mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
908e47cc03
* support generalized substructure search in the SubstructLibrary * simplify namespaces * support the new functionality in the swig wrappers * update mac swig version in CI * ensure swig4 * switch mac_java ci builds to conda-forge * change in response to review * add copy ctor to extendedquerymol * Back to the way it was
391 lines
14 KiB
Java
391 lines
14 KiB
Java
/*
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*
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* Copyright (c) 2018, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import org.junit.*;
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public class SubstructLibraryTests extends GraphMolTest {
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private ROMol mol;
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private ROMol m;
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@Before public void setUp() {
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}
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@Test
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public void test1Basics() {
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SubstructLibrary lib = new SubstructLibrary();
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assertEquals(0, lib.size());
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// mol holders
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MolHolder mh = new MolHolder();
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assertEquals(0, mh.size());
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CachedMolHolder cmh = new CachedMolHolder();
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assertEquals(0, cmh.size());
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CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
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assertEquals(0, csmh.size());
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CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
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assertEquals(0, ctsmh.size());
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KeyFromPropHolder keys = new KeyFromPropHolder();
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// fpholder - can we create it...
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PatternHolder ph = new PatternHolder();
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TautomerPatternHolder tph = new TautomerPatternHolder();
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// Now lets make some molecules
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mol = RWMol.MolFromSmiles("c1ccccc1");
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String smiles = mol.MolToSmiles();
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mol.setProp("_Name", "foo");
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mh.addMol(mol);
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assertEquals(1, mh.size());
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cmh.addMol(mol);
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assertEquals(1, cmh.size());
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csmh.addMol(mol);
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assertEquals(1, csmh.size());
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ctsmh.addMol(mol);
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assertEquals(1, ctsmh.size());
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keys.addMol(mol);
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assertEquals(1, keys.size());
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m = mh.getMol(0);
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assertEquals(smiles, m.MolToSmiles());
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m = cmh.getMol(0);
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assertEquals(smiles, m.MolToSmiles());
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m = csmh.getMol(0);
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assertEquals(smiles, m.MolToSmiles());
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m = ctsmh.getMol(0);
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assertEquals(smiles, m.MolToSmiles());
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assertEquals("foo", keys.getKey(0));
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mol = RWMol.MolFromSmiles("CCN");
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mol.setProp("_Name", "bar");
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smiles = mol.MolToSmiles();
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mh.addMol(mol);
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assertEquals(2, mh.size());
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cmh.addMol(mol);
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assertEquals(2, mh.size());
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keys.addMol(mol);
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assertEquals(2, keys.size());
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csmh.addSmiles("CCN");
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assertEquals(2, csmh.size());
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ctsmh.addSmiles("CCN");
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assertEquals(2, ctsmh.size());
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m = mh.getMol(1);
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assertEquals(smiles, m.MolToSmiles());
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m = cmh.getMol(1);
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assertEquals(smiles, m.MolToSmiles());
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m = csmh.getMol(1);
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assertEquals(smiles, m.MolToSmiles());
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m = ctsmh.getMol(1);
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assertEquals(smiles, m.MolToSmiles());
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assertEquals("bar", keys.getKey(1));
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}
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@Test
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public void test2Basics() {
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MolHolder mh = new MolHolder();
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assertEquals(0, mh.size());
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CachedMolHolder cmh = new CachedMolHolder();
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assertEquals(0, cmh.size());
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CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
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assertEquals(0, csmh.size());
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CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
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assertEquals(0, ctsmh.size());
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mol = RWMol.MolFromSmiles("c1ccccc1");
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// mol holder
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SubstructLibrary lib = new SubstructLibrary(mh);
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SubstructLibrary lib2;
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lib.addMol(mol);
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UInt_Vect matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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if(lib.canSerialize()) {
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byte pickle[] = lib.Serialize();
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assertTrue(pickle != null);
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lib2 = SubstructLibrary.Deserialize(pickle);
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assertFalse(lib2 == null);
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assertEquals(lib.size(), 1);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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}
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// cached mol holder
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lib = new SubstructLibrary(cmh);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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assertEquals(1, lib.countMatches(mol));
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assertTrue(lib.hasMatch(mol));
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if(lib.canSerialize()) {
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byte pickle[] = lib.Serialize();
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assertTrue(pickle != null);
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lib2 = SubstructLibrary.Deserialize(pickle);
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assertFalse(lib2 == null);
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assertEquals(lib.size(), 1);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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assertEquals(1, lib.countMatches(mol));
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assertTrue(lib.hasMatch(mol));
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}
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// cached smiles mol holder
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lib = new SubstructLibrary(csmh);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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if(lib.canSerialize()) {
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byte pickle[] = lib.Serialize();
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assertTrue(pickle != null);
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lib2 = SubstructLibrary.Deserialize(pickle);
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assertFalse(lib2 == null);
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assertEquals(lib.size(), 1);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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}
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// cached trusted smiles mol holder
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lib = new SubstructLibrary(ctsmh);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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if(lib.canSerialize()) {
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byte pickle[] = lib.Serialize();
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assertTrue(pickle != null);
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lib2 = SubstructLibrary.Deserialize(pickle);
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assertFalse(lib2 == null);
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assertEquals(lib.size(), 1);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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}
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}
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@Test
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public void test3Basics() {
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MolHolder mh = new MolHolder();
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PatternHolder pat = new PatternHolder();
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assertEquals(0, mh.size());
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CachedMolHolder cmh = new CachedMolHolder();
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assertEquals(0, cmh.size());
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CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
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assertEquals(0, csmh.size());
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CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
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assertEquals(0, ctsmh.size());
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mol = RWMol.MolFromSmiles("c1ccccc1");
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// mol holder
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SubstructLibrary lib = new SubstructLibrary(mh, pat);
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lib.addMol(mol);
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UInt_Vect matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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// cached mol holder
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try {
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lib = new SubstructLibrary(cmh, pat);
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lib.addMol(mol);
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assertTrue(false); // shouldn't get here can't share patternholder and addmol
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} catch(Exception e) {
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// ok to get here
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}
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cmh = new CachedMolHolder();
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pat = new PatternHolder();
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lib = new SubstructLibrary(cmh, pat);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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// cached smiles mol holder
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pat = new PatternHolder();
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lib = new SubstructLibrary(csmh, pat);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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// cached trusted smiles mol holder
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pat = new PatternHolder();
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lib = new SubstructLibrary(ctsmh, pat);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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}
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@Test
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public void test4Basics() {
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MolHolder mh = new MolHolder();
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TautomerPatternHolder pat = new TautomerPatternHolder();
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assertEquals(0, mh.size());
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CachedMolHolder cmh = new CachedMolHolder();
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assertEquals(0, cmh.size());
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CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
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assertEquals(0, csmh.size());
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CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
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assertEquals(0, ctsmh.size());
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mol = RWMol.MolFromSmiles("c1ccccc1");
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TautomerQuery tautomerQuery = TautomerQuery.fromMol(mol);
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// mol holder
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SubstructLibrary lib = new SubstructLibrary(mh, pat);
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lib.addMol(mol);
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UInt_Vect matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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matches = lib.getMatches(tautomerQuery);
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assertEquals(1, matches.size());
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assertEquals(1, lib.countMatches(mol));
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assertEquals(1, lib.countMatches(tautomerQuery));
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// cached mol holder
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try {
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lib = new SubstructLibrary(cmh, pat);
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lib.addMol(mol);
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assertTrue(false); // shouldn't get here can't share patternholder and addmol
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} catch(Exception e) {
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// ok to get here
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}
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cmh = new CachedMolHolder();
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pat = new TautomerPatternHolder();
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lib = new SubstructLibrary(cmh, pat);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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matches = lib.getMatches(tautomerQuery);
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assertEquals(1, matches.size());
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assertEquals(1, lib.countMatches(mol));
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assertEquals(1, lib.countMatches(tautomerQuery));
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// cached smiles mol holder
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pat = new TautomerPatternHolder();
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lib = new SubstructLibrary(csmh, pat);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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matches = lib.getMatches(tautomerQuery);
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assertEquals(1, matches.size());
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assertEquals(1, lib.countMatches(mol));
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assertEquals(1, lib.countMatches(tautomerQuery));
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// cached trusted smiles mol holder
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pat = new TautomerPatternHolder();
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lib = new SubstructLibrary(ctsmh, pat);
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lib.addMol(mol);
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matches = lib.getMatches(mol);
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assertEquals(1, matches.size());
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matches = lib.getMatches(tautomerQuery);
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assertEquals(1, matches.size());
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assertEquals(1, lib.countMatches(mol));
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assertEquals(1, lib.countMatches(tautomerQuery));
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}
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@Test
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public void test5Basics() {
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MolHolder mh = new MolHolder();
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MolHolder mh2 = new MolHolder();
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PatternHolder pat = new PatternHolder();
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assertEquals(0, mh.size());
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CachedMolHolder cmh = new CachedMolHolder();
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assertEquals(0, cmh.size());
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mol = RWMol.MolFromSmiles("c1ccccc1");
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mol.setProp("_Name", "foo");
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KeyFromPropHolder keys = new KeyFromPropHolder();
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KeyFromPropHolder keys2 = new KeyFromPropHolder();
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// mol holder
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SubstructLibrary lib = new SubstructLibrary(mh, pat, keys);
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lib.addMol(mol);
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SubstructLibrary lib2 = new SubstructLibrary(mh2, keys2);
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lib2.addMol(mol);
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UInt_Vect matches = lib.getMatches(mol);
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UInt_Vect matches2 = lib2.getMatches(mol);
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assertEquals(1, matches.size());
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assertEquals(matches.get(0), matches.get(0));
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Str_Vect ids = lib.getKeys().getKeys(matches);
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Str_Vect ids2 = lib2.getKeys().getKeys(matches2);
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assertEquals(ids.get(0), "foo");
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assertEquals(ids2.get(0), "foo");
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}
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@Test
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public void test6XQM() {
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MolHolder mh = new MolHolder();
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PatternHolder pat = new TautomerPatternHolder();
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assertEquals(0, mh.size());
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// mol holder
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SubstructLibrary lib = new SubstructLibrary(mh, pat);
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mol = RWMol.MolFromSmiles("COCC=O");
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lib.addMol(mol);
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mol = RWMol.MolFromSmiles("COOCC=O");
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lib.addMol(mol);
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mol = RWMol.MolFromSmiles("COOOCC=O");
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lib.addMol(mol);
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mol = RWMol.MolFromSmiles("COOOOCC=O");
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lib.addMol(mol);
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RWMol rwm = RWMol.MolFromSmiles("COC=CO |LN:1:1.3|");
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ExtendedQueryMol qry = RDKFuncs.createExtendedQueryMol(rwm);
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UInt_Vect matches = lib.getMatches(qry);
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assertEquals(3, matches.size());
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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.SubstructLibraryTests");
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}
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}
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