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/*
*
* Copyright (c) 2019 Greg Landrum and T5 Informatics GmbH
* All rights reserved.
*
* This file is part of the RDKit.
* The contents are covered by the terms of the BSD license
* which is included in the file license.txt, found at the root
* of the RDKit source tree.
*/
package org.RDKit;
import static org.junit.Assert.*;
import org.junit.*;
public class AbbreviationsTests extends GraphMolTest {
@Before public void setUp() {
}
@Test
public void test1Basics() {
AbbreviationDefinition_Vect abbrevs = RDKFuncs.getDefaultAbbreviations();
RWMol mol = RWMol.MolFromSmiles("C1CCC1C(F)(F)F");
assertEquals(mol.getNumAtoms(),8);
RDKFuncs.condenseMolAbbreviations(mol,abbrevs);
// no changes here due to the threshold
assertEquals(mol.getNumAtoms(),8);
RDKFuncs.condenseMolAbbreviations(mol,abbrevs, 1.0);
assertEquals(mol.getNumAtoms(),5);
assertEquals(RDKFuncs.MolToCXSmiles(mol),"*C1CCC1 |$CF3;;;;$|");
}
@Test
public void test2LinkerBasics() {
AbbreviationDefinition_Vect abbrevs = RDKFuncs.getDefaultLinkers();
RWMol mol = RWMol.MolFromSmiles("COCCOCCOCCOCCCl");
assertEquals(mol.getNumAtoms(),14);
RDKFuncs.condenseMolAbbreviations(mol,abbrevs);
// no changes here due to the threshold
assertEquals(mol.getNumAtoms(),14);
RDKFuncs.condenseMolAbbreviations(mol,abbrevs, 1.0);
assertEquals(mol.getNumAtoms(),3);
assertEquals(RDKFuncs.MolToCXSmiles(mol),"C*Cl |$;PEG4;$|");
}
@Test
public void test3Matching() {
AbbreviationDefinition_Vect abbrevs = RDKFuncs.getDefaultAbbreviations();
RWMol mol = RWMol.MolFromSmiles("C1CCC1C(F)(F)F");
assertEquals(mol.getNumAtoms(),8);
AbbreviationMatch_Vect matches = RDKFuncs.findApplicableAbbreviationMatches(mol,abbrevs,1.0);
assertEquals(matches.size(),1);
assertEquals(matches.get(0).getAbbrev().getLabel(),"CF3");
RDKFuncs.applyMatches(mol,matches);
assertEquals(mol.getNumAtoms(),5);
assertEquals(RDKFuncs.MolToCXSmiles(mol),"*C1CCC1 |$CF3;;;;$|");
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.AbbreviationsTests");
}
}
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