
public void test99MemoryLeak() {
ChemicalReaction rxn =
ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn );;
assertEquals( 2,rxn.getNumReactantTemplates() );
assertEquals( 1,rxn.getNumProductTemplates() );
assertTrue(rxn.getImplicitPropertiesFlag());
ROMol_Vect reacts = new ROMol_Vect();
for (String react : new String[] {"C(=O)O","N"})
reacts.add(RWMol.MolFromSmiles(react));
// Do not need the initReactantMatchers call here
for(Integer i=0;i<1000000;i++){
ROMol_Vect_Vect prods = rxn.runReactants(reacts);;
assertEquals( 1,prods.size() );
assertEquals( 1,prods.get(0).size() );
assertEquals( 3,prods.get(0).get(0).getNumAtoms() );
//prods.get(0).get(0).delete();
//prods.get(0).delete();
//prods.delete();
}
}
@Test
public void test100RunSingleReactant() {
ChemicalReaction rxn =
ChemicalReaction.ReactionFromSmarts("[N;$(N-[#6]):3]=[C;$(C=S):1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);!$([ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[N:3]-[C:1]-[N+0:2]");
ROMol reag1 = RWMol.MolFromSmiles("C=CCN=C=S");
ROMol reag2 = RWMol.MolFromSmiles("NCc1ncc(Cl)cc1Br");
ROMol_Vect_Vect prods0 = rxn.runReactant(reag1, 0);
ROMol expected_result0 = RWMol.MolFromSmiles("C=CCNC(N)=S");
ROMol expected_sidechain0 = RWMol.MolFromSmiles("[1*:1]=S.[3*:3]CC=C");
assertEquals( 1, prods0.size() );
assertEquals( 1, prods0.get(0).size() );
assertEquals( 1, prods0.size() );
assertEquals( 1, prods0.get(0).size() );
assertEquals( expected_result0.MolToSmiles(), prods0.get(0).get(0).MolToSmiles() );
assertEquals( expected_sidechain0.MolToSmiles(),
ChemicalReaction.ReduceProductToSideChains(prods0.get(0).get(0)).MolToSmiles());
ROMol_Vect_Vect prods1 = rxn.runReactant(reag2, 1);
ROMol expected_result1 = RWMol.MolFromSmiles("NCNCc1ncc(Cl)cc1Br");
ROMol expected_sidechain1 = RWMol.MolFromSmiles("[2*:2]Cc1ncc(Cl)cc1Br");
ROMol expected_sidechain1_nodummies = RWMol.MolFromSmiles("Cc1ncc(Cl)cc1Br");
assertEquals( 1, prods1.size() );
assertEquals( 1, prods1.get(0).size() );
assertEquals( 1, prods1.size() );
assertEquals( 1, prods1.get(0).size() );
assertEquals( expected_result1.MolToSmiles(), prods1.get(0).get(0).MolToSmiles() );
assertEquals( expected_sidechain1.MolToSmiles(),
ChemicalReaction.ReduceProductToSideChains(prods1.get(0).get(0)).MolToSmiles());
assertEquals( expected_sidechain1_nodummies.MolToSmiles(),
ChemicalReaction.ReduceProductToSideChains(
prods1.get(0).get(0),false).MolToSmiles());
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.ChemReactionTests");
}
}
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