mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
af6d413ccc
* SWIG wrap SubstructLibrary * Fix tests * Fix virtual overload for tagAtoms * Add SubstructLibrary to swig
247 lines
8.9 KiB
Java
247 lines
8.9 KiB
Java
/*
|
|
*
|
|
* 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());
|
|
|
|
// fpholder - can we create it...
|
|
PatternHolder ph = new PatternHolder();
|
|
|
|
// Now lets make some molecules
|
|
mol = RWMol.MolFromSmiles("c1ccccc1");
|
|
String smiles = mol.MolToSmiles();
|
|
|
|
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());
|
|
|
|
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());
|
|
|
|
mol = RWMol.MolFromSmiles("CCN");
|
|
smiles = mol.MolToSmiles();
|
|
|
|
mh.addMol(mol);
|
|
assertEquals(2, mh.size());
|
|
cmh.addMol(mol);
|
|
assertEquals(2, mh.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());
|
|
}
|
|
|
|
|
|
@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());
|
|
|
|
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 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());
|
|
}
|
|
|
|
|
|
|
|
public static void main(String args[]) {
|
|
org.junit.runner.JUnitCore.main("org.RDKit.SubstructLibraryTests");
|
|
}
|
|
|
|
}
|