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https://github.com/rdkit/rdkit.git
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aa336f3faf
* extend the allowed valences of the alkali earths make it possible to have preferred and arbitrary valence states (I thought this already worked) * backup * maybe needed * copy in some swig3 files; at this point the tests all work * remove SWIG version lock * changes in response to review
287 lines
10 KiB
Java
287 lines
10 KiB
Java
/*
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* $Id: AtomPairsTests.java 4395 2011-01-28 16:54:48Z landrgr1 $
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*
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* Copyright (c) 2010, 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 java.io.File;
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import org.junit.*;
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public class AtomPairsTests extends GraphMolTest {
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@Test
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public void testAtomCodes_1() {
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ROMol mol = RWMol.MolFromSmiles("C=C");
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Atom atom0 = mol.getAtomWithIdx(0);
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Atom atom1 = mol.getAtomWithIdx(1);
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assertNotNull(atom0);
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assertNotNull(atom1);
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assertEquals(RDKFuncs.getAtomCode(atom0), RDKFuncs.getAtomCode(atom1));
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long tgt = 1 | (1 | 1 << RDKFuncs.getNumPiBits()) << RDKFuncs.getNumBranchBits();
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assertEquals(tgt, RDKFuncs.getAtomCode(atom0));
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tgt = 1 << RDKFuncs.getNumBranchBits() | 1 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(atom0, 1));
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}
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@Test
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public void testAtomCodes_2() {
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ROMol mol = RWMol.MolFromSmiles("C#CO");
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long tgt = 1 | 2 << RDKFuncs.getNumBranchBits() | 1 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(0)));
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tgt = 2 | 2 << RDKFuncs.getNumBranchBits() | 1 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(1)));
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tgt = 1 | 0 << RDKFuncs.getNumBranchBits() | 3 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(2)));
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}
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@Test
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public void testAtomCodes_3() {
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ROMol mol = RWMol.MolFromSmiles("CC(O)C(O)(O)C");
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long tgt = 1 | 0 << RDKFuncs.getNumBranchBits() | 1 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(1), 2));
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tgt = 2 | 0 << RDKFuncs.getNumBranchBits() | 1 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(3), 2));
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}
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@Test
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public void testAtomCodes_4() {
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ROMol mol = RWMol.MolFromSmiles("C=CC(=O)O");
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long tgt = 0 | 0 << RDKFuncs.getNumBranchBits() | 3 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(4), 1));
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tgt = 3 | 1 << RDKFuncs.getNumBranchBits() | 1 << (RDKFuncs.getNumBranchBits() + RDKFuncs.getNumPiBits());
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assertEquals(tgt, RDKFuncs.getAtomCode(mol.getAtomWithIdx(2)));
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}
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@Test
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public void testAtomPairs() {
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ROMol mol = RWMol.MolFromSmiles("CCCCC");
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SparseIntVect32 fp;
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long tgt, c1, c2, c3;
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c1 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(0));
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c2 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(1));
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c3 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(2));
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tgt = 1 | (Math.min(c1, c2) | Math.max(c1, c2) << RDKFuncs.getCodeSize()) << RDKFuncs.getNumPathBits();
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assertEquals(tgt, RDKFuncs.getAtomPairCode(c1, c2, 1));
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assertEquals(tgt, RDKFuncs.getAtomPairCode(c2, c1, 1));
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tgt = 2 | (Math.min(c1, c3) | Math.max(c1, c3) << RDKFuncs.getCodeSize()) << RDKFuncs.getNumPathBits();
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assertEquals(tgt, RDKFuncs.getAtomPairCode(c1, c3, 2));
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assertEquals(tgt, RDKFuncs.getAtomPairCode(c3, c1, 2));
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mol = RWMol.MolFromSmiles("CCC");
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fp = RDKFuncs.getAtomPairFingerprint(mol);
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assertEquals(3, fp.getTotalVal());
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assertEquals(2, fp.getNonzero().size());
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c1 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(0));
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c2 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(1));
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c3 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(2));
