/* * * Copyright (c) 2018, 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 org.junit.*; public class SubstructLibraryTests extends GraphMolTest { private ROMol mol; private ROMol m; @Before public void setUp() { } @Test public void test1Basics() { SubstructLibrary lib = new SubstructLibrary(); assertEquals(0, lib.size()); // mol holders MolHolder mh = new MolHolder(); assertEquals(0, mh.size()); CachedMolHolder cmh = new CachedMolHolder(); assertEquals(0, cmh.size()); CachedSmilesMolHolder csmh = new CachedSmilesMolHolder(); assertEquals(0, csmh.size()); CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder(); assertEquals(0, ctsmh.size()); KeyFromPropHolder keys = new KeyFromPropHolder(); // fpholder - can we create it... PatternHolder ph = new PatternHolder(); TautomerPatternHolder tph = new TautomerPatternHolder(); // Now lets make some molecules mol = RWMol.MolFromSmiles("c1ccccc1"); String smiles = mol.MolToSmiles(); mol.setProp("_Name", "foo"); mh.addMol(mol); assertEquals(1, mh.size()); cmh.addMol(mol); assertEquals(1, cmh.size()); csmh.addMol(mol); assertEquals(1, csmh.size()); ctsmh.addMol(mol); assertEquals(1, ctsmh.size()); keys.addMol(mol); assertEquals(1, keys.size()); m = mh.getMol(0); assertEquals(smiles, m.MolToSmiles()); m = cmh.getMol(0); assertEquals(smiles, m.MolToSmiles()); m = csmh.getMol(0); assertEquals(smiles, m.MolToSmiles()); m = ctsmh.getMol(0); assertEquals(smiles, m.MolToSmiles()); assertEquals("foo", keys.getKey(0)); mol = RWMol.MolFromSmiles("CCN"); mol.setProp("_Name", "bar"); smiles = mol.MolToSmiles(); mh.addMol(mol); assertEquals(2, mh.size()); cmh.addMol(mol); assertEquals(2, mh.size()); keys.addMol(mol); assertEquals(2, keys.size()); csmh.addSmiles("CCN"); assertEquals(2, csmh.size()); ctsmh.addSmiles("CCN"); assertEquals(2, ctsmh.size()); m = mh.getMol(1); assertEquals(smiles, m.MolToSmiles()); m = cmh.getMol(1); assertEquals(smiles, m.MolToSmiles()); m = csmh.getMol(1); assertEquals(smiles, m.MolToSmiles()); m = ctsmh.getMol(1); assertEquals(smiles, m.MolToSmiles()); assertEquals("bar", keys.getKey(1)); } @Test public void test2Basics() { MolHolder mh = new MolHolder(); assertEquals(0, mh.size()); CachedMolHolder cmh = new CachedMolHolder(); assertEquals(0, cmh.size()); CachedSmilesMolHolder csmh = new CachedSmilesMolHolder(); assertEquals(0, csmh.size()); CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder(); assertEquals(0, ctsmh.size()); mol = RWMol.MolFromSmiles("c1ccccc1"); // mol holder SubstructLibrary lib = new SubstructLibrary(mh); SubstructLibrary lib2; lib.addMol(mol); UInt_Vect matches = lib.getMatches(mol); assertEquals(1, matches.size()); if(lib.canSerialize()) { byte pickle[] = lib.Serialize(); assertTrue(pickle != null); lib2 = SubstructLibrary.Deserialize(pickle); assertFalse(lib2 == null); assertEquals(lib.size(), 1); matches = lib.getMatches(mol); assertEquals(1, matches.size()); } // cached mol holder lib = new SubstructLibrary(cmh); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); assertEquals(1, lib.countMatches(mol)); assertTrue(lib.hasMatch(mol)); if(lib.canSerialize()) { byte pickle[] = lib.Serialize(); assertTrue(pickle != null); lib2 = SubstructLibrary.Deserialize(pickle); assertFalse(lib2 == null); assertEquals(lib.size(), 1); matches = lib.getMatches(mol); assertEquals(1, matches.size()); assertEquals(1, lib.countMatches(mol)); assertTrue(lib.hasMatch(mol)); } // cached smiles mol holder lib = new SubstructLibrary(csmh); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); if(lib.canSerialize()) { byte pickle[] = lib.Serialize(); assertTrue(pickle != null); lib2 = SubstructLibrary.Deserialize(pickle); assertFalse(lib2 == null); assertEquals(lib.size(), 1); matches = lib.getMatches(mol); assertEquals(1, matches.size()); } // cached trusted smiles mol holder lib = new SubstructLibrary(ctsmh); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); if(lib.canSerialize()) { byte pickle[] = lib.Serialize(); assertTrue(pickle != null); lib2 = SubstructLibrary.Deserialize(pickle); assertFalse(lib2 == null); assertEquals(lib.size(), 1); matches = lib.getMatches(mol); assertEquals(1, matches.size()); } } @Test public void test3Basics() { MolHolder mh = new MolHolder(); PatternHolder pat = new PatternHolder(); assertEquals(0, mh.size()); CachedMolHolder cmh = new CachedMolHolder(); assertEquals(0, cmh.size()); CachedSmilesMolHolder csmh = new CachedSmilesMolHolder(); assertEquals(0, csmh.size()); CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder(); assertEquals(0, ctsmh.size()); mol = RWMol.MolFromSmiles("c1ccccc1"); // mol holder SubstructLibrary lib = new SubstructLibrary(mh, pat); lib.addMol(mol); UInt_Vect matches = lib.getMatches(mol); assertEquals(1, matches.size()); // cached mol holder try { lib = new SubstructLibrary(cmh, pat); lib.addMol(mol); assertTrue(false); // shouldn't get here can't share patternholder and addmol } catch(Exception e) { // ok to get here } cmh = new CachedMolHolder(); pat = new PatternHolder(); lib = new SubstructLibrary(cmh, pat); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); // cached smiles mol holder pat = new PatternHolder(); lib = new SubstructLibrary(csmh, pat); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); // cached trusted smiles mol holder pat = new PatternHolder(); lib = new SubstructLibrary(ctsmh, pat); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); } @Test public void test4Basics() { MolHolder mh = new MolHolder(); TautomerPatternHolder pat = new TautomerPatternHolder(); assertEquals(0, mh.size()); CachedMolHolder cmh = new CachedMolHolder(); assertEquals(0, cmh.size()); CachedSmilesMolHolder csmh = new CachedSmilesMolHolder(); assertEquals(0, csmh.size()); CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder(); assertEquals(0, ctsmh.size()); mol = RWMol.MolFromSmiles("c1ccccc1"); TautomerQuery tautomerQuery = TautomerQuery.fromMol(mol); // mol holder SubstructLibrary lib = new SubstructLibrary(mh, pat); lib.addMol(mol); UInt_Vect matches = lib.getMatches(mol); assertEquals(1, matches.size()); matches = lib.getMatches(tautomerQuery); assertEquals(1, matches.size()); assertEquals(1, lib.countMatches(mol)); assertEquals(1, lib.countMatches(tautomerQuery)); // cached mol holder try { lib = new SubstructLibrary(cmh, pat); lib.addMol(mol); assertTrue(false); // shouldn't get here can't share patternholder and addmol } catch(Exception e) { // ok to get here } cmh = new CachedMolHolder(); pat = new TautomerPatternHolder(); lib = new SubstructLibrary(cmh, pat); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); matches = lib.getMatches(tautomerQuery); assertEquals(1, matches.size()); assertEquals(1, lib.countMatches(mol)); assertEquals(1, lib.countMatches(tautomerQuery)); // cached smiles mol holder pat = new TautomerPatternHolder(); lib = new SubstructLibrary(csmh, pat); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); matches = lib.getMatches(tautomerQuery); assertEquals(1, matches.size()); assertEquals(1, lib.countMatches(mol)); assertEquals(1, lib.countMatches(tautomerQuery)); // cached trusted smiles mol holder pat = new TautomerPatternHolder(); lib = new SubstructLibrary(ctsmh, pat); lib.addMol(mol); matches = lib.getMatches(mol); assertEquals(1, matches.size()); matches = lib.getMatches(tautomerQuery); assertEquals(1, matches.size()); assertEquals(1, lib.countMatches(mol)); assertEquals(1, lib.countMatches(tautomerQuery)); } @Test public void test5Basics() { MolHolder mh = new MolHolder(); MolHolder mh2 = new MolHolder(); PatternHolder pat = new PatternHolder(); assertEquals(0, mh.size()); CachedMolHolder cmh = new CachedMolHolder(); assertEquals(0, cmh.size()); mol = RWMol.MolFromSmiles("c1ccccc1"); mol.setProp("_Name", "foo"); KeyFromPropHolder keys = new KeyFromPropHolder(); KeyFromPropHolder keys2 = new KeyFromPropHolder(); // mol holder SubstructLibrary lib = new SubstructLibrary(mh, pat, keys); lib.addMol(mol); SubstructLibrary lib2 = new SubstructLibrary(mh2, keys2); lib2.addMol(mol); UInt_Vect matches = lib.getMatches(mol); UInt_Vect matches2 = lib2.getMatches(mol); assertEquals(1, matches.size()); assertEquals(matches.get(0), matches.get(0)); Str_Vect ids = lib.getKeys().getKeys(matches); Str_Vect ids2 = lib2.getKeys().getKeys(matches2); assertEquals(ids.get(0), "foo"); assertEquals(ids2.get(0), "foo"); } @Test public void test6XQM() { MolHolder mh = new MolHolder(); PatternHolder pat = new TautomerPatternHolder(); assertEquals(0, mh.size()); // mol holder SubstructLibrary lib = new SubstructLibrary(mh, pat); mol = RWMol.MolFromSmiles("COCC=O"); lib.addMol(mol); mol = RWMol.MolFromSmiles("COOCC=O"); lib.addMol(mol); mol = RWMol.MolFromSmiles("COOOCC=O"); lib.addMol(mol); mol = RWMol.MolFromSmiles("COOOOCC=O"); lib.addMol(mol); RWMol rwm = RWMol.MolFromSmiles("COC=CO |LN:1:1.3|"); ExtendedQueryMol qry = RDKFuncs.createExtendedQueryMol(rwm); UInt_Vect matches = lib.getMatches(qry); assertEquals(3, matches.size()); } public static void main(String args[]) { org.junit.runner.JUnitCore.main("org.RDKit.SubstructLibraryTests"); } }