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//
// Created by Gareth Jones on 9/4/2020.
//
// Copyright 2020 Schrodinger, Inc
// @@ 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 org.junit.Test;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
public class SubstanceGroupTests extends GraphMolTest {
private RWMol getMol(String file) {
file = getRdBase() + "/Code/GraphMol/test_data/"+file;
try {
String block = new String(Files.readAllBytes(Paths.get(file)));
return RDKFuncs.MolBlockToMol(block);
} catch (IOException ex) {
throw new RuntimeException("IO Exception reading " + file, ex);
}
}
@Test
public void supGroupTest() {
RWMol mol = getMol("sgroups_and_marvin_metal.mol");
assertNotNull(mol);
long sgroupCount = RDKFuncs.getSubstanceGroupCount(mol);
assertEquals(1, sgroupCount);
SubstanceGroup supGroup = RDKFuncs.getSubstanceGroupWithIdx(mol, 0);
assertTrue(supGroup.hasProp("TYPE"));
assertTrue(supGroup.hasProp("index"));
assertTrue(supGroup.hasProp("LABEL"));
assertTrue(supGroup.hasProp("DATAFIELDS"));
assertEquals("SUP", supGroup.getStringProp("TYPE"));
assertEquals(1, supGroup.getUIntProp("index"));
assertEquals("M", supGroup.getStringProp("LABEL"));
assertEquals(0, supGroup.getStringVectProp("DATAFIELDS").size());
assertEquals(1, supGroup.getAtoms().size());
assertEquals(0, supGroup.getBonds().size());
assertEquals(1, supGroup.getAtoms().get(0));
}
@Test
public void polymerTest() {
RWMol mol = getMol("sgroups_copolymer2.mol");
assertNotNull(mol);
long sgroupCount = RDKFuncs.getSubstanceGroupCount(mol);
assertEquals(3, sgroupCount);
assertEquals(9, mol.getNumAtoms());
SubstanceGroup substanceGroup = RDKFuncs.getSubstanceGroupWithIdx(mol, 0);
assertTrue(substanceGroup.hasProp("index"));
assertEquals(2, substanceGroup.getUIntProp("index") );
assertEquals(2, substanceGroup.getAtoms().size());
assertEquals(3, substanceGroup.getAtoms().get(0));
assertEquals(2, substanceGroup.getAtoms().get(1));
assertEquals(2, substanceGroup.getBonds().size());;
assertEquals(1, substanceGroup.getBonds().get(0));
assertEquals(3, substanceGroup.getBonds().get(1));
assertTrue(substanceGroup.hasProp("PARENT"));
assertEquals(10, substanceGroup.getUIntProp("PARENT"));
substanceGroup = RDKFuncs.getSubstanceGroupWithIdx(mol, 2);
assertTrue(substanceGroup.hasProp("index"));
assertEquals(10, substanceGroup.getUIntProp("index") );
assertEquals(5, substanceGroup.getAtoms().size());
assertEquals(3, substanceGroup.getAtoms().get(0));
assertEquals(2, substanceGroup.getAtoms().get(1));
assertEquals(4, substanceGroup.getAtoms().get(2));
assertEquals(5, substanceGroup.getAtoms().get(3));
assertEquals(7, substanceGroup.getAtoms().get(4));
assertEquals(2, substanceGroup.getBonds().size());;
assertEquals(1, substanceGroup.getBonds().get(0));
assertEquals(5, substanceGroup.getBonds().get(1));
assertFalse(substanceGroup.hasProp("PARENT"));
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.SubstanceGroupTests");
}
}
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