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assertEquals(2, fp.getVal((int) RDKFuncs.getAtomPairCode(c1, c2, 1)));
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assertEquals(1, fp.getVal((int) RDKFuncs.getAtomPairCode(c1, c3, 2)));
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mol = RWMol.MolFromSmiles("CC=O.Cl");
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fp = RDKFuncs.getAtomPairFingerprint(mol);
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assertEquals(3, fp.getTotalVal());
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assertEquals(3, fp.getNonzero().size());
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c1 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(0));
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c2 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(1));
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c3 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(2));
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assertEquals(1, fp.getVal((int) RDKFuncs.getAtomPairCode(c1, c2, 1)));
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assertEquals(1, fp.getVal((int) RDKFuncs.getAtomPairCode(c1, c2, 1)));
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assertEquals(1, fp.getVal((int) RDKFuncs.getAtomPairCode(c2, c3, 1)));
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}
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@Test
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public void testAtomPairs2() {
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ROMol mol;
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SparseIntVect32 fp;
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mol = RWMol.MolFromSmiles("CCC");
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fp = RDKFuncs.getAtomPairFingerprint(mol, 1, 2);
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assertEquals(3, fp.getTotalVal());
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assertEquals(2, fp.getNonzero().size());
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fp = RDKFuncs.getAtomPairFingerprint(mol, 2, 2);
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assertEquals(1, fp.getTotalVal());
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assertEquals(1, fp.getNonzero().size());
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}
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@Test
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public void testHashedAtomPairs() {
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ROMol mol = RWMol.MolFromSmiles("c1ccccc1");
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SparseIntVect32 fp1, fp2;
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fp1 = RDKFuncs.getHashedAtomPairFingerprint(mol);
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fp2 = RDKFuncs.getHashedAtomPairFingerprint(mol);
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assertEquals(1.0, RDKFuncs.DiceSimilarity(fp1, fp2), 0.0);
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assertTrue( fp1.eq(fp2) );
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mol = RWMol.MolFromSmiles("c1ccccn1");
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fp2 = RDKFuncs.getHashedAtomPairFingerprint(mol);
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assertEquals(0.0, RDKFuncs.DiceSimilarity(fp1, fp2), 1.0);
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mol = RWMol.MolFromSmiles("c1ccccc1");
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fp1 = RDKFuncs.getHashedAtomPairFingerprint(mol, 2048);
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fp2 = RDKFuncs.getHashedAtomPairFingerprint(mol, 2048, 1, 3);
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assertEquals(1.0, RDKFuncs.DiceSimilarity(fp1, fp2), 0.0);
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assertTrue( fp1.eq(fp2) );
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fp2 = RDKFuncs.getHashedAtomPairFingerprint(mol, 2048, 1, 2);
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assertEquals(0.0, RDKFuncs.DiceSimilarity(fp1, fp2), 1.0);
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}
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@Test
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public void testTorsions() {
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ROMol mol = RWMol.MolFromSmiles("CCCC");
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SparseIntVect64 fp;
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double tgt;
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long c1, c2, c3, c4;
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UInt_Vect codes = new UInt_Vect();
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mol = RWMol.MolFromSmiles("CCCC");
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c1 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(0)) - 1;
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c2 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(1)) - 2;
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c3 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(2)) - 2;
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c4 = RDKFuncs.getAtomCode(mol.getAtomWithIdx(3)) - 1;
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tgt = c1 | (c2 | (c3 | c4 << RDKFuncs.getCodeSize()) << RDKFuncs.getCodeSize()) << RDKFuncs.getCodeSize();
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codes.clear();
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codes.add(c1);
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codes.add(c2);
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codes.add(c3);
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codes.add(c4);
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assertEquals(tgt, RDKFuncs.getTopologicalTorsionCode(codes).doubleValue(), 0.0);
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fp = RDKFuncs.getTopologicalTorsionFingerprint(mol);
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assertEquals(1, fp.getTotalVal());
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assertEquals(1, fp.getNonzero().size());
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mol = RWMol.MolFromSmiles("CCCCO.Cl");
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fp = RDKFuncs.getTopologicalTorsionFingerprint(mol);
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assertEquals(2, fp.getTotalVal());
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assertEquals(2, fp.getNonzero().size());
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fp = RDKFuncs.getTopologicalTorsionFingerprint(mol, 3);
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assertEquals(3, fp.getTotalVal());
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assertEquals(3, fp.getNonzero().size());
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}
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@Test
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public void testHashedTorsions() {
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ROMol mol = RWMol.MolFromSmiles("c1ccccc1");
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SparseIntVect64 fp1, fp2;
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fp1 = RDKFuncs.getHashedTopologicalTorsionFingerprint(mol);
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fp2 = RDKFuncs.getHashedTopologicalTorsionFingerprint(mol);
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assertEquals(1.0, RDKFuncs.DiceSimilarity(fp1, fp2), 0.0);
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assertTrue( fp1.eq(fp2) );
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mol = RWMol.MolFromSmiles("c1ccccn1");
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fp2 = RDKFuncs.getHashedTopologicalTorsionFingerprint(mol);
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assertEquals(0.0, RDKFuncs.DiceSimilarity(fp1, fp2), 1.0);
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mol = RWMol.MolFromSmiles("c1ccccc1");
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fp1 = RDKFuncs.getHashedTopologicalTorsionFingerprint(mol, 2048, 6);
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fp2 = RDKFuncs.getHashedTopologicalTorsionFingerprint(mol, 2048, 6);
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assertEquals(1.0, RDKFuncs.DiceSimilarity(fp1, fp2), 0.0);
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assertTrue( fp1.eq(fp2) );
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mol = RWMol.MolFromSmiles("c1ccccn1");
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fp2 = RDKFuncs.getHashedTopologicalTorsionFingerprint(mol, 2048, 6);
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assertEquals(0.0, RDKFuncs.DiceSimilarity(fp1, fp2), 1.0);
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}
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@Test
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public void testBulkTorsions() {
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String fName = new File(getRdBase(), "/Projects/DbCLI/testData/pubchem.200.sdf").getPath();
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SDMolSupplier suppl = new SDMolSupplier(fName);
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while (!suppl.atEnd()) {
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ROMol mol = suppl.next();
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SparseIntVect64 fp;
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fp = RDKFuncs.getTopologicalTorsionFingerprint(mol);
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assertTrue(fp.getTotalVal() > 1);
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}
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}
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@Test
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public void testRootedAtomPairs() {
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ROMol mol = RWMol.MolFromSmiles("OCCCCC");
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SparseIntVect32 fp1, fp2;
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UInt_Vect roots = new UInt_Vect();
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fp1 = RDKFuncs.getAtomPairFingerprint(mol);
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Match_Vect nz1 = fp1.getNonzero();
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assertTrue(nz1.size() > 0);
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roots.add(0L);
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fp2 = RDKFuncs.getAtomPairFingerprint(mol, roots);
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Match_Vect nz2 = fp2.getNonzero();
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assertTrue(nz2.size() > 0);
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assertTrue(nz2.size() < nz1.size());
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for (int i = 0; i < nz2.size(); i++) {
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Int_Pair pair = nz2.get(i);
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assertEquals(pair.getSecond() , fp2.getVal(pair.getFirst()));
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}
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}
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@Test
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public void testRootedTorsions() {
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SparseIntVect64 fp1, fp2;
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ROMol mol = RWMol.MolFromSmiles("OCCCC");
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UInt_Vect roots = new UInt_Vect();
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roots.add(0L);
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fp1 = RDKFuncs.getTopologicalTorsionFingerprint(mol);
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Long_Pair_Vect nz1 = fp1.getNonzero();
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assertTrue(nz1.size() > 0);
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fp2 = RDKFuncs.getTopologicalTorsionFingerprint(mol, 4, roots);
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Long_Pair_Vect nz2 = fp2.getNonzero();
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assertTrue(nz2.size() > 0);
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assertTrue(nz2.size() < nz1.size());
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for (int i = 0; i < nz2.size(); ++i) {
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Long_Pair pair = nz2.get(i);
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assertTrue(pair.getSecond() <= fp2.getVal(pair.getFirst()));
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}
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main(AtomPairsTests.class.getName());
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}
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}
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