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9a864f4238
* Changes to use SubstanceGroups in Java * Forgot to add SWIG file * Java test for SubstanceGroup wrappers * Added RDKit boilerplate
99 lines
3.7 KiB
Java
99 lines
3.7 KiB
Java
//
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// Created by Gareth Jones on 9/4/2020.
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//
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// Copyright 2020 Schrodinger, Inc
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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package org.RDKit;
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import org.junit.Test;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Paths;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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public class SubstanceGroupTests extends GraphMolTest {
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private RWMol getMol(String file) {
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file = getRdBase() + "/Code/GraphMol/test_data/"+file;
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try {
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String block = new String(Files.readAllBytes(Paths.get(file)));
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return RDKFuncs.MolBlockToMol(block);
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} catch (IOException ex) {
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throw new RuntimeException("IO Exception reading " + file, ex);
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}
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}
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@Test
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public void supGroupTest() {
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RWMol mol = getMol("sgroups_and_marvin_metal.mol");
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assertNotNull(mol);
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long sgroupCount = RDKFuncs.getSubstanceGroupCount(mol);
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assertEquals(1, sgroupCount);
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SubstanceGroup supGroup = RDKFuncs.getSubstanceGroupWithIdx(mol, 0);
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assertTrue(supGroup.hasProp("TYPE"));
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assertTrue(supGroup.hasProp("index"));
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assertTrue(supGroup.hasProp("LABEL"));
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assertTrue(supGroup.hasProp("DATAFIELDS"));
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assertEquals("SUP", supGroup.getStringProp("TYPE"));
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assertEquals(1, supGroup.getUIntProp("index"));
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assertEquals("M", supGroup.getStringProp("LABEL"));
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assertEquals(0, supGroup.getStringVectProp("DATAFIELDS").size());
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assertEquals(1, supGroup.getAtoms().size());
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assertEquals(0, supGroup.getBonds().size());
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assertEquals(1, supGroup.getAtoms().get(0));
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}
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@Test
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public void polymerTest() {
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RWMol mol = getMol("sgroups_copolymer2.mol");
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assertNotNull(mol);
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long sgroupCount = RDKFuncs.getSubstanceGroupCount(mol);
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assertEquals(3, sgroupCount);
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assertEquals(9, mol.getNumAtoms());
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SubstanceGroup substanceGroup = RDKFuncs.getSubstanceGroupWithIdx(mol, 0);
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assertTrue(substanceGroup.hasProp("index"));
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assertEquals(2, substanceGroup.getUIntProp("index") );
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assertEquals(2, substanceGroup.getAtoms().size());
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assertEquals(3, substanceGroup.getAtoms().get(0));
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assertEquals(2, substanceGroup.getAtoms().get(1));
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assertEquals(2, substanceGroup.getBonds().size());;
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assertEquals(1, substanceGroup.getBonds().get(0));
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assertEquals(3, substanceGroup.getBonds().get(1));
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assertTrue(substanceGroup.hasProp("PARENT"));
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assertEquals(10, substanceGroup.getUIntProp("PARENT"));
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substanceGroup = RDKFuncs.getSubstanceGroupWithIdx(mol, 2);
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assertTrue(substanceGroup.hasProp("index"));
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assertEquals(10, substanceGroup.getUIntProp("index") );
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assertEquals(5, substanceGroup.getAtoms().size());
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assertEquals(3, substanceGroup.getAtoms().get(0));
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assertEquals(2, substanceGroup.getAtoms().get(1));
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assertEquals(4, substanceGroup.getAtoms().get(2));
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assertEquals(5, substanceGroup.getAtoms().get(3));
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assertEquals(7, substanceGroup.getAtoms().get(4));
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assertEquals(2, substanceGroup.getBonds().size());;
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assertEquals(1, substanceGroup.getBonds().get(0));
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assertEquals(5, substanceGroup.getBonds().get(1));
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assertFalse(substanceGroup.hasProp("PARENT"));
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.SubstanceGroupTests");
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}
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}
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