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/*
*
* 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");
}
}
